diff options
Diffstat (limited to 'reproduce')
67 files changed, 2781 insertions, 1529 deletions
diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh index bea88d5..16950b5 100755 --- a/reproduce/analysis/bash/download-multi-try.sh +++ b/reproduce/analysis/bash/download-multi-try.sh @@ -31,7 +31,7 @@ # reason, you don't want to use a lock file, set the 'lockfile' name to # 'nolock'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index 5860806..7373503 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -105,7 +105,7 @@ # also called '%' (if your local copy of the input dataset and the only # repository names are the same, be sure to set '%' accordingly). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index ba8c960..80eb60a 100644 --- a/reproduce/analysis/config/delete-me-squared-num.conf +++ b/reproduce/analysis/config/delete-me-squared-num.conf @@ -1,6 +1,6 @@ # Number of samples in the demonstration analysis (to be deleted). # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf index 1ab7de1..4c95c2f 100644 --- a/reproduce/analysis/config/metadata.conf +++ b/reproduce/analysis/config/metadata.conf @@ -15,7 +15,7 @@ # and the copyright license name and standard link to the fully copyright # license. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf index 7821306..e0400d3 100644 --- a/reproduce/analysis/config/pdf-build.conf +++ b/reproduce/analysis/config/pdf-build.conf @@ -12,7 +12,7 @@ # LaTeX. Otherwise, a notice will just printed that, no PDF will be # created. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index 031085d..09cca90 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,6 +1,6 @@ # To enable verification of output datasets set this variable to 'yes'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index a20abc6..1377395 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -1,6 +1,6 @@ # Dummy Makefile to create a random dataset for plotting. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index c51f910..7aefd3f 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -265,16 +265,8 @@ clean: # executing 'build'. rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf -# Delete all the built outputs except the dependency programs. We'll -# use Bash's extended options builtin ('shopt') to enable "extended -# glob" (for listing of files). It allows extended features like -# ignoring the listing of a file with '!()' that we are using -# afterwards. - shopt -s extglob - rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex) - rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir)) - rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/* - rm -rf $(badir)/preparation-done.mk +# Delete the full 'badir' (containing all analysis outputs). + rm -rf $(badir) distclean: clean # Without cleaning the Git hooks, we won't be able to easily commit @@ -285,7 +277,7 @@ distclean: clean # 'rm' program. So for this recipe, we'll use the host system's 'rm', # not our own. $$sys_rm -rf $(BDIR) - $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf + $$sys_rm -f .local .build @@ -329,12 +321,11 @@ $(project-package-contents): paper.pdf | $(texdir) paper.tex > $$dir/paper.tex # Copy ONLY the version-controlled files in 'reproduce' and -# 'tex/src'. This is important because files like 'LOCAL.conf' (in -# 'reproduce/software/config') should not be archived, they contain -# information about the host computer and are irrelevant for -# others. Also some project authors may have temporary files here -# that are not under version control and thus shouldn't be archived -# (although this is bad practice, but that is up to the user). +# 'tex/src'. This is important because the git commit hash goes in +# the tarball name (should correspond to it) and some project authors +# may have temporary files here that are not under version control +# and thus shouldn't be archived (although this is bad practice, but +# that is up to the user). # # To keep the sub-directory structure, we are packaging the files # with Tar, piping it, and unpacking it in the archive directory. So @@ -362,17 +353,20 @@ $(project-package-contents): paper.pdf | $(texdir) rm -rf $$dir/tex/build/build* # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or -# PGFPlots was used to generate them), copy them too. +# PGFPlots was used to generate them), copy them too. Note that in +# the main project source, 'tex/tikz' is just a symbolic link to +# 'tex/build/tikz'. But inside the tarball we do not want to have +# symbolic links and they should be independent. if ls tex/tikz/*.pdf &> /dev/null; then cp tex/tikz/*.pdf $$dir/tex/tikz fi # When submitting to places like arXiv, they will just run LaTeX once -# and won't run 'biber'. So we need to also keep the '.bbl' file into -# the distributing tarball. However, BibLaTeX is particularly -# sensitive to versioning (a '.bbl' file has to be read by the same -# BibLaTeX version that created it). This is hard to do with -# non-up-to-date places like arXiv. Therefore, we thus just copy the +# and won't run 'biber' or 'biblatex'. So we need to also keep the +# '.bbl' file into the distributing tarball. However, BibLaTeX is +# particularly sensitive to versioning (a '.bbl' file has to be read +# by the same BibLaTeX version that created it). This is hard to do +# with non-up-to-date places like arXiv. Therefore, we just copy the # whole of BibLaTeX's source (the version we are using) into the top # tarball directory. In this way, arXiv's LaTeX engine will use the # same BibLaTeX version to interpret the '.bbl' file. TIP: you can @@ -521,7 +515,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) # Unrecognized format. *) - echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;; + printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! " + printf "Please see the description of this variable in " + printf "'$(bsdir)/config/LOCAL.conf' for the acceptable " + printf "values."; exit 1;; esac fi diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 3c06ce3..c218cdd 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -19,6 +19,21 @@ +# Software info in TeX +# -------------------- +# +# The information of the installed software is placed in the +# '.build/software' directory (which the TeX build should not depend +# on). Therefore, we should copy those macros here in the LaTeX build +# directory, so the TeX directory is completely independent from each +# other. +$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex + cp $(bsdir)/config/*.tex $(mtexdir)/ + + + + + # LaTeX macros for paper # ---------------------- # @@ -40,19 +55,36 @@ # Note that if you don't want the final PDF and just want the processing # and file outputs, you can give any value other than 'yes' to # 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'. -$(mtexdir)/project.tex: $(mtexdir)/verify.tex +$(mtexdir)/project.tex: $(mtexdir)/verify.tex $(mtexdir)/dependencies.tex # If no PDF is requested, or if LaTeX isn't available, don't continue # to building the final PDF. Otherwise, merge all the TeX macros into # one for building the PDF. - @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then + @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; + then # Put a LaTeX input command for all the necessary macro files. -# 'hardware-parameters.tex' is created in 'configure.sh'. +# Note that 'hardware-parameters.tex' is created in 'configure.sh' +# (which is why it is first in the list). projecttex=$(mtexdir)/project.tex rm -f $$projecttex - for t in $(subst paper,,$(makesrc)) hardware-parameters; do - echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex + for t in hardware-parameters $(subst paper,,$(makesrc)); do + +# Only add the macro file to 'project.tex' if the macro file is +# not empty. Empty macro files are not a bug in Maneage alone: 1) +# the processing of a sub-Makefile may not need to produce any +# written macro for the PDF, and that is perfectly fine. 2) LaTeX +# can also '\input' an empty file. However, it is important for +# for publication servers (like arXiv) that do not allow +# uploading empty files. Therefore, when 'project.tex' contains +# empty files, such severs will not be able compile the PDF +# because the file name is mentioned in 'project.tex', but cannot +# be found in the uploaded files. + tfile=tex/build/macros/$$t.tex + if [ -s $$tfile ]; then + echo "\input{$$tfile}" >> $$projecttex + fi + done # Possibly highlight the '\new' parts of the text. @@ -105,23 +137,6 @@ else texbdir:=$(texdir)/build-$(shell whoami) endif tikzdir:=$(texbdir)/tikz -$(texbdir):; mkdir $@ -$(tikzdir): | $(texbdir); mkdir $@ - - - - - -# Software info in TeX -# -------------------- -# -# The information of the installed software is placed in the -# '.build/software' directory (which the TeX build should not depend -# on). Therefore, we should copy those macros here in the LaTeX build -# directory, so the TeX directory is completely independent from each -# other. -$(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex - cp $(bsdir)/tex/*.tex $(mtexdir)/ @@ -139,8 +154,7 @@ $(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex # recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't # been modified, we don't want to re-build the bibliography, only the final # PDF. -$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ - | $(mtexdir)/project.tex $(tikzdir) +$(texbdir)/paper.bbl: tex/src/references.tex | $(mtexdir)/project.tex # If '$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) @@ -166,9 +180,9 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ # for details. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper fi @@ -200,9 +214,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # option '-shell-escape'. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index ffb2a3c..352fd00 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ # Basic preparations, called by './project make'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 2689e64..7286ca6 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -1,6 +1,6 @@ # Top-level Makefile (first to be loaded). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -19,9 +19,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index ea40f39..8d1c2e0 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -4,7 +4,7 @@ # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -23,9 +23,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index c74f8ca..91c4b77 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -1,6 +1,6 @@ # Verify the project outputs before building the paper. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -138,11 +138,44 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) # Verify TeX macros (the values that go into the PDF text). for m in $(verify-check); do - file=$(mtexdir)/$$m.tex - if [ $$m == delete-me ]; then s=711e2f7fa1f16ecbeeb3df6bcb4ec705 - else echo; echo "'$$m' not recognized."; exit 1 + +# Set the macro file name, make sure it exists (the user may have +# forgot to create it in the respective sub-Makefile). + tfile=$(mtexdir)/$$m.tex + if ! [ -f $$tfile ]; then + printf "$$tfile: ERROR: does not exist! If you do not " + printf "(currently) plan macros to be added to the final " + printf "PDF from that sub-Makefile, do the following to " + printf "avoid this error: put a 'touch \$$@' as the recipe " + printf "of the '\$$(mtexdir)/$$m.tex' target (at the bottom " + printf "of 'reproduce/analysis/make/$$m.mk'). If you later " + printf "decide to define macros there, simply replace the " + printf "temporary 'touch \$$@' command with the command(s) " + printf "to prepare/write the macro (see 'initialize.mk' " + printf "as an example)\n"; + exit 1 fi - $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp) + +# Check the hash for this file and verify it. + case $$m in + delete-me) s=711e2f7fa1f16ecbeeb3df6bcb4ec705;; + *) # This file's hash is not in the list above. + +# If the file is empty, we can skip it (with the 'continue' +# command). Otherwise, the user should be informed with an +# error. + if [ -s $$tfile ]; then + printf "$$tfile: ERROR: please add the hash of this " + printf "macro file to the list of hashes above this " + printf "error message (in " + printf "'reproduce/analysis/make/verify.mk')\n"; exit 1 + else + continue + fi + ;; + esac + $(call verify-txt-no-comments-no-space, $$tfile, $$s, $@.tmp) + done # Move temporary file to final target. diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex index 5697885..3c012cf 100644 --- a/reproduce/software/bibtex/astrometrynet.tex +++ b/reproduce/software/bibtex/astrometrynet.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex index 3df1aa1..aa9d162 100644 --- a/reproduce/software/bibtex/astropy.tex +++ b/reproduce/software/bibtex/astropy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/corner.tex b/reproduce/software/bibtex/corner.tex index fd7ea76..164adda 100644 --- a/reproduce/software/bibtex/corner.tex +++ b/reproduce/software/bibtex/corner.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex index 311072d..0c761ce 100644 --- a/reproduce/software/bibtex/cython.tex +++ b/reproduce/software/bibtex/cython.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex index 15c5c62..f5f4069 100644 --- a/reproduce/software/bibtex/fftw.tex +++ b/reproduce/software/bibtex/fftw.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex index bbfdec1..c3cd7d6 100644 --- a/reproduce/software/bibtex/galsim.tex +++ b/reproduce/software/bibtex/galsim.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex index 7d56e3e..8f97305 100644 --- a/reproduce/software/bibtex/gnuastro.tex +++ b/reproduce/software/bibtex/gnuastro.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex index afdd6a6..6063722 100644 --- a/reproduce/software/bibtex/healpix.tex +++ b/reproduce/software/bibtex/healpix.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex index 1d5270b..a1f8b4d 100644 --- a/reproduce/software/bibtex/imfit.tex +++ b/reproduce/software/bibtex/imfit.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/kiwisolver.tex b/reproduce/software/bibtex/kiwisolver.tex index 47d3f56..62df2a2 100644 --- a/reproduce/software/bibtex/kiwisolver.tex +++ b/reproduce/software/bibtex/kiwisolver.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2025-2025 Boud Roukema <boud@cosmo.torun.pl> +%% Copyright (C) 2025-2026 Boud Roukema <boud@cosmo.torun.pl> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex index ec7bab4..68d648a 100644 --- a/reproduce/software/bibtex/matplotlib.tex +++ b/reproduce/software/bibtex/matplotlib.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex index 83510dd..b973248 100644 --- a/reproduce/software/bibtex/missfits.tex +++ b/reproduce/software/bibtex/missfits.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2020-2025 Surena Fatemi <surena.fatemi@ipm.ir> +%% Copyright (C) 2020-2026 Surena Fatemi <surena.fatemi@ipm.ir> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex index 10e0e74..6125251 100644 --- a/reproduce/software/bibtex/mpi4py.tex +++ b/reproduce/software/bibtex/mpi4py.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex index fb017c4..8955d3d 100644 --- a/reproduce/software/bibtex/numpy.tex +++ b/reproduce/software/bibtex/numpy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/parallel.tex b/reproduce/software/bibtex/parallel.tex new file mode 100644 index 0000000..1ba1018 --- /dev/null +++ b/reproduce/software/bibtex/parallel.tex @@ -0,0 +1,15 @@ +%% Copyright (C) 2026-2026 Boud Roukema <boud@cosmo.torun.pl> +%% +%% Copying and distribution of this file, with or without modification, +%% are permitted in any medium without royalty provided the copyright +%% notice and this notice are preserved. This file is offered as-is, +%% without any warranty. + +@ARTICLE{parallel, + author = {{Tange}, Ole}, + title = "{GNU Parallel 20260322, https://doi.org/10.5281/zenodo.19321428}", + journal = {Zenodo.19321428}, + year = 2026, + month = mar, + doi = {10.5281/zenodo.19321428}, +} diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex index c58eeeb..f17fc3a 100644 --- a/reproduce/software/bibtex/r-cran.tex +++ b/reproduce/software/bibtex/r-cran.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2022-2025 Boud Roukema <boud@cosmo.torun.pl> -%% Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2022-2026 Boud Roukema <boud@cosmo.torun.pl> +%% Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex index b5c4da9..271a09e 100644 --- a/reproduce/software/bibtex/scamp.tex +++ b/reproduce/software/bibtex/scamp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex index 1296393..0574891 100644 --- a/reproduce/software/bibtex/scipy.tex +++ b/reproduce/software/bibtex/scipy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex index 818f04a..33ec1e8 100644 --- a/reproduce/software/bibtex/sextractor.tex +++ b/reproduce/software/bibtex/sextractor.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sip_tpv.tex b/reproduce/software/bibtex/sip_tpv.tex index 0d52e33..d9b7cdd 100644 --- a/reproduce/software/bibtex/sip_tpv.tex +++ b/reproduce/software/bibtex/sip_tpv.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex index e0989f9..813942d 100644 --- a/reproduce/software/bibtex/swarp.tex +++ b/reproduce/software/bibtex/swarp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex index 01e481b..18e4254 100644 --- a/reproduce/software/bibtex/sympy.tex +++ b/reproduce/software/bibtex/sympy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex index caf1500..00d8195 100644 --- a/reproduce/software/bibtex/tides.tex +++ b/reproduce/software/bibtex/tides.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index 341a78e..7d45d06 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -3,18 +3,37 @@ # This is just a template for the './project configure' script to fill # in. Please don't make any change to this file. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. -BDIR = @bdir@ -INDIR = @indir@ + + + + +# Local system settings +# --------------------- +# +# Build directory (mandatory). All the created files of the project will be +# within this directory. +BDIR = @bdir@ + +# Input data directory. This can be empty or a non-existant location. If +# so, then the inputs will be downloaded from the 'INPUTS.conf' into the +# build directory. +INDIR = @indir@ + +# Software source code directory. This can be empty or a non-existant +# location. If so, the software tarballs will be downloaded. DEPENDENCIES-DIR = @ddir@ -SYS_CPATH = @sys_cpath@ -DOWNLOADER = @downloader@ -GROUP-NAME = @groupname@ + +# Other local settings (compiler, downloader and user). +SYS_CPATH = @sys_cpath@ +GROUP-NAME = @groupname@ +DOWNLOADER = @downloader@ +SYS_LIBRARY_SH_PATH = @sys_library_sh_path@ diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index 716fd41..51791a5 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -1,7 +1,7 @@ # Necessary high-level software to build in this project. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -42,5 +42,7 @@ top-level-programs = gnuastro top-level-python = # R libraries/modules -# [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all] +# +# As of 2022-01-02: to have all of the R packages, select 'r-cran-cowplot +# r-cran-gridExtra'. top-level-r-cran = diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 89738ce..9e1c437 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -1,8 +1,8 @@ # sha512 checksums of all the necessary software tarballs. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -15,43 +15,42 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = 52fa7d14e5f05d7b1b5f64ca110388db119fd6b8d4cc25011e0e25848491507e610259091c56f3ca7a7688ee2547f8a98de2005626b35c29558e71f28e29b848 -binutils-checksum = efbc5957bd22804a860261886598778347e82f9cbc0728d21d26748b7296e34328fdc16252868169594a001a301babbcd0964d9c508523736bc79cac2aff8efc +bash-checksum = b905e107403ceb25ad92f26ab71d6a7f12b1cadbcb27de9f5fefa7da31e96de0be281f8095170ed36e3fc22237dcfc252ff674925e6123638f6a3e11f3c5ecfd +binutils-checksum = ad7bbebc0c4e537c15d7537027246e2c1c0d355efcd6a369c7ef91c6491ec6a6e9af24c60b7df7508213abeedbd2e53c41549889073ac1f629b0746b78ee894b bzip2-checksum = 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df45f00e9eaeae2f27f813f31591590c961da2f6bff15bba6fb2a14d529c221f39b29894b8da408fe49cd4b760840a0e05c4baef377ccfacd9983c0bba83d6d8 diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg index c3cea11..40f672c 100644 --- a/reproduce/software/config/numpy-scipy.cfg +++ b/reproduce/software/config/numpy-scipy.cfg @@ -7,8 +7,8 @@ # appropriate sections. Not all packages will use all sections so you # should leave out sections that your package does not use. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index f0e040e..26c992f 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -3,7 +3,7 @@ # is irrelevant). Note that this is not a to be read as a variable but will # be parsed as a list. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh index deae01b..e2c7bb7 100755 --- a/reproduce/software/config/software_acknowledge_context.sh +++ b/reproduce/software/config/software_acknowledge_context.sh @@ -10,8 +10,8 @@ # your project to make a smoothly readable English text. Afterwards, please # feel free to modify them as you wish. # -# Copyright (C) 2021-2025 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index e68a771..7210fd5 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -4,8 +4,8 @@ # name to this variable (you can check in 'ctan.org' to find the official # name). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2022-2025 Boud Roukema <boud@astro.uni.torun.pl> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Boud Roukema <boud@astro.uni.torun.pl> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf index 0babd69..56f1129 100644 --- a/reproduce/software/config/texlive.conf +++ b/reproduce/software/config/texlive.conf @@ -2,7 +2,7 @@ # # installdir: Install directory # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 8bf7b23..f976930 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -3,8 +3,8 @@ # If un-commented the URLs of this file will be used. Otherwise default # servers (primarily on 'zenodo.org') will be checked for the tarball. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2020-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -25,7 +25,7 @@ #curl-url = https://curl.haxx.se/download #dash-url = http://gondor.apana.org.au/~herbert/dash/files #diffutils-url = http://ftp.gnu.org/gnu/diffutils -#file-url = ftp://ftp.astron.com/pub/file +#file-url = http://ftp.astron.com/pub/file #findutils-url = http://ftp.gnu.org/gnu/findutils #flock-url = https://github.com/discoteq/flock/releases #gawk-url = http://ftp.gnu.org/gnu/gawk @@ -35,12 +35,12 @@ #gmp-url = https://gmplib.org/download/gmp #grep-url = http://ftp.gnu.org/gnu/grep #gzip-url = http://akhlaghi.org/src -#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure +#isl-url = http://gcc.gnu.org/pub/gcc/infrastructure #less-url = http://www.greenwoodsoftware.com/less/ #libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv #libtool-url = http://ftp.gnu.org/gnu/libtool #libunistring-url = http://ftp.gnu.org/gnu/libunistring -#libxml2-url = ftp://xmlsoft.org/libxml2 +#libxml2-url = https://download.gnome.org/sources/libxml2 #lzip-url = https://download.savannah.gnu.org/releases/lzip/ #m4-url = http://akhlaghi.org/maneage-software #make-url = http://akhlaghi.org/src @@ -52,7 +52,6 @@ #patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version) #perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}')) #pkgconfig-url = http://pkg-config.freedesktop.org/releases -#podlators-url = https://www.eyrie.org/~eagle/software/podlators/ #readline-url = http://ftp.gnu.org/gnu/readline #sed-url = http://ftp.gnu.org/gnu/sed #tar-url = http://ftp.gnu.org/gnu/tar @@ -94,6 +93,9 @@ #expat-url = https://github.com/libexpat/libexpat/releases #fftw-url = https://fftw.org #flex-url = https://github.com/westes/flex/files/981163 +#framel: 2025-05-23 from https://software.igwn.org/lscsoft/source/framel-8.47.3.tar.xz; +# see also https://git.ligo.org/virgo/virgoapp/Fr +#framel-url = https://software.igwn.org/lscsoft/source #freetype-url = https://download.savannah.gnu.org/releases/freetype #gdb-url = http://ftp.gnu.org/gnu/gdb #ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html @@ -140,13 +142,16 @@ #scamp-url = http://akhlaghi.org/maneage-software #scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download #sextractor-url = http://akhlaghi.org/maneage-software +#sqlite-url - https://sqlite.org #swarp-url = https://www.astromatic.net/download/swarp #swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) +#tcltk-defaults - 2025-05-24 - repacked from Debian/testing https://packages.debian.org/source/testing/tcltk-defaults #tides-url = http://akhlaghi.org/maneage-software +#tzdb-url = https://www.iana.org/time-zones #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.40 #valgrind-url = https://sourceware.org/pub/valgrind #vim-url = ftp://ftp.vim.org/pub/vim/unix -#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib +#wcslib-url = https://www.atnf.csiro.au/computing/software/wcs/wcslib-releases #xlsxio-url = https://github.com/brechtsanders/xlsxio/archive #yaml-url = pyyaml.org/download/libyaml @@ -195,8 +200,10 @@ # But be sure to send us a link to the tarball so we upload it to Maneage's # backup servers. #astropy-url = https://files.pythonhosted.org/packages/45/12/a1c582b3f9df5e2680eae0ed82c8057ae06d6130a1f7a5c0770fa899737e +#astropy-healpix-url = https://files.pythonhosted.org/packages/5c/8a/dfd71e4db13706383ca2cea0b2831eb10da2c286d4494f183f80fc03cbc2 #astropy-iers-data-url = https://files.pythonhosted.org/packages/a1/4d/b9511aba29d4330437497166a7049ab9bac53e344c54e44a35390724ca37 #contourpy-url = https://files.pythonhosted.org/packages/25/c2/fc7193cc5383637ff390a712e88e4ded0452c9fbcf84abe3de5ea3df1866 +#cosmodesi-mpytools = https://github.com/cosmodesi/mpytools/archive #cppy-url = https://files.pythonhosted.org/packages/45/ed/b35645a1b285bce356f30cc0fe77a042375c385660ccd61e0cdc4c1f7c44 #cycler-url = https://files.pythonhosted.org/packages/a9/95/a3dbbb5028f35eafb79008e7522a75244477d2838f38cbb722248dabc2a8 #cython-url = https://files.pythonhosted.org/packages/5a/25/886e197c97a4b8e254173002cdc141441e878ff29aaa7d9ba560cd6e4866 @@ -205,7 +212,9 @@ #flit-core-url = https://files.pythonhosted.org/packages/bc/18/b9b81cab2b8f63e6e7f72e1ba2766a0454fcd563e7a77b8299cb917ba805 #fonttools-url = https://files.pythonhosted.org/packages/1c/8c/9ffa2a555af0e5e5d0e2ed7fdd8c9bef474ed676995bb4c57c9cd0014248 #gpep517-url = https://files.pythonhosted.org/packages/1c/53/e6ad6aa7036d62ac009986e1e5180465353344afd958ddc8ac15e3b632bc +#healpy-url = https://files.pythonhosted.org/packages/a4/db/4d1e7fcd429151edb1e2c6d10365f86de217097e276c0b44dbc197028d21 #kiwisolver-url = https://files.pythonhosted.org/packages/82/59/7c91426a8ac292e1cdd53a63b6d9439abd573c875c3f92c146767dd33faf +#ligo-skymap-url = https://files.pythonhosted.org/packages/f5/f5/fa82a88c104a9d1fcf863e05a56b213b512db05bc72b5c4f1c7c7d3bc118 #matplotlib-url = https://files.pythonhosted.org/packages/68/dd/fa2e1a45fce2d09f4aea3cee169760e672c8262325aa5796c49d543dc7e6 #meson-url = https://files.pythonhosted.org/packages/02/98/bbcaf6caaaa0510a68834f119ac793a8abade6ff827fc2791eeb6f8b4a66 #meson-python-url = https://files.pythonhosted.org/packages/67/66/91d242ea8dd1729addd36069318ba2cd03874872764f316c3bb51b633ed2 diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 9c82c8d..3e4ec9a 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -1,8 +1,8 @@ # Versions of the various dependencies # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -17,42 +17,35 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier for 'awk'; don't modify this line) -bash-version = 5.2.37 -binutils-version = 2.43.1 +bash-version = 5.3.9 +binutils-version = 2.45.1 bison-version = 3.8.2 -coreutils-version = 9.6 -curl-version = 8.11.1 -dash-version = 0.5.12 -diffutils-version = 3.10 -file-version = 5.46 +coreutils-version = 9.11 +curl-version = 8.17.0 +diffutils-version = 3.12 findutils-version = 4.10.0 flock-version = 0.4.0 -gawk-version = 5.3.1 -gcc-version = 14.2.0 -gettext-version = 0.23.1 -git-version = 2.48.1 -gmp-version = 6.3.0 -grep-version = 3.11 -gzip-version = 1.13 +gawk-version = 5.3.2 +gettext-version = 1.0 +git-version = 2.52.0 +grep-version = 3.12 +gzip-version = 1.14 help2man-version = 1.49.3 isl-version = 0.27 -less-version = 668 +less-version = 685 libiconv-version = 1.18 libtool-version = 2.5.4 -libunistring-version = 1.3 -libxml2-version = 2.13.5 +libunistring-version = 1.4.2 +libxml2-version = 2.15.1 lzip-version = 1.25 -m4-version = 1.4.19 +m4-version = 1.4.21 make-version = 4.4.1 mpc-version = 1.3.1 -mpfr-version = 4.2.1 -nano-version = 8.3 -ncurses-version = 6.5 -openssl-version = 3.4.0 -perl-version = 5.40.1 -pkgconfig-version = 0.29.2 -podlators-version = 6.0.2 -readline-version = 8.2.13 +mpfr-version = 4.2.2 +nano-version = 9.0 +openssl-version = 3.6.0 +perl-version = 5.42.0 +readline-version = 8.3.3 sed-version = 4.9 tar-version = 1.35 texinfo-version = 7.2 @@ -60,7 +53,6 @@ unzip-version = 6.0 wget-version = 1.25.0 which-version = 2.23 xz-version = 5.6.3 -zip-version = 3.0 zlib-version = 1.3.1 # Version-dependent build @@ -90,6 +82,38 @@ certpem-version = 2025-02-10 # supported. patchelf-version = 0.13 +# Dash +# ---- +# +# Dash 0.5.13.1 causes the build of pkg-config to put the building of +# Maneage within apptainer to go into the background! Forcing the user to +# run 'fg' to continue the build. When updating to a later version, be +# careful about this: that it does not cause this issue. +dash-version = 0.5.12 + +# Not working with C23 +# -------------------- +# +# As of GCC 15.1, the default C standard has been changed from C17 to C23 +# and the following software cannot be built with C23. So we have added +# '-std=$(GNU_STD_OLD)' to the CFLAGS environment variable in their build +# rules. A test is done in 'configure.sh' to see if the host compiler has +# 'gnu17' and if not, to use 'gnu99'. After updating a package's version +# (and if you have GCC 15.1 or later) first remove '-std=$(GNU_STD_OLD)' +# and then try the build. If it works, move the software package back up to +# the main list before making a commit. +gmp-version = 6.3.0 +file-version = 5.46 +ncurses-version = 6.5 +pkgconfig-version = 0.29.2 + +# GCC +# --- +# +# There is a version-specific 'sed -e' fix for a bug in this version of GCC +# that should no longer be necessary in future versions. +gcc-version = 15.2.0 + @@ -112,21 +136,23 @@ automake-version = 1.17 boost-version = 1.87.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 4.5.0 +cfitsio-version = 4.6.3 cmake-version = 3.31.5 eigen-version = 3.4.0 emacs-version = 28.1 expat-version = 2.6.4 fftw-version = 3.3.10 flex-version = 2.6.4-410-74a89fd +framel-version = 8.47.3 freetype-version = 2.13.3 gdb-version = 11.1 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -ghostscript-version = 10.04.0 -gnuastro-version = 0.23 +ghostscript-version = 10.06.0 +gnuastro-version = 0.24 gperf-version = 3.1 gsl-version = 2.8 +healpix-version = 3.83-2024Nov13 icu-version = 70.1 imagemagick-version = 7.1.0-13 imfit-version = 1.6.1 @@ -140,14 +166,17 @@ libpaper-version = 1.1.29 libpng-version = 1.6.46 libtiff-version = 4.7.0 libtirpc-version = 1.2.6 +metaio-version = 8.5.0-a5da19d metastore-version = 1.1.2-23-fa9170b missfits-version = 2.8.0 -ninjabuild-version = 1.12.1 +ninjabuild-version = 1.13.2 openblas-version = 0.3.29 -openmpi-version = 4.1.1 +openmpi-version = 5.0.10 openssh-version = 8.0p1 +parallel-version = 20260322 patch-version = 2.7.6 pcre-version = 8.44 +pcre2-version = 10.45 pixman-version = 0.40.0 plplot-version = 5.15.0 r-cran-version = 4.1.2 @@ -155,15 +184,19 @@ rpcsvc-proto-version = 1.4 scamp-version = 2.10.0 scons-version = 3.0.5 sextractor-version = 2.25.0 +sqlite-version = 3.53.0 swarp-version = 2.41.5 -swig-version = 4.0.2 +swig-version = 4.3.1 +tcl-version = 9.1a1 tides-version = 2.0 -util-linux-version = 2.40.4 +tk-version = 9.1a1 +tzdb-version = 2026a +util-linux-version = 2.41.3 valgrind-version = 3.18.1 -vim-version = 9.0 -wcslib-version = 8.4 +wcslib-version = 8.5 xlsxio-version = 0.2.21 yaml-version = 0.2.5 +zip-version = 3.0-15 # Xorg packages fontconfig-version = 2.16.0 @@ -181,8 +214,12 @@ xcb-proto-version = 1.17.0 xorgproto-version = 2024.1 xtrans-version = 1.5.2 -# Version-dependent build -# ----------------------- +# Not working with C23 (similar to same topic in basic): future versions +# may have fixed this problem, so when updating, first remove '-std=gnu17' +# and if it builds without crashing, put this back in the normal list. +vim-version = 9.0 + +# Version is in the build recipe lapack-version = 3.8.0 libgit2-version = 1.9.0 @@ -202,6 +239,17 @@ minizip-version = $(zlib-version) # version 1.12.0. hdf5-version = 1.13.1 +# The lalsuite tarball within Maneage is based on the upstream commit +# 678514ed of 21 May 2025 of https://git.ligo.org/lscsoft/lalsuite. But +# instead of being a 950 Mb '.tar.gz' file including the '.git/' directory +# (or a 320 Mb '.tar.gz' file without the '.git/' directory), our tarball +# is a 25 Mb '.tar.lz' file (a factor of 30 to 10 times smaller). The main +# difference (apart from the extra compression provided by lzip) is that +# this light tarball does not include the big test data files. A +# description of how this tarball was made and what files have been removed +# is in the 'README-Maneage-LightWeight.md' file that is within the +# tarball. +lalsuite-version = v7.26-15-g1e4c5e5080 @@ -216,74 +264,77 @@ hdf5-version = 1.13.1 # URL in 'reproduce/software/make/python.mk'. # # CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line) -asn1crypto-version = 0.24.0 -asteval-version = 0.9.16 -astropy-version = 7.0.1 +astropy-healpix-version = 1.1.2 astropy-iers-data-version = 0.2025.2.24.0.34.4 +astropy-version = 7.1.0 beautifulsoup4-version = 4.10.0 -beniget-version = 0.4.1 -certifi-version = 2018.11.29 cffi-version = 1.15.0 -chardet-version = 3.0.4 +colorama-version = 0.4.6 contourpy-version = 1.3.1 -corner-version = 2.0.1 +cosmodesi-mpytools-version = 1.0.0-04369fc9 cppy-version = 1.3.1 cycler-version = 0.12.1 cython-version = 3.0.12 -eigency-version = 1.77 -emcee-version = 3.0.1 -entrypoints-version = 0.3 -esutil-version = 0.6.9 +exceptiongroup-version = 1.3.0 extension-helpers-version = 1.2.0 features-version = 0.5.12 flake8-version = 3.7.8 flit-core-version = 3.11.0 +flit-scm-version = 1.7.0 fonttools-version = 4.56.0 -future-version = 0.18.1 galsim-version = 2.3.5 -gast-version = 0.5.3 gpep517-version = 16 h5py-version = 2.10.0 +hatch-vcs-version = 0.5.0 +hatchling-version = 1.27.0 +healpy-version = 1.18.1 html5lib-version = 1.0.1 -idna-version = 2.8 -jeepney-version = 0.4 +igwn-ligolw-version = 2.1.0 +igwn-segments-version = 2.1.0 +iniconfig-version = 2.1.0 jinja2-version = 3.0.3 +joblib-version = 1.5.0 kiwisolver-version = 1.4.8 +ligo-skymap-version = 2.4.0 lmfit-version = 0.9.14 +lscsoft-glue-version = 4.1.0 lsstdesccoord-version = 1.2.0 -markupsafe-version = 2.0.1 -meson-version = 1.7.0 meson-python-version = 0.17.1 -mpi4py-version = 3.1.3 -mpmath-version = 1.1.0 +meson-version = 1.7.0 +mpi4py-version = 4.0.3 +networkx-version = 3.5 numpy-version = 2.2.3 packaging-version = 24.2 -pexpect-version = 4.7.0 +pandas-version = 2.2.3 +pathspec-version = 0.12.1 pillow-version = 11.1.0 pip-version = 19.0.2 -ply-version = 3.11 +pluggy-version = 1.6.0 pybind11-version = 2.13.6 -pycodestyle-version = 2.5.0 -pycparser-version = 2.19 pyerfa-version = 2.0.1.5 -pyflakes-version = 2.1.1 -pyproject-metadata-version = 0.9.0 +pyfftw-version = 0.15.1 +pygments-version = 2.19.2 pyparsing-version = 3.2.1 -pypkgconfig-version = 1.5.1 +pyproject-metadata-version = 0.9.0 +pytest-version = 8.4.1 python-dateutil-version = 2.9.0.post0 python-installer-version = 0.7.0 +python3-fitsio-version = 1.3.0 pythran-version = 0.11.0 +pytz-version = 2025.2 pyyaml-version = 6.0.2 requests-version = 2.21.0 -setuptools-version = 75.8.0 +scikit-base-version = 0.12.2 +scikit-learn-version = 1.6.1 setuptools-scm-version = 8.2.0 +setuptools-version = 80.8.0 sip_tpv-version = 1.1 six-version = 1.17.0 -soupsieve-version = 1.8 sympy-version = 1.4 -uncertainties-version = 3.1.6 -urllib3-version = 1.24.1 -webencodings-version = 0.5.1 +threadpoolctl-version = 3.6.0 +tqdm-version = 4.67.1 +trove-classifiers-version = 2025.5.9.12 +versioneer-version = 0.29 wheel-version = 0.45.1 # Matplotlib and Scipy are big packages that may have difficulty resolving @@ -293,26 +344,11 @@ scipy-version = 1.15.2 # CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line) -# Special Python modules: -# -# Healpy: When any Python module is requested, healpix will also build its -# Python module Healpy. -# -# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting -# it here. When future versions fix the problem, we'll un-comment it again. -#healpy-version = xxxxx - -# Problematic software that are currently ignored: - -# Healpix 3.80 has different installation scheme that is not yet -# implemented here, and unfortunately healpix 3.50 has conflicts with -# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring -# it. -#healpix-version = 3.50 +# Problematic software that is currently ignored: # Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731), # so it and its dependencies are being ignored: 'cryptography', and thus @@ -324,6 +360,34 @@ semantic-version-version = 2.10.0 #keyring-version = 18.0.0 #astroquery-version = 0.4 +# Not yet adated to the GPEP517 build method: +#asn1crypto-version = 0.24.0 +#asteval-version = 0.9.16 +#beniget-version = 0.4.1 +#certifi-version = 2018.11.29 +#chardet-version = 3.0.4 +#corner-version = 2.0.1 +#eigency-version = 1.77 +#emcee-version = 3.0.1 +#entrypoints-version = 0.3 +#esutil-version = 0.6.9 +#future-version = 0.18.1 +#gast-version = 0.5.3 +#idna-version = 2.8 +#jeepney-version = 0.4 +#markupsafe-version = 2.0.1 +#mpmath-version = 1.1.0 +#pexpect-version = 4.7.0 +#ply-version = 3.11 +#pycodestyle-version = 2.5.0 +#pycparser-version = 2.19 +#pyflakes-version = 2.1.1 +#pypkgconfig-version = 1.5.1 +#soupsieve-version = 1.8 +#uncertainties-version = 3.1.6 +#urllib3-version = 1.24.1 +#webencodings-version = 0.5.1 + diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md index 00afef4..0d1464d 100644 --- a/reproduce/software/make/README.md +++ b/reproduce/software/make/README.md @@ -1,7 +1,7 @@ Software building instructions ------------------------------ -Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This directory contains Makefiles that are called by the high-level diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk index 6e7d415..a20f558 100644 --- a/reproduce/software/make/atlas-multiple.mk +++ b/reproduce/software/make/atlas-multiple.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk index 2b68677..79f5b42 100644 --- a/reproduce/software/make/atlas-single.mk +++ b/reproduce/software/make/atlas-single.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 40c5a4e..92fa8f0 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -21,9 +21,9 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -39,7 +39,7 @@ # along with this Makefile. If not, see <http://www.gnu.org/licenses/>. # Top level environment -include reproduce/software/config/LOCAL.conf +include .build/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk include reproduce/software/config/versions.conf include reproduce/software/config/checksums.conf @@ -63,10 +63,13 @@ ibidir = $(BDIR)/software/installed/version-info/proglib # editor) is installed by default, it is recommended to have it in the # 'basic.mk', so Maneaged projects can be edited on any system (even when # there is no command-line text editor available). +# +# The recipe is '@echo > /dev/null' so Make does not print "make: Nothing +# to be done for 'all'." targets-proglib = low-level-links \ gcc-$(gcc-version) \ nano-$(nano-version) -all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) +all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)); @echo > /dev/null # Define the shell environment # ---------------------------- @@ -102,12 +105,13 @@ endif export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) # This is the "basic" tools where we are relying on the host operating -# system, but are slowly populating our basic software envirnoment. To run -# (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here, -# we'll first tell the programs to look into any possible pre-defined -# 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries. We -# will also make sure that there is no "current directory" in it (by -# removing a starting or trailing ':' and any occurance of '::'. +# system, but are slowly populating our basic software envirnoment. So +# here, we are also appending the host's 'LD_LIBRARY_PATH' to Maneage's +# installed library path. It is just important to keep Maneage's library +# directories first so when something has been built, the newly built +# software use (link-with) Maneage's libraries, not the host's. We will +# also make sure that there is no "current directory" in it (by removing a +# starting or trailing ':' and any occurance of '::'). # # But first: in case LD_LIBRARY_PATH is empty, give it the default value of # $(sys_library_sh_path) (which was the location of the libraries needed by @@ -117,7 +121,7 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) ifeq ($(strip $(LD_LIBRARY_PATH)),) export LD_LIBRARY_PATH=$(sys_library_sh_path) endif -export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \ +export LD_LIBRARY_PATH := $(shell echo $(ildir):$(LD_LIBRARY_PATH) \ | sed -e's/::/:/g' -e's/^://' -e's/:$$//') # RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is @@ -250,6 +254,23 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ # systems) $(call makelink,ldd) +# zic: On some systems like Debian GNU/Linux, 'zic' may be in +# '/usr/sbin' and is available to users. But it is not normally in +# the 'PATH' of a non-root user. This is because the executables +# there are normally system-level commands, and most are executable +# only by the root user. + $(call makelink,zic) + if [ "x$$(command -v zic)" = x ]; then + zicfullpath=$$(PATH=$${PATH}:/usr/sbin command -v zic) + if [ "x$${zicfullpath}" = x ]; then + printf "Warning: 'zic' not found. You may need it for" + printf " higher-level packages such as 'tzdb'. Install" + printf " 'zic' if needed.\n" + else + ln -sf $$(realpath $${zicfullpath}) $(ibdir)/zic + fi + fi + # We want this to be empty (so it doesn't interefere with the other # files in 'ibidir'. touch $@ @@ -341,24 +362,22 @@ $(ibidir)/zlib-$(zlib-version): | $(ibdir) $(ildir) $(lockdir) echo "Zlib $(zlib-version)" > $@ # GNU Tar: When built statically, tar gives a segmentation fault on -# unpacking Bash. So we'll build it dynamically. Note that technically, zip -# and unzip aren't dependencies of Tar, but for a clean build, we'll set -# Tar to be the last compression-related software (the first-set of -# software to be built). +# unpacking Bash. So we'll build it dynamically. $(ibidir)/tar-$(tar-version): \ $(ibidir)/xz-$(xz-version) \ $(ibidir)/gzip-$(gzip-version) \ $(ibidir)/zlib-$(zlib-version) \ $(ibidir)/bzip2-$(bzip2-version) -# Since all later programs depend on Tar, the configuration will hit -# a bottleneck here: only making Tar. So its more efficient to built -# it on multiple threads (even when the user's Make doesn't pass down -# the number of threads). +# About the onfigurations: nls and iconv were creating problems with +# the dependencies on MacOs and are not relevant in the context of +# Maneage, hence, they are disabled. $(call unsafe-config) tarball=tar-$(tar-version).tar.lz $(call import-source, $(tar-url), $(tar-checksum)) - $(call gbuild, tar-$(tar-version), , , -j$(numthreads) V=1) + $(call gbuild, tar-$(tar-version), , \ + --disable-nls am_cv_func_iconv=no, \ + -j$(numthreads) V=1) echo "GNU Tar $(tar-version)" > $@ @@ -375,8 +394,8 @@ $(ibidir)/tar-$(tar-version): \ # Patchelf is necessary for some software on GNU/Linux systems, its job is # to manually insert RPATH into the dynamically-linked executable. Since # all the other software depend on Pathelf, to avoid manually repeating as -# a prerequisite (and forgetting in others causing bugs), we'll put it as a -# dependancy of 'tar'. +# a prerequisite (and forgetting in others causing bugs), it is installed +# in this phase (right after 'tar'). $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) tarball=patchelf-$(patchelf-version).tar.lz $(call import-source, $(patchelf-url), $(patchelf-checksum)) @@ -387,7 +406,47 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) echo "PatchELF $(patchelf-version)" > $@ fi +$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version) +# Download the tarball. + tarball=pkg-config-$(pkgconfig-version).tar.lz + $(call import-source, $(pkgconfig-url), $(pkgconfig-checksum)) + +# An existing 'libiconv' can cause a conflict with 'pkg-config' (this +# is why 'libiconv' depends on 'pkg-config'). On a clean build, +# 'pkg-config' is built first. But when we don't have a clean build +# (and 'libiconv' exists) there will be a problem. So before +# re-building 'pkg-config', we'll remove any installation of +# 'libiconv'. + rm -f $(ildir)/libiconv* $(idir)/include/iconv.h + +# Some Mac OS systems may have a version of the GNU C Compiler (GCC) +# installed that doesn't support some necessary features of building +# Glib (as part of pkg-config), so we will disable pkg-config's +# internal Glib for Mac systems, and to be further safe, we'll make +# sure it will use LLVM's Clang. +# +# On macOS systems, to ensure that Clang can build pkg-config, take +# the following steps: +# 1. Install the latest Glib via Homebrew: +# brew install glib +# 2. Set these environment variables before configuring Maneage: +# export GLIB_CFLAGS=$(pkg-config --cflags glib-2.0) +# export GLIB_LIBS=$(pkg-config --libs glib-2.0) +# 3. Ensure PKG_CONFIG_PATH includes Homebrew's pkgconfig: +# export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH + if [ x$(on_mac_os) = xyes ]; then + extra_pkgconf="" + export compiler="CC=clang" + else + export compiler="" + extra_pkgconf="--with-internal-glib" + fi + export CFLAGS="-std=$(std_c_old) $$CFLAGS" + $(call gbuild, pkg-config-$(pkgconfig-version), static, \ + $$compiler $$extra_pkgconf \ + --with-pc-path=$(ildir)/pkgconfig, V=1) + echo "pkg-config $(pkgconfig-version)" > $@ @@ -407,7 +466,10 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version) # function (for tilde expansion). The first can be disabled with # '--disable-load', but unfortunately I don't know any way to fix the # second. So, we'll have to build it dynamically for now. -$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) \ + $(ibidir)/pkg-config-$(pkgconfig-version) + +# Prepare the input. tarball=ncurses-$(ncurses-version).tar.lz $(call import-source, $(ncurses-url), $(ncurses-checksum)) @@ -423,11 +485,18 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk* # Standard build process. + export CFLAGS="-std=$(std_c_old) $$CFLAGS" $(call gbuild, ncurses-$(ncurses-version), static, \ - --with-shared --enable-rpath --without-normal \ - --without-debug --with-cxx-binding \ - --with-cxx-shared --enable-widec --enable-pc-files \ - --with-pkg-config=$(ildir)/pkgconfig, -j$(numthreads)) + --with-shared \ + --enable-rpath \ + --enable-widec \ + --without-debug \ + --without-normal \ + --enable-pc-files \ + --with-cxx-shared \ + --with-cxx-binding \ + --with-pkg-config=$(ildir)/pkgconfig, \ + -j$(numthreads)) # Unfortunately there are many problems with 'ncurses' using "normal" # (or 8-bit) characters. The standard way that will work is to build @@ -536,6 +605,7 @@ $(ibidir)/readline-$(readline-version): \ # pname=bash50-$(printf "%03d" $i); \ # wget http://ftp.gnu.org/gnu/bash/bash-5.0-patches/$pname -O ../$pname;\ # patch -p0 -i ../$pname; \ +# rm ../$pname; \ # done # $ cd .. # $ mv bash-5.0 bash-5.0.$number @@ -564,7 +634,7 @@ $(ibidir)/bash-$(bash-version): \ export CFLAGS="$$CFLAGS \ -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \ -DSTANDARD_UTILS_PATH='\"$(ibdir)\"' \ - -DSYS_BASHRC='\"$(BASH_ENV)\"' " + -DSYS_BASHRC='\"$(BASH_ENV)\"'" $(call gbuild, bash-$(bash-version),, $$stopt \ --with-installed-readline=$(ildir) \ --with-curses=yes, \ @@ -581,9 +651,6 @@ $(ibidir)/bash-$(bash-version): \ # shell. By convention, 'sh' is just a symbolic link to the preferred # shell executable. So we'll define '$(ibdir)/sh' as a symbolic link # to the Bash that we just built and installed. -# -# Just to be sure that the installation step above went well, before -# making the link, we'll see if the file actually exists there. ln -fs $(ibdir)/bash $(ibdir)/sh echo "GNU Bash $(bash-version)" > $@ @@ -596,6 +663,7 @@ $(ibidir)/bash-$(bash-version): \ + # Level 4: Most other programs # ---------------------------- @@ -609,15 +677,21 @@ perl-conflddlflags = else perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS" endif -$(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/perl-$(perl-version): $(ibidir)/tar-$(tar-version) + +# Import tarball. tarball=perl-$(perl-version).tar.lz $(call import-source, $(perl-url), $(perl-checksum)) + +# Extract the version strings. major_version=$$(echo $(perl-version) \ | sed -e's/\./ /g' \ | awk '{printf("%d", $$1)}') base_version=$$(echo $(perl-version) \ | sed -e's/\./ /g' \ | awk '{printf("%d.%d", $$1, $$2)}') + +# Unpack, build and install. cd $(ddir) rm -rf perl-$(perl-version) tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions @@ -628,15 +702,15 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) -Duseshrplib \ -Dprefix=$(idir) \ -Dvendorprefix=$(idir) \ - -Dprivlib=$(idir)/share/perl$$major_version/core_perl \ - -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \ - -Dsitelib=$(idir)/share/perl$$major_version/site_perl \ - -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/site_perl \ - -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \ - -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \ - -Dscriptdir=$(idir)/bin/core_perl \ - -Dsitescript=$(idir)/bin/site_perl \ - -Dvendorscript=$(idir)/bin/vendor_perl \ + -Dprivlib=$(idir)/share/perl$$major_version/perl-core \ + -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/perl-core \ + -Dsitelib=$(idir)/share/perl$$major_version/perl-site \ + -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/perl-site \ + -Dvendorlib=$(idir)/share/perl$$major_version/perl-vendor \ + -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/perl-vendor \ + -Dscriptdir=$(idir)/bin/perl-core \ + -Dsitescript=$(idir)/bin/perl-site \ + -Dvendorscript=$(idir)/bin/perl-vendor \ -Dinc_version_list=none \ -Dman1ext=1perl \ -Dman3ext=3perl \ @@ -647,7 +721,14 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) make install cd .. rm -rf perl-$(perl-version) - cd $$topdir + +# Symbolic links to necessary Perl programs (that Perl installs in +# the 'perl-core' directory. + ln -sf $(ibdir)/perl-core/xsubpp $(ibdir)/xsubpp + ln -sf $(ibdir)/perl-core/pod2man $(ibdir)/pod2man + ln -sf $(ibdir)/perl-core/pod2text $(ibdir)/pod2text + +# Final target. echo "Perl $(perl-version)" > $@ @@ -716,29 +797,6 @@ $(ibidir)/coreutils-$(coreutils-version): \ rm -rf coreutils-$(coreutils-version) echo "GNU Coreutils $(coreutils-version)" > $@ -# Podlators -# -# POD is short for "Plain Old Documentation", that is the format used in -# Perl's documentation. Podlators provies two executables pod2man and -# pod2text convert this into the roff format (used in man pages) or pod2 It -# is used by some software like OpenSSL to create their man pages. -$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) - tarball=podlators-$(podlators-version).tar.lz - $(call import-source, $(podlators-url), $(podlators-checksum)) - cd $(ddir) - rm -rf podlators-$(podlators-version) - tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions - cd podlators-$(podlators-version) - $(shsrcdir)/prep-source.sh $(ibdir) - perl Makefile.PL - make - make install - ln -sf $(ibdir)/site_perl/pod2man $(ibdir)/pod2man - ln -sf $(ibdir)/site_perl/pod2text $(ibdir)/pod2text - cd .. - rm -rf podlators-$(podlators-version) - echo "podlators $(podlators-version)" > $@ - # OpenSSL # # Until we find a nice and generic way to create an updated CA file in the @@ -746,8 +804,9 @@ $(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) # along with the other tarballs. $(idir)/etc:; mkdir $@ $(idir)/etc/ssl: | $(idir)/etc; mkdir $@ -$(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \ - | $(idir)/etc/ssl +$(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \ + $(ibidir)/patchelf-$(patchelf-version) \ + | $(idir)/etc/ssl # First download the certificates and copy them into the # installation directory. @@ -903,7 +962,7 @@ $(ibidir)/diffutils-$(diffutils-version): \ echo "GNU Diffutils $(diffutils-version)" > $@ $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version) - export CFLAGS="-std=c99 $$CFLAGS" + export CFLAGS="-std=$(std_c_old) $$CFLAGS" tarball=file-$(file-version).tar.lz $(call import-source, $(file-url), $(file-checksum)) $(call gbuild, file-$(file-version), static, \ @@ -955,6 +1014,8 @@ $(ibidir)/help2man-$(help2man-version): \ $(call gbuild, help2man-$(help2man-version), static, ,V=1) echo "Help2man $(Help2man-version)" > $@ +# Even though libiconv does not use pkg-config, pkg-config conflicts with +# it, see the comments in pkg-config for more. $(ibidir)/libiconv-$(libiconv-version): \ $(ibidir)/pkg-config-$(pkgconfig-version) tarball=libiconv-$(libiconv-version).tar.lz @@ -970,12 +1031,14 @@ $(ibidir)/libunistring-$(libunistring-version): \ -j$(numthreads)) echo "GNU libunistring $(libunistring-version)" > $@ -$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/tar-$(tar-version) # The libxml2 tarball also contains Python bindings which are built # and installed to a system directory by default. If you don't need # the Python bindings, the easiest solution is to compile without # Python support: './configure --without-python'. If you really need -# the Python bindings, use '--with-python-install-dir=DIR' instead. +# its Python bindings: +# 1. Add the Python dependency. +# 2. Add the '--with-python-install-dir=DIR' configure option. tarball=libxml2-$(libxml2-version).tar.lz $(call import-source, $(libxml2-url), $(libxml2-checksum)) $(call gbuild, libxml2-$(libxml2-version), static, \ @@ -1014,6 +1077,7 @@ $(ibidir)/gmp-$(gmp-version): \ $(ibidir)/coreutils-$(coreutils-version) tarball=gmp-$(gmp-version).tar.lz $(call import-source, $(gmp-url), $(gmp-checksum)) + export CFLAGS="-std=$(std_c_old) $$CFLAGS" $(call gbuild, gmp-$(gmp-version), static, \ --enable-cxx --enable-fat, \ -j$(numthreads)) @@ -1060,10 +1124,6 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) -j$(numthreads) V=1) echo "GNU Grep $(grep-version)" > $@ -# M4 doesn't depend on PatchELF, but just to be consistent with the -# levels/phases introduced here (where the compressors are level 1, -# PatchELF is level 2, and ...), we'll set it as a dependency. -# # The '--with-syscmd-shell' is used as the default shell and if not given, # 'm4' will use '/bin/sh' (which is not under Maneage control and can cause # problems in 'high-level.mk' because it closes off the system's @@ -1071,7 +1131,7 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) # library, the high-level programs will not be built). We are setting this # default shell to Dash because M4 is built before our own Bash. Recall # that Dash is built before we enter this Makefile. -$(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) +$(ibidir)/m4-$(m4-version): $(ibidir)/libiconv-$(libiconv-version) tarball=m4-$(m4-version).tar.lz $(call import-source, $(m4-url), $(m4-checksum)) $(call gbuild, m4-$(m4-version), static, \ @@ -1085,32 +1145,6 @@ $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version) $(call gbuild, mpfr-$(mpfr-version), static) echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@ -$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version) - -# Download the tarball. - tarball=pkg-config-$(pkgconfig-version).tar.lz - $(call import-source, $(pkgconfig-url), $(pkgconfig-checksum)) - -# An existing 'libiconv' can cause a conflict with 'pkg-config', this -# is why 'libiconv' depends on 'pkg-config'. On a clean build, -# 'pkg-config' is built first. But when we don't have a clean build -# (and 'libiconv' exists) there will be a problem. So before -# re-building 'pkg-config', we'll remove any installation of -# 'libiconv'. - rm -f $(ildir)/libiconv* $(idir)/include/iconv.h - -# Some Mac OS systems may have a version of the GNU C Compiler (GCC) -# installed that doesn't support some necessary features of building -# Glib (as part of pkg-config). So to be safe, for Mac systems, we'll -# make sure it will use LLVM's Clang. - if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang" - else export compiler="" - fi - $(call gbuild, pkg-config-$(pkgconfig-version), static, \ - $$compiler --with-internal-glib \ - --with-pc-path=$(ildir)/pkgconfig, V=1) - echo "pkg-config $(pkgconfig-version)" > $@ - $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version) tarball=sed-$(sed-version).tar.lz $(call import-source, $(sed-url), $(sed-checksum)) @@ -1218,6 +1252,7 @@ $(ibidir)/binutils-$(binutils-version): \ $(call makelink,ld) $(call makelink,nm) $(call makelink,ps) + $(call makelink,lipo) $(call makelink,strip) $(call makelink,ranlib) echo "" > $@ @@ -1441,6 +1476,14 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \ -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +# Bug in GCC 15.2.0 using glibc 2.43 (see [1]) as fixed in [2]. +# [1] https://patchwork.ozlabs.org/project/gcc/patch/e1679277-d7c9-49aa-8365-a8dca082d9bd@web.de +# [2] https://github.com/johnny-mnemonic/toolchain-autobuilds/commit/9585fdfc + sed -e's|char \*q = strchr (p + 1,|const char \*q = strchr (p + 1,|' \ + libgomp/affinity-fmt.c > affinity-fmt-tmp.c + mv affinity-fmt-tmp.c libgomp/affinity-fmt.c + + # Set the build directory for the processing. mkdir build cd build diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index 463fbbf..984d0bf 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -3,7 +3,7 @@ # imported into 'basic.mk' and 'high-level.mk'. They should be activated # with Make's 'Call' function. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 4ed5d62..d059544 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -29,7 +29,7 @@ # along with this Makefile. If not, see <http://www.gnu.org/licenses/>. # Top level environment (same as 'basic.mk') -include reproduce/software/config/LOCAL.conf +include .build/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk include reproduce/software/config/versions.conf include reproduce/software/config/checksums.conf @@ -123,11 +123,12 @@ ifneq ($(strip $(offline)),1) target-texlive := $(itidir)/texlive endif -# Ultimate Makefile target. +# Ultimate Makefile target. The recipe is '@echo > /dev/null' so Make does +# not print "make: Nothing to be done for 'all'." all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \ $(foreach p, $(targets-python), $(ipydir)/$(p)) \ $(foreach p, $(targets-r-cran), $(ircrandir)/$(p)) \ - $(target-texlive) + $(target-texlive); @echo > /dev/null # Define the shell environment # ---------------------------- @@ -437,6 +438,23 @@ $(ibidir)/cfitsio-$(cfitsio-version): tar cf $$customtar cfitsio-$(cfitsio-version) cd $$topdir +# Add SSE2 optimization only when we are on a Linux kernel or using +# macOS on an Intel CPU. + arch=$$(uname -m) + unames=$$(uname -s) + if [ "$$unames" = "Linux" ]; then + confopts="$$confopts --enable-sse2" + elif [ "$$unames" = "Darwin" ] && [ "$$arch" = "x86_64" ]; then + confopts="$$confopts --enable-sse2" + fi + +# On macOS, system libraries (e.g., libSystem) are inside the SDK, +# not standard paths. 'xcrun' provides the correct SDK path; use $$ +# so it is evaluated by the shell (not Make). + if [ $(on_mac_os) = yes ]; then + export SDKROOT=$$(xcrun --show-sdk-path) + fi + # Continue the standard build on the customized tarball. Note that # with the installation of CFITSIO, 'fpack' and 'funpack' are not # installed by default. Because of that, they are added explicity. @@ -445,7 +463,10 @@ $(ibidir)/cfitsio-$(cfitsio-version): # specific 'shared' target for the building of the shared libraries. export gbuild_tar=$(ddir)/$$customtar $(call gbuild, cfitsio-$(cfitsio-version), , \ - --enable-sse2 --enable-reentrant \ + $$confopts \ + --disable-curl \ + --disable-fortran \ + --enable-reentrant \ --with-bzip2=$(idir), , \ make fpack funpack) rm $$customtar @@ -504,36 +525,62 @@ $(ibidir)/expat-$(expat-version): $(call gbuild, expat-$(expat-version), static) echo "Expat $(expat-version)" > $@ +# FFTW manual customizations: +# +# - To activate the OpenMPI features of FFTW, add OpenMPI as a dependency +# of FFTW: the necessary flags are automatically added if OpenMPI was +# installed before FFTW. +# +# - There are Intel-specific optimizations that can be enabled by adding +# the following two options to 'opts' +# +# --enable-avx --enable-sse2 +# +# However, they cause crashes on non-Intel processors (has been confirmed +# in ARM's aarch64). So in the generic scenario they are +# removed. Checking how these optimizations affect the numerical accuracy +# of the result (and thus optionally adding them for Intel-based +# processors) should be studied before they are optionally added for +# Intel-based CPUs (and ignored for others). $(ibidir)/fftw-$(fftw-version): # Prepare the source tarball. tarball=fftw-$(fftw-version).tar.lz $(call import-source, $(fftw-url), $(fftw-checksum)) -# FFTW's single and double precision libraries must be built -# independently: for the the single-precision library, we need to add -# the '--enable-float' option. We will build this first, then the -# default double-precision library. -# -# There are Intel-specific optimizations that can be enabled by -# adding the following two options to 'confop' -# -# --enable-avx --enable-sse2 -# -# However, they cause crashs on non-Intel processors (has been -# confirmed in ARM's aarch64). So in the generic scenario they are -# removed. Checking how these optimizations affect the numeric -# accuracy of the result (and thus optionally adding them for -# Intel-based processors) should be studied before they are -# optionally added for Intel-based CPUs (and ignored for others). - confop="--enable-shared --enable-threads" - $(call gbuild, fftw-$(fftw-version), static, \ - $$confop --enable-float) - $(call gbuild, fftw-$(fftw-version), static, \ - $$confop) - cp $(dtexdir)/fftw.tex $(ictdir)/ +# Specific customizations: you can add the options mentioned above +# after the 'if' statements, for example: "opts=$$opts EXTRA". + opts="--enable-shared --enable-threads" + if [ x$(on_mac_os) = xyes ]; then opts="$$opts --disable-fortran" + else + if [ -f $(ibidir)/openmpi-$(openmpi-version) ]; then + opts="$$opts --enable-openmp --enable-mpi" + fi + fi + +# FFTW's single, double and long-double precision libraries must be +# built separately (fully independent builds and installs). + $(call gbuild, fftw-$(fftw-version), static, $$opts) + $(call gbuild, fftw-$(fftw-version), static, $$opts \ + --enable-float) + $(call gbuild, fftw-$(fftw-version), static, $$opts \ + --enable-long-double) + cp -pv $(dtexdir)/fftw.tex $(ictdir)/ echo "FFTW $(fftw-version) \citep{fftw}" > $@ +# 2026-02-20 'framel' is needed by the python package lalsuite, which is +# needed by ligo-skymap; currently the compile of 'framel' 8.49.0 fails with +# +# error: initialization of 'void (*)(void)' from incompatible +# pointer type 'void (*)(int, char *)' [-Wincompatible-pointer-types] +# +# Hints: try using gcc -std=gnu99 or -std=gnu11 (default is -std=gnu17). +$(ibidir)/framel-$(framel-version): $(ibidir)/cmake-$(cmake-version) + tarball=framel-$(framel-version).tar.lz + $(call import-source, $(framel-url), $(framel-checksum)) + $(call cbuild, framel-$(framel-version), static) + echo "Framel $(framel-version)" > $@ + $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version) # As of version 2.13.2, FreeType doesn't account for the 'SHELL' # environment variable. The issue has been reported to the @@ -570,64 +617,114 @@ $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version) echo "HDF5 library $(hdf5-version)" > $@ # HEALPix includes the source of its C, C++, Python (and several other -# languages) libraries within one tarball. We will include the Python -# installation only when any other Python module is requested (in -# 'TARGETS.conf'). +# languages) libraries within one tarball. However, we do not build the +# python version here; instead we provide 'healpy' as a separate package; +# see 'python.mk' for the build rule. # # Note that the default './configure' script is an interactive script which # is hard to automate. So we need to go into the 'autotools' directory of # the 'C' and 'cxx' directories and configure the GNU Build System (with # 'autoreconf', which uses 'autoconf' and 'automake') to easily build the # HEALPix C/C++ libraries in batch mode. -ifeq ($(strip $(targets-python)),) -healpix-python-dep = -else -healpix-python-dep = $(ipydir)/matplotlib-$(matplotlib-version) \ - $(ipydir)/astropy-$(astropy-version) -endif -$(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \ +$(ibidir)/healpix-$(healpix-version): \ $(ibidir)/cfitsio-$(cfitsio-version) \ $(ibidir)/autoconf-$(autoconf-version) \ $(ibidir)/automake-$(automake-version) + +# Import the tarball. tarball=healpix-$(healpix-version).tar.lz $(call import-source, $(healpix-url), $(healpix-checksum)) - if [ x"$(healpix-python-dep)" = x ]; then - pycommand1="echo no-healpy-because-no-other-python" - pycommand2="echo no-healpy-because-no-other-python" - else - pycommand1="python setup.py build" - pycommand2="python setup.py install" - fi - rm -rf $(ddir)/Healpix_$(healpix-version) + +# Setup the build directory + rm -rf $(ddir)/healpix-$(healpix-version) topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions - cd Healpix_$(healpix-version) + cd healpix-$(healpix-version) $(shsrcdir)/prep-source.sh $(ibdir) - cd src/C/autotools + +# Compile and install libsharp: + cd src/common_libraries/libsharp autoreconf --install ./configure --prefix=$(idir) make V=1 -j$(numthreads) SHELL=$(ibdir)/bash make install - cd ../../cxx/autotools/ + +# Compile and install the C version: + cd ../../C/autotools + printf "\n\nDEBUG ONLY\n\n"; /bin/pwd; printf "\nGUBED\n\n\n" + autoreconf --install + ./configure --prefix=$(idir) + make V=1 -j$(numthreads) SHELL=$(ibdir)/bash + make install + +# Compile and install the C++ version: + cd ../../cxx/ + printf "\n\nDEBUG.BBBB ONLY\n\n"; /bin/pwd; printf "\nBBB.GUBED\n\n\n" autoreconf --install ./configure --prefix=$(idir) # With CFITSIO 4.0, the 'CFITSIO_VERSION' macro has three -# components. But this version of Healpix doesn't yet account for -# this. +# components. But this (which?) version of Healpix doesn't yet +# account for this. sed -i -e's/CFITSIO_VERSION/fitsversion/' cxxsupport/fitshandle.cc # Continue with the building. make V=1 -j$(numthreads) SHELL=$(ibdir)/bash make install - cd ../../healpy - $$pycommand1 - $$pycommand2 + +# Finalize the build cd $$topdir - rm -rf $(ddir)/Healpix_$(healpix-version) + rm -rf $(ddir)/healpix-$(healpix-version) cp $(dtexdir)/healpix.tex $(ictdir)/ echo "HEALPix $(healpix-version) \citep{healpix}" > $@ +# 2025-05-24 The build rules here for 'lalsuite' include git initialisation +# with a dummy commit of all the source files since this is required for an +# install unless the .git/ directory (currently 650 Mb) is included in the +# tarball. Our lalsuite tarball also has many big data test files removed, +# since these are unlikely to be needed in typically astronomy usage; this +# brings the .tar.lz file down to 25 Mb from the default of about 950 Mb +# (tar.gz) or 740 Mb (tar.lz). +# +# If you need to do full gravitational wave work with 'lalsuite', then you +# should provide an alternative tarball and edit the three files +# reproduce/software/config/{versions,checksums,urls}.conf in order to use +# your preferred tarball. +$(ipydir)/lalsuite-$(lalsuite-version): \ + $(ibidir)/automake-$(automake-version) \ + $(ibidir)/swig-$(swig-version) \ + $(ibidir)/metaio-$(metaio-version) \ + $(ibidir)/framel-$(framel-version) \ + $(ipydir)/astropy-$(astropy-version) \ + $(ipydir)/igwn-segments-$(igwn-segments-version) \ + $(ipydir)/lscsoft-glue-$(lscsoft-glue-version) \ + $(ipydir)/python-dateutil-$(python-dateutil-version) + tarball=lalsuite-$(lalsuite-version).tar.lz + $(call import-source, $(lalsuite-url), \ + $(lalsuite-checksum)) + +# First: build from source as if it's a C source only. + cd $(ddir) + unpackdir=lalsuite-$(lalsuite-version) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) + +# A git commit is needed to generate version-control files; the +# strings in these will be rather arbitrary and should be ignored. + git init && git add . + git commit -a --no-edit -m "Dummy commit" \ + --author "Tarball <tar@ball.only>" + autoreconf + ./configure --prefix="$(idir)" --enable-swig-python + make + make install + +# Clean up and build final tarball + cd $(ddir); rm -fr $$unpackdir + echo "LALSuite $(lalsuite-version)" > $@ + $(ibidir)/libbsd-$(libbsd-version): $(ibidir)/libmd-$(libmd-version) tarball=libbsd-$(libbsd-version).tar.lz $(call import-source, $(libbsd-url), $(libbsd-checksum)) @@ -730,7 +827,8 @@ $(ibidir)/libtiff-$(libtiff-version): $(ibidir)/libjpeg-$(libjpeg-version) $(call gbuild, libtiff-$(libtiff-version), static, \ --disable-jbig \ --disable-webp \ - --disable-zstd) + --disable-zstd \ + --disable-libdeflate ) echo "Libtiff $(libtiff-version)" > $@ $(ibidir)/libtirpc-$(libtirpc-version): @@ -838,9 +936,52 @@ $(ibidir)/ninjabuild-$(ninjabuild-version): $(ibidir)/cmake-$(cmake-version) echo "Ninja build system $(ninjabuild-version)" > $@ $(ibidir)/openblas-$(openblas-version): + +# Import the tarball. tarball=openblas-$(openblas-version).tar.lz $(call import-source, $(openblas-url), $(openblas-checksum)) - if [ x$(on_mac_os) = xyes ]; then export CC=clang; fi + +# If 'gcc' is actually a symbolic link to 'clang', then print the +# following message to guide the user on how to prepare their +# environment. + if $$CC --version | grep clang &> /dev/null; then + +# Print message. + echo; echo + printf "*********************************************\n" + printf "OpenBlas could not be installed with Clang!\n\n" + printf "In order to install OpenBLAS, GCC and Gfortran are " + printf "needed. You can take the following steps to fix " + printf "this:\n\n" + printf "1. Install GCC with Homebrew.\n" + printf "2. Get the full path of 'gcc', 'g++', and 'gfortran' " + printf "(for example with 'which gcc').\n" + printf "3. Comment the 'exit 1' and un-comment (and edit) the " + printf "'export's that are below this message (in the " + printf "'openblas' rule of " + printf "'reproduce/software/make/high-level.mk', within the " + printf "'openblas' rule):\n\n" + printf " exit 1\n" + printf " #export CC=/opt/homebrew/bin/gcc-XX\n" + printf " #export CXX=/opt/homebrew/bin/g++-XX\n" + printf " #export FC=/opt/homebrew/bin/gfortran-XX\n\n" + printf " with the lines:\n\n" + printf " #exit 1\n" + printf " export CC=/opt/homebrew/bin/gcc-15\n" + printf " export CXX=/opt/homebrew/bin/g++-15\n" + printf " export FC=/opt/homebrew/bin/gfortran-15\n\n" + printf "5. Re-configure Maneage.\n" + printf "*********************************************\n" + echo; echo + +# Parts to modify when the message above is printed. + exit 1 + #export CC=/opt/homebrew/bin/gcc-XX + #export CXX=/opt/homebrew/bin/g++-XX + #export FC=/opt/homebrew/bin/gfortran-XX + fi + +# Do the build. cd $(ddir) tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions cd openblas-$(openblas-version) @@ -907,6 +1048,209 @@ $(ibidir)/tides-$(tides-version): cp $(dtexdir)/tides.tex $(ictdir)/ echo "TIDES $(tides-version) \citep{tides}" > $@ +$(ibidir)/sqlite-$(sqlite-version): $(ibidir)/tcl-$(tcl-version) + tarball=sqlite-$(sqlite-version).tar.lz + $(call import-source, $(sqlite-url), $(sqlite-checksum)) + $(call gbuild, sqlite-$(sqlite-version),, \ + --enable-all --enable-static --enable-shared) + echo "Sqlite $(sqlite-version)" > $@ + +$(ibidir)/tcl-$(tcl-version): $(ibidir)/zlib-$(zlib-version) \ + $(ibidir)/tzdb-$(tzdb-version) + +# If both the tcl and tk packages are needed, then they must be built +# together, with identical version numbers. Thus, for simplicity in +# the build system, whether or not we build only tcl, or both tcl and +# tk, we must check that the versions are identical. + if [ "x$(tcl-version)" != "x$(tk-version)" ]; then + printf "Error: This build system requires identical tcl and " + printf "tk versions to be selected **even if** tk is not " + printf "going to be built. However, tcl-version=$(tcl-version) " + printf "while tk-version=$(tk-version)\n" + exit 1 + fi + +# Prepare the input tarball. + tarball=tcl-$(tcl-version).tar.lz + $(call import-source, $(tcl-url), $(tcl-checksum)) + +# Setup the build directory + cd $(ddir) + unpackdir_tcl=tcl-$(tcl-version) + rm -rf $${unpackdir_tcl} + +# Install TCL + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd - # return to the top maneage directory + cd $(ddir)/$${unpackdir_tcl}/unix + $(shsrcdir)/prep-source.sh $(ibdir) + ./configure --prefix="$(idir)" + make -j$(numthreads) + make install + cd - # return to the top maneage directory + +# Setup the 'tclsh' symbolic link. + maj_min_version=$$(printf $(tcl-version)| \ + sed -e "s;^\([0-9]*\.[0-9]*\).*\';\1;") + printf "Will symlink tclsh$${maj_min_version} as tclsh ...\n" + cd $(ibdir) + rm -fv tclsh && ln -sv tclsh$${maj_min_version} tclsh + cd - + cd $(ddir) + +# Finalize. + if (printf "$$unpackdir_tcl" | grep "[a-z][a-z]"); then \ + rm -fr $$unpackdir_tcl + fi + echo "Tcl $(tcl-version)" > $(ibidir)/tcl-$(tcl-version) + + +# The tk library needs the X11 library for building GUIs, and should not +# normally be needed for a non-interactive project. However, GUIs built +# with tk might be convenient during development of a project, since visual +# checks within the maneage shell may be useful. +# +# We need to rebuild tcl temporarily in the temporary build area in order +# to build tk. However, we want the tk target to be dependent on tcl as a +# prerequisite to avoid the possibility of parallel builds that risk +# conflicting within the build area because of duplicate use of the same +# tcl package directory after untarring the archive. +$(ibidir)/tk-$(tk-version): $(ibidir)/zip-$(zip-version) \ + $(ibidir)/tcl-$(tcl-version) \ + $(ibidir)/libx11-$(libx11-version) \ + +# Prepare the tarball. + tarball=tk-$(tk-version).tar.lz + $(call import-source, $(tk-url), $(tk-checksum)) + +# If both the tcl and tk packages are needed, then they must be built +# together, with identical version numbers. Thus, for simplicity in +# the build system, whether or not we build only tcl, or both tcl and +# tk, we must check that the versions are identical. + if [ "x$(tcl-version)" != "x$(tk-version)" ]; then + printf "Error: This build system requires identical tcl and " + printf "tk versions to be selected **even if** tk is not " + printf "going to be built. However, tcl-version=$(tcl-version) " + printf "while tk-version=$(tk-version)\n" + exit 1 + fi + +# Make sure no temporary directory exists. + cd $(ddir) + unpackdir=tk-$(tk-version) + if (printf "$$unpackdir" | grep "[a-z][a-z]"); then + rm -rf $$unpackdir + fi + +# Install TK: zipfs is being disabled because of the problem with +# installing zip (see the comments above zip). + cd $(ddir) + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir/unix + $(shsrcdir)/prep-source.sh $(ibdir) + ./configure --prefix="$(idir)" --with-tcl=$(ildir) + make -j$(numthreads) + make install + +# Finalize. + cd $(ddir) + if (printf "$$unpackdir" | grep "[a-z][a-z]"); then \ + rm -fr $$unpackdir; fi + echo "Tk $(tk-version)" > $(ibidir)/tk-$(tk-version) + + + +# WARNING: Dependence on glibc: tzdb (time zone data base) uses the 'zic' +# program from the GNU C library. Until Maneage builds its own glibc, it is +# imported from the host operating system in the 'low-level-links' step of +# 'basic.mk'. +$(ibidir)/tzdb-$(tzdb-version): + +# Import the tarball + tarball=tzdb-$(tzdb-version).tar.lz + $(call import-source, $(tzdb-url), $(tzdb-checksum)) + +# Unpack the tarball. + cd $(ddir) + unpackdir=tzdb-$(tzdb-version) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd $$unpackdir + +# Make necessary corrections. + TZGEN=$(strip $(ddir))/$$unpackdir/tzgen + printf "\n\n\n_____TZGEN=$${TZGEN}_____\n\n\n" + make AWK=gawk BACKWARD="backward" PACKRATDATA=backzone \ + PACKRATLIST=zone.tab VERSION_DEPS= tzdata.zi leapseconds + +# Build the timezone data +# +# The '-b fat' option was created in glibc by around 2020, when +# '-b slim' became the default. Allowing the default of '-b slim' +# could potentially lead to a #Y2038 bug [3]. +# +# Some other hacks are also needed for older glibc. +# +# [1] https://mm.icann.org/pipermail/tz-announce/2020-October/000059.html +# [2] https://github.com/stub42/pytz/issues/48 +# [3] https://en.wikipedia.org/wiki/Year_2038_problem + BFAT_OPTION=$$(if (zic -b fat 2>/dev/null); then \ + printf "%sb fat" "-"; else printf ""; fi) + if [ "x$${BFAT_OPTION}" = "x" ]; then \ + sed -e 's/Sa\([^a-zA-Z]\)/Sat\1/g' \ + -e 's/Su\([^a-zA-Z]\)/Sun\1/g' \ + -e 's/^\(.\|..\) Sat/\1 Sa/' \ + -e "s/lastSu\'/lastSun/" tzdata.zi \ + | grep -v "^L" \ + > tzdata.zi.3letter.days + zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null \ + tzdata.zi.3letter.days + zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \ + tzdata.zi.3letter.days + else + zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null tzdata.zi + zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \ + tzdata.zi + fi + +# Replace hardlinks by symlinks + if [ "x$${BFAT_OPTION}" = "x" ]; then + +# Older method of creating symbolic links: + grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \ + | while read L target name ; do + absolute_name="$${TZGEN}/$$name" + relative_target=$$(realpath -m -s \ + --relative-to="$${absolute_name%/*}" \ + "$${TZGEN}/$$target") + maybe_newdir=$$(printf $$name | sed -e "s;/[^/]*\';;") + mkdir -p $${TZGEN}/$${maybe_newdir} + mkdir -p $${TZGEN}/right/$${maybe_newdir} + ln -sf "$$relative_target" "$${TZGEN}/$$name" + ln -sf "$$relative_target" "$${TZGEN}/right/$$name" + done + + else + +# More recent (2025-05-25) method of creating symbolic links: + grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \ + | while read L target name ; do + absolute_name="$${TZGEN}/$$name" + relative_target=$$(realpath -m -s \ + --relative-to="$${absolute_name%/*}" \ + "$${TZGEN}/$$target") + ln -sf "$$relative_target" "$${TZGEN}/$$name" + ln -sf "$$relative_target" "$${TZGEN}/right/$$name" + done + fi + +# Generate a posixrules file (with a UTC timezone) and install. + ln -s Etc/UTC $${TZGEN}/posixrules + mkdir -p $(idir)/share/zoneinfo + cp -rv $${TZGEN}/* $(idir)/share/zoneinfo/ + cd $(ddir); rm -rf $$unpackdir + echo "IANA Time Zone Database (tzdb) $(tzdb-version)" > $@ + $(ibidir)/valgrind-$(valgrind-version): tarball=valgrind-$(valgrind-version).tar.lz $(call import-source, $(valgrind-url), $(valgrind-checksum)) @@ -962,7 +1306,19 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) tarball=wcslib-$(wcslib-version).tar.lz $(call import-source, $(wcslib-url), $(wcslib-checksum)) +# macOS arm64 fix: reserve extra space in binary headers so +# install_name_tool (called bellow, after installation) can safely +# update library paths. Without this, we get the following error: +# "larger updated load commands do not fit". SDKROOT is also +# necessary for system libraries. + if [ x$(on_mac_os) = xyes ]; then + sdk=$$(xcrun --show-sdk-path) + LDFLAGS="$$LDFLAGS -isysroot $$sdk" + export LDFLAGS="$$LDFLAGS -Wl,-headerpad_max_install_names" + fi + # Build WCSLIB while disabling some features: +# # - Fortran is disabled because as of May 2023, on macOS systems # where we do not install GCC (and thus a standard 'gfortran'), the # LLVM Fortran compiler is not complete and will cause a crash. If @@ -971,11 +1327,18 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) # systems. Hopefully some time in the future, GCC will also be # install-able on macOS within Maneage or LLVM's 'gfortran' will # also be complete and will not cause a crash. +# # - PGPLOT is disabled because it has many manual steps in its # installation. Therefore, we currently do not build PGPlots in # Maneage. Once (if) it is added, we can remove '--without-pgplot'. +# +# - Flex is disabled because we have not made it a prerequisite for +# the 'wcslib' target, and we don't want the behaviour to differ +# between host OSes that may or may not have 'flex', or may have +# different versions of 'flex'. $(call gbuild, wcslib-$(wcslib-version), , \ LIBS="-pthread -lcurl -lm" \ + --disable-flex \ --without-pgplot \ --disable-fortran \ --with-cfitsiolib=$(ildir) \ @@ -1185,6 +1548,13 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tarball=ghostscript-$(ghostscript-version).tar.lz $(call import-source, $(ghostscript-url), $(ghostscript-checksum)) +# On macOS we use the system compiler and linker. The system linker +# there doesn't support '--copy-dt-needed-entries', while the one on +# Linux crashes if we remove it. So we only activate it on macOS. + if [ x$(on_mac_os) = xno ]; then + export LDFLAGS="$$LDFLAGS -Wl,--copy-dt-needed-entries" + fi + # Unpack it and configure Ghostscript. The option # '-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library from being # required at compile time. @@ -1192,13 +1562,12 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions cd ghostscript-$(ghostscript-version) $(shsrcdir)/prep-source.sh $(ibdir) - ./configure --prefix=$(idir) \ - --disable-cups \ + ./configure --disable-cups \ + --prefix=$(idir) \ --enable-dynamic \ --disable-compile-inits \ - --disable-hidden-visibility \ - CFLAGS="-DPNG_ARM_NEON_OPT=0" \ - LDFLAGS=-Wl,--copy-dt-needed-entries + --disable-hidden-visibility \ + CFLAGS="-DPNG_ARM_NEON_OPT=0" # Build and install the program and the shared libraries. make V=1 -j$(numthreads) @@ -1223,18 +1592,61 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ rm -rf ghostscript-$(ghostscript-version) echo "GPL Ghostscript $(ghostscript-version)" > $@ +# Gnuastro can optionally depend on libgit2, but it is not included as a +# dependency here for the two reasons below. If you would like to have it, +# add it as a dependency (its build instruction and dependencies are here +# already), then remove the '--without-libgit2' configure option) and also +# comment the following two generic configuration lines: 'outfitsnocommit' +# and 'outfitsnoconfig'. +# - Within Maneage, we have everything under Git already and users are +# expected to include the version in all their products. +# - libgit2 can only be built with CMake (which takes extremely long to +# compile: possibly even longer than GCC!). +# - Maneage is often run on HPCs that can have network connections +# between the storage and processer and the necessary libgit2 +# operations on every created file can have a performance impact. $(ibidir)/gnuastro-$(gnuastro-version): \ $(ibidir)/gsl-$(gsl-version) \ $(ibidir)/wcslib-$(wcslib-version) \ $(ibidir)/libjpeg-$(libjpeg-version) \ $(ibidir)/libtiff-$(libtiff-version) \ - $(ibidir)/libgit2-$(libgit2-version) \ $(ibidir)/ghostscript-$(ghostscript-version) + +# Generic installation. tarball=gnuastro-$(gnuastro-version).tar.lz $(call import-source, $(gnuastro-url), $(gnuastro-checksum)) - $(call gbuild, gnuastro-$(gnuastro-version), static, , \ - -j$(numthreads)) + $(call gbuild, gnuastro-$(gnuastro-version), static, \ + --without-libgit2, -j$(numthreads)) cp $(dtexdir)/gnuastro.tex $(ictdir)/ + +# Generally, besides the Git commit, we are also disabling the +# default mode of printing any type of metadata and versions of +# dependencies in output headers (through the installation-wide +# configuration file). This is done because within a large pipeline, +# Gnuastro is used to create many intermediate files (that are +# deleted shortly after being created) and it is not worth the +# overhread to keep this information in those intermediate products: +# it is the pipeline's responsibility to put them in the final +# outputs. We recommend to use the Gnuastro Fits program's keyword +# writing options to add as much contextual metadata on your final +# products as possible. Some tips: +# - The creation date is not good (because it is not reproducible +# and will make simple validation hard). The project's Commit +# should be used instead. +# - Define a keyword to keep the public URL of the repository of +# the Maneage'd project. In this way, a person who gets your +# final product can easily check that for all the information +# (including software versions and configuration options). + gconf=$(idir)/etc/gnuastro/gnuastro.conf + echo "" >> $$gconf + echo "# Maneage specific (see Gnuastro build rule for details)." \ + >> $$gconf + echo " outfitsnocommit = 1" >> $$gconf + echo " outfitsnoconfig = 1" >> $$gconf + echo " outfitsnodate = 1" >> $$gconf + echo " outfitsnoversions = 1" >> $$gconf + +# Final target. echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version) @@ -1352,6 +1764,16 @@ $(ibidir)/imfit-$(imfit-version): \ rm -rf $$unpackdir echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ +# This is the LIGO lscsoft package 'metaio' [1] (to be distinguished from +# some other packages with the same name). +# +# [1] https://git.ligo.org/lscsoft/metaio +$(ibidir)/metaio-$(metaio-version): + tarball=metaio-$(metaio-version).tar.lz + $(call import-source, $(metaio-url), $(metaio-checksum)) + $(call gbuild, metaio-$(metaio-version), static) + echo "Lscsoft Metaio $(metaio-version)" > $@ + # Minizip 1.x is actually distributed within zlib. It doesn't have its own # independent tarball. So we need a custom build, which include the GNU # Autotools (Autoconf and Automake). Note that Minizip 2.x isn't like this @@ -1458,6 +1880,25 @@ $(ibidir)/netpbm-$(netpbm-version): \ rm -rf $$unpackdir echo "Netpbm $(netpbm-version)" > $@ +$(ibidir)/parallel-$(parallel-version): + +# Prepare the tarball and build it. + tarball=parallel-$(parallel-version).tar.lz + $(call import-source, $(parallel-url), $(parallel-checksum)) + $(call gbuild, parallel-$(parallel-version), static) + +# GNU Parallel requires the users to acknowledge that they will cite +# it. Otherwise, it prints a warning on every run: reminding the user +# to cite it. In Maneage, we make sure that all software that request +# citation are cited automatically, so there is no need for a +# Maneager to get this warning and we can automatically ensure the +# developer that it will be cited. + echo "will cite" | $(ibdir)/parallel --citation + +# Copy the BibTeX source of the citation and finish. + cp -pv $(dtexdir)/parallel.tex $(ictdir)/ + echo "GNU Parallel $(parallel-version) \citep{parallel}" > $@ + $(ibidir)/patch-$(patch-version): tarball=patch-$(patch-version).tar.gz $(call import-source, $(patch-url), $(patch-checksum)) @@ -1476,6 +1917,13 @@ $(ibidir)/pcre-$(pcre-version): , V=1 -j$(numthreads)) echo "Perl Compatible Regular Expressions $(pcre-version)" > $@ +$(ibidir)/pcre2-$(pcre2-version): + tarball=pcre2-$(pcre2-version).tar.lz + $(call import-source, $(pcre2-url), $(pcre2-checksum)) + $(call gbuild, pcre2-$(pcre2-version), static) + echo "Perl Compatible Regular Expressions 2 $(pcre2-version)" > $@ + + # On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0 # needs the 'finite' function of 'math.h' which has been deprecated in # macOS. By manually adding "#define finite isfinite" in 'math.h' like @@ -1642,15 +2090,13 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version) cp $(dtexdir)/swarp.tex $(ictdir)/ echo "SWarp $(swarp-version) \citep{swarp}" > $@ -$(ibidir)/swig-$(swig-version): - -# Option --without-pcre was a suggestion once the configure step was -# tried and it failed. It was not recommended but it works! pcr is a -# dependency of swig +$(ibidir)/swig-$(swig-version): \ + $(ibidir)/pcre2-$(pcre2-version) +# Not disabling pcre, since PCRE is needed for lalsuite (python). tarball=swig-$(swig-version).tar.lz $(call import-source, $(swig-url), $(swig-checksum)) $(call gbuild, swig-$(swig-version), static, \ - --without-pcre --without-tcl) + --without-tcl) echo "Swig $(swig-version)" > $@ # The disables: @@ -1717,8 +2163,19 @@ $(ibidir)/util-linux-$(util-linux-version): \ # manually by commenting the relevant files in the # 'configure.ac'. sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \ + -e's|UL_BUILD_INIT(\[bits\], \[yes\])|UL_BUILD_INIT(\[bits\], \[no\])|' \ -i configure.ac +# 'autogen.sh' checks for dependencies, but 'flex' (that is not built +# in Maneage) is not needed when compiling from tarball (see: +# https://github.com/util-linux/util-linux/pull/2531#issuecomment-1798020594) + sed -i '/flex/d' autogen.sh + ./autogen.sh + +# The 'autogen.sh' call resets the 'SHELL' (that was corrected in +# 'prep-source.sh') to '/bin/sh'. Therefore, we need to correct it. + sed -i -e's|SHELL = /bin/sh|SHELL = $(SHELL)|' po/Makefile.in.in + # Having updated 'configure.ac', we need to re-generate the # './configure' script with 'autoreconf' (which is part of Autoconf # and needs Automake; hence why they are dependencies. @@ -1728,7 +2185,6 @@ $(ibidir)/util-linux-$(util-linux-version): \ export CONFIG_SHELL=$(ibdir)/bash ./configure --prefix=$(idircustom)/util-linux \ --disable-dependency-tracking \ - --enable-libmount-support-mtab \ --disable-silent-rules \ --disable-liblastlog2 \ --disable-mountpoint \ @@ -1807,6 +2263,7 @@ $(ibidir)/vim-$(vim-version): unpackdir=vim-$(vim-version) cd $(ddir)/$$unpackdir $(shsrcdir)/prep-source.sh $(ibdir) + export CFLAGS="-std=gnu17 $$CFLAGS" ./configure --prefix=$(idir) \ --disable-canberra \ --enable-multibyte \ @@ -1832,16 +2289,28 @@ $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version) BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) echo "Unzip $(unzip-version)" > $@ -$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version) +$(ibidir)/zip-$(zip-version): + +# Prepare the tarball and build directory. tarball=zip-$(zip-version).tar.lz $(call import-source, $(zip-url), $(zip-checksum)) - $(call gbuild, zip-$(zip-version), static,, \ - -f unix/Makefile generic \ - CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ - -f unix/Makefile generic \ - BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) - echo "Zip $(zip-version)" > $@ +# Unpack and go into the directory. + export LDFLAGS="$$LDFLAGS -static" + cd $(ddir) + rm -fr zip-$(zip-version)/ + tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions + cd zip-$(zip-version)/ + +# Build and install + make SHELL=$(ibdir)/bash -f unix/Makefile generic + make SHELL=$(ibdir)/bash install -f unix/Makefile \ + generic BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 + +# Go back to the top build directory, clean up and finalize. + cd $(ddir) + rm -rf zip-$(zip-version)/ + echo "Zip $(zip-version)" > $@ @@ -2020,7 +2489,7 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ # We do not build TeXLive from source and for its installation it # downloads components from the web internally; and those # components can use '/bin/sh' (which needs 'sys_library_sh_path'). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" + export LD_LIBRARY_PATH="$(sys_library_sh_path)" # To update itself, tlmgr needs a backup directory. backupdir=$(idir)/texlive/backups @@ -2049,7 +2518,6 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ # files (this is because we do no yet install LaTeX from source): cdir=$$(pwd) cd $(idir)/texlive - $(shsrcdir)/prep-source.sh $(ibdir) cd $$cdir # Get all the necessary versions. diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index c994e3f..6153f0a 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -83,7 +83,11 @@ $(ibidir)/libffi-$(libffi-version): fi echo "Libffi $(libffi-version)" > $@ -$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) +# 2025-05-26 '--with-system-ffi' seems to be obsolete +# TODO: For a recommended list of dependencies, see +# https://github.com/pyenv/pyenv/wiki#suggested-build-environment +$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) \ + $(ibidir)/sqlite-$(sqlite-version) # Download the source. tarball=python-$(python-version).tar.lz @@ -346,12 +350,27 @@ $(ipydir)/astropy-$(astropy-version): \ rm -fv $(idir)/bin/fits{diff,check,header,info,2bitmap} rm -fv $(idir)/bin/{samp_hub,showtable,volint,wcslint} +# Uncomment the 'export' command below only when building from a git +# tarball, e.g. for testing if a bug still occurs: +# export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ASTROPY=7.2.0.87 + # Do the basic build. $(call pybuild, tar -xf, astropy-$(astropy-version),,, \ GPEP517) cp -pv $(dtexdir)/astropy.tex $(ictdir)/ echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@ +$(ipydir)/astropy-healpix-$(astropy-healpix-version): \ + $(ipydir)/extension-helpers-$(extension-helpers-version) \ + $(ipydir)/numpy-$(numpy-version) + tarball=astropy-healpix-$(astropy-healpix-version).tar.lz + $(call import-source, $(astropy-healpix-url), \ + $(astropy-healpix-checksum)) + $(call pybuild, tar -xf, \ + astropy-healpix-$(astropy-healpix-version),,, \ + GPEP517) + echo "Astropy-healpix $(astropy-healpix-version)" > $@ + $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \ $(ipydir)/setuptools-$(setuptools-version) tarball=astropy-iers-data-$(astropy-iers-data-version).tar.lz @@ -360,7 +379,7 @@ $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \ $(call pybuild, tar -xf, \ astropy-iers-data-$(astropy-iers-data-version),,, \ GPEP517) - echo "Astropy-Iers-Data $(astropy-iers-data-version)" > $@ + echo "Astropy-IERS-data $(astropy-iers-data-version)" > $@ $(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \ $(ipydir)/soupsieve-$(soupsieve-version) @@ -400,6 +419,13 @@ $(ipydir)/chardet-$(chardet-version): \ $(call pybuild, tar -xf, chardet-$(chardet-version), , \ Chardet $(chardet-version)) +$(ipydir)/colorama-$(colorama-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=colorama-$(colorama-version).tar.lz + $(call import-source, $(colorama-url), $(colorama-checksum)) + $(call pybuild, tar -xf, \ + colorama-$(colorama-version),,, GPEP517) + $(ipydir)/contourpy-$(contourpy-version): \ $(ipydir)/pybind11-$(pybind11-version) \ $(ipydir)/meson-python-$(meson-python-version) @@ -417,6 +443,15 @@ $(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version) cp $(dtexdir)/corner.tex $(ictdir)/ echo "Corner $(corner-version) \citep{corner}" > $@ +$(ipydir)/cosmodesi-mpytools-$(cosmodesi-mpytools-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=cosmodesi-mpytools-$(cosmodesi-mpytools-version).tar.lz + $(call import-source, $(cosmodesi-mpytools-url), $(cosmodesi-mpytools-checksum)) + $(call pybuild, tar -xf, cosmodesi-mpytools-$(cosmodesi-mpytools-version), , \ + Cosmodesi-mpytools $(cosmodesi-mpytools-version), GPEP517) + echo "Cosmodesi-mpytools $(cosmodesi-mpytools-version)" > $@ + $(ipydir)/cppy-$(cppy-version): \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) tarball=cppy-$(cppy-version).tar.lz @@ -482,6 +517,15 @@ $(ipydir)/entrypoints-$(entrypoints-version): \ $(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \ EntryPoints $(entrypoints-version)) +$(ipydir)/exceptiongroup-$(exceptiongroup-version): \ + $(ipydir)/setuptools-$(setuptools-version) \ + $(ipydir)/flit-scm-$(flit-scm-version) + tarball=exceptiongroup-$(exceptiongroup-version).tar.lz + $(call import-source, $(exceptiongroup-url), $(exceptiongroup-checksum)) + $(call pybuild, tar -xf, exceptiongroup-$(exceptiongroup-version), , \ + Exceptiongroup $(exceptiongroup-version), GPEP517) + + $(ipydir)/extension-helpers-$(extension-helpers-version): \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) tarball=extension-helpers-$(extension-helpers-version).tar.lz @@ -507,6 +551,16 @@ $(ipydir)/flit-core-$(flit-core-version): \ $(call pybuild, tar -xf, flit-core-$(flit-core-version), , \ Flit-core $(flit-core-version), GPEP517) + +$(ipydir)/flit-scm-$(flit-scm-version): \ + $(ipydir)/flit-core-$(flit-core-version) \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=flit-scm-$(flit-scm-version).tar.lz + $(call import-source, $(flit-scm-url), $(flit-scm-checksum)) + $(call pybuild, tar -xf, flit-scm-$(flit-scm-version), , \ + flit-scm $(flit-scm-version), GPEP517) + + # Although cython is not an obligatory prerequisite of fonttools, we force # it as a prerequisite for reproducibility; otherwise build parallelism may # lead to some builds with and some builds without cython, depending on how @@ -558,6 +612,23 @@ $(ipydir)/gpep517-$(gpep517-version): \ BOOT_GPEP517) echo "gpep517 $(gpep517-version)" > $@ +$(ipydir)/hatchling-$(hatchling-version): \ + $(ipydir)/packaging-$(packaging-version) \ + $(ipydir)/pathspec-$(pathspec-version) \ + $(ipydir)/pluggy-$(pluggy-version) \ + $(ipydir)/trove-classifiers-$(trove-classifiers-version) + tarball=hatchling-$(hatchling-version).tar.lz + $(call import-source, $(hatchling-url), $(hatchling-checksum)) + $(call pybuild, tar -xf, \ + hatchling-$(hatchling-version),,, GPEP517) + +$(ipydir)/hatch-vcs-$(hatch-vcs-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=hatch-vcs-$(hatch-vcs-version).tar.lz + $(call import-source, $(hatch-vcs-url), $(hatch-vcs-checksum)) + $(call pybuild, tar -xf, hatch-vcs-$(hatch-vcs-version), , \ + Hatch-vcs $(hatch-vcs-version), GPEP517) + $(ipydir)/h5py-$(h5py-version): \ $(ipydir)/six-$(six-version) \ $(ibidir)/hdf5-$(hdf5-version) \ @@ -572,15 +643,38 @@ $(ipydir)/h5py-$(h5py-version): \ $(call pybuild, tar -xf, h5py-$(h5py-version), , \ h5py $(h5py-version)) -# 'healpy' is actually installed as part of the HEALPix package. It will be -# installed with its C/C++ libraries if any other Python library is -# requested with HEALPix. So actually calling for 'healpix' (when 'healpix' -# is requested) is not necessary. But some users might not know about this -# and just ask for 'healpy'. To avoid confusion in such cases, we'll just -# set 'healpy' to be dependent on 'healpix' and not download any tarball -# for it, or write anything in the final target. -$(ipydir)/healpy-$(healpy-version): $(ibidir)/healpix-$(healpix-version) - touch $@ +# As of 2025-05-20, there are at least three python healpix packages at +# pypi.org, with versions: +# +# https://pypi.org/project/healpy 1.18.1 +# https://pypi.org/project/healpix 2024.2 +# https://pypi.org/project/astropy-healpix 1.1.2 +# +# Maneage provides both 'healpy' and 'astropy-healpix', independently. We +# ignore pypix 'healpix', whose name risks confusion with the C/C++/fortran +# version of healpix. +# +# For simplicity and error tracing, you should best install either healpy +# or astropy-healpix, not both. For example, astropy_healpix/healpy.py has +# an interface to provide 'healpy' type function names. However, it may be +# possible to use both if your python imports avoid namespace clashes. See +# the documentation and source code of the respective packages to study how +# they relate to one another. +# +# The 'healpy' package requires the C/C++ 'healpix' package to be built +# in order to use the shared 'libsharp' library. +$(ipydir)/healpy-$(healpy-version): \ + $(ibidir)/healpix-$(healpix-version) \ + $(ipydir)/matplotlib-$(matplotlib-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=healpy-$(healpy-version).tar.lz + $(call import-source, $(healpy-url), \ + $(healpy-checksum)) + $(call pybuild, tar -xf, \ + healpy-$(healpy-version),,, \ + GPEP517) + echo "Healpy $(healpy-version)" > $@ + $(ipydir)/html5lib-$(html5lib-version): \ $(ipydir)/six-$(six-version) \ @@ -612,6 +706,13 @@ $(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version) $(call pybuild, tar -xf, jinja2-$(jinja2-version), , \ Jinja2 $(jinja2-version)) +$(ipydir)/joblib-$(joblib-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=joblib-$(joblib-version).tar.lz + $(call import-source, $(joblib-url), $(joblib-checksum)) + $(call pybuild, tar -xf, \ + joblib-$(joblib-version),,, GPEP517) + $(ipydir)/keyring-$(keyring-version): \ $(ipydir)/entrypoints-$(entrypoints-version) \ $(ipydir)/secretstorage-$(secretstorage-version) \ @@ -631,6 +732,48 @@ $(ipydir)/kiwisolver-$(kiwisolver-version): \ cp -pv $(dtexdir)/kiwisolver.tex $(ictdir)/ echo "Kiwisolver $(kiwisolver-version) \citep{cassowary2001}" > $@ +# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining +# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these +# to igwn-ligolw and igwn-segments, respectively [1]. +# [1] https://github.com/ahnitz/ligo-segments/issues/1 +$(ipydir)/igwn-segments-$(igwn-segments-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=igwn-segments-$(igwn-segments-version).tar.lz + $(call import-source, $(igwn-segments-url), $(igwn-segments-checksum)) + $(call pybuild, tar -xf, \ + igwn-segments-$(igwn-segments-version),, \ + Igwn-segments $(igwn-segments-version), GPEP517) + + +$(ipydir)/iniconfig-$(iniconfig-version): \ + $(ipydir)/hatch-vcs-$(hatch-vcs-version) + tarball=iniconfig-$(iniconfig-version).tar.lz + $(call import-source, $(iniconfig-url), $(iniconfig-checksum)) + $(call pybuild, tar -xf, iniconfig-$(iniconfig-version), , \ + Iniconfig $(iniconfig-version), GPEP517) + +# Upstream this is called ligo.skymap with a full stop '.'; we replace it +# by a hyphen '-' to reduce the chance of regex errors. +# +# 2025-05-19 Warning: this might have some undetected dependencies. +$(ipydir)/ligo-skymap-$(ligo-skymap-version): \ + $(ibidir)/gsl-$(gsl-version) \ + $(ipydir)/tqdm-$(tqdm-version) \ + $(ibidir)/sqlite-$(sqlite3-version) \ + $(ipydir)/astropy-$(astropy-version) \ + $(ipydir)/lalsuite-$(lalsuite-version) \ + $(ipydir)/igwn-ligolw-$(igwn-ligolw-version) \ + $(ipydir)/igwn-segments-$(igwn-segments-version) \ + $(ipydir)/astropy-healpix-$(astropy-healpix-version) + tarball=ligo-skymap-$(ligo-skymap-version).tar.lz + $(call import-source, $(ligo-skymap-url), \ + $(ligo-skymap-checksum)) + $(call pybuild, tar -xf, \ + ligo-skymap-$(ligo-skymap-version),,, \ + GPEP517) + echo "ligo-skymap $(ligo-skymap-version)" > $@ + + $(ipydir)/lmfit-$(lmfit-version): \ $(ipydir)/six-$(six-version) \ $(ipydir)/scipy-$(scipy-version) \ @@ -644,6 +787,14 @@ $(ipydir)/lmfit-$(lmfit-version): \ $(call pybuild, tar -xf, lmfit-$(lmfit-version), , \ LMFIT $(lmfit-version)) +$(ipydir)/lscsoft-glue-$(lscsoft-glue-version): \ + $(ipydir)/gpep517-$(gpep517-version) \ + $(ipydir)/python-installer-$(python-installer-version) + tarball=lscsoft-glue-$(lscsoft-glue-version).tar.lz + $(call import-source, $(lscsoft-glue-url), $(lscsoft-glue-checksum)) + $(call pybuild, tar -xf, \ + lscsoft-glue-$(lscsoft-glue-version),,, GPEP517) + $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \ $(ipydir)/cffi-$(cffi-version) \ $(ipydir)/numpy-$(numpy-version) \ @@ -661,11 +812,19 @@ $(ipydir)/markupsafe-$(markupsafe-version): \ $(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \ MarkupSafe $(markupsafe-version)) +# As of 2026-04-19: Matplotlib needs internet to download and build its +# custom versions of 'freetype' and 'qhull'. The proposed option to 'python +# -m pip instsall' in [1] for using system libraries was tested, but did +# not work in this setup (our 'pybuild' uses 'python -m gpep517 +# install-from-source', not 'pip'). +# +# [1] https://matplotlib.org/stable/install/dependencies.html $(ipydir)/matplotlib-$(matplotlib-version): \ $(itidir)/texlive \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/cycler-$(cycler-version) \ $(ipydir)/pillow-$(pillow-version) \ + $(ibidir)/freetype-$(freetype-version) \ $(ipydir)/fonttools-$(fonttools-version) \ $(ipydir)/contourpy-$(contourpy-version) \ $(ipydir)/kiwisolver-$(kiwisolver-version) \ @@ -706,12 +865,11 @@ $(ipydir)/meson-python-$(meson-python-version): \ echo "Meson-Python $(meson-python-version)" > $@ $(ipydir)/mpi4py-$(mpi4py-version): \ - $(ipydir)/gpep517-$(gpep517-version) \ $(ibidir)/openmpi-$(openmpi-version) \ - $(ipydir)/python-installer-$(python-installer-version) + $(ipydir)/cython-$(cython-version) tarball=mpi4py-$(mpi4py-version).tar.lz $(call import-source, $(mpi4py-url), $(mpi4py-checksum)) - $(call pybuild, tar -xf, mpi4py-$(mpi4py-version)) + $(call pybuild, tar -xf, mpi4py-$(mpi4py-version),,, GPEP517) cp $(dtexdir)/mpi4py.tex $(ictdir)/ echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@ @@ -723,8 +881,17 @@ $(ipydir)/mpmath-$(mpmath-version): \ $(call pybuild, tar -xf, mpmath-$(mpmath-version), , \ mpmath $(mpmath-version)) -# Until 2025-02-22: we had 'export CFLAGS="--std=c99 $$CFLAGS"' before -# calling pybuild; but that doesn't seem to be necessary. +$(ipydir)/networkx-$(networkx-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=networkx-$(networkx-version).tar.lz + $(call import-source, $(networkx-url), $(networkx-checksum)) + $(call pybuild, tar -xf, \ + networkx-$(networkx-version),,, \ + GPEP517) + echo "networkx $(networkx-version)" > $@ + +# Numpy's MacOS builds using Xcode prior to 26.3 needed the following flags +# added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'. $(ipydir)/numpy-$(numpy-version): \ $(ipydir)/cython-$(cython-version) \ $(ibidir)/openblas-$(openblas-version) \ @@ -732,9 +899,6 @@ $(ipydir)/numpy-$(numpy-version): \ $(ipydir)/meson-python-$(meson-python-version) tarball=numpy-$(numpy-version).tar.lz $(call import-source, $(numpy-url), $(numpy-checksum)) - if [ x$(on_mac_os) = xyes ]; then - export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle" - fi conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" $(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version), GPEP517) @@ -748,6 +912,23 @@ $(ipydir)/packaging-$(packaging-version): \ $(call pybuild, tar -xf, packaging-$(packaging-version), , \ Packaging $(packaging-version), GPEP517) +$(ipydir)/pandas-$(pandas-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/versioneer-$(versioneer-version) \ + $(ipydir)/pytz-$(pytz-version) + tarball=pandas-$(pandas-version).tar.lz + $(call import-source, $(pandas-url), $(pandas-checksum)) + $(call pybuild, tar -xf, pandas-$(pandas-version), , \ + Pandas $(pandas-version), GPEP517) + echo "pandas $(pandas-version)" > $@ + +$(ipydir)/pathspec-$(pathspec-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pathspec-$(pathspec-version).tar.lz + $(call import-source, $(pathspec-url), $(pathspec-checksum)) + $(call pybuild, tar -xf, \ + pathspec-$(pathspec-version),,, GPEP517) + $(ipydir)/pexpect-$(pexpect-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/python-installer-$(python-installer-version) @@ -773,6 +954,13 @@ $(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \ # $(call pybuild, tar -xf, pip-$(pip-version), , \ # PiP $(pip-version)) +$(ipydir)/pluggy-$(pluggy-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pluggy-$(pluggy-version).tar.lz + $(call import-source, $(pluggy-url), $(pluggy-checksum)) + $(call pybuild, tar -xf, \ + pluggy-$(pluggy-version),,, GPEP517) + $(ipydir)/ply-$(ply-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/python-installer-$(python-installer-version) @@ -828,6 +1016,13 @@ $(ipydir)/pyflakes-$(pyflakes-version): \ $(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \ pyflakes $(pyflakes-version)) +$(ipydir)/pygments-$(pygments-version): \ + $(ipydir)/hatchling-$(hatchling-version) + tarball=pygments-$(pygments-version).tar.lz + $(call import-source, $(pygments-url), $(pygments-checksum)) + $(call pybuild, tar -xf, pygments-$(pygments-version), , \ + Pygments $(pygments-version), GPEP517) + $(ipydir)/pyparsing-$(pyparsing-version): \ $(ipydir)/gpep517-$(gpep517-version) \ $(ipydir)/flit-core-$(flit-core-version) \ @@ -854,8 +1049,26 @@ $(ipydir)/pyproject-metadata-$(pyproject-metadata-version): \ $(call pybuild, tar -xf, \ pyproject-metadata-$(pyproject-metadata-version),,, GPEP517) + +$(ipydir)/pytest-$(pytest-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) \ + $(ipydir)/colorama-$(colorama-version) \ + $(ipydir)/exceptiongroup-$(exceptiongroup-version) \ + $(ipydir)/iniconfig-$(iniconfig-version) \ + $(ipydir)/packaging-$(packaging-version) \ + $(ipydir)/pluggy-$(pluggy-version) \ + $(ipydir)/pygments-$(pygments-version) + tarball=pytest-$(pytest-version).tar.lz + $(call import-source, $(pytest-url), $(pytest-checksum)) + $(call pybuild, tar -xf, \ + pytest-$(pytest-version),,, \ + GPEP517) + echo "pytest $(pytest-version)" > $@ + + $(ipydir)/python-dateutil-$(python-dateutil-version): \ - $(ipydir)/setuptools-scm-$(setuptools-scm-version) + $(ipydir)/setuptools-scm-$(setuptools-scm-version) \ + $(ipydir)/six-$(six-version) tarball=python-dateutil-$(python-dateutil-version).tar.lz $(call import-source, $(python-dateutil-url), $(python-dateutil-checksum)) $(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \ @@ -885,6 +1098,37 @@ $(ipydir)/python-installer-$(python-installer-version): \ BOOT_INSTALLER) echo "Python-installer $(python-installer-version)" > $@ +# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining +# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these +# to igwn-ligolw and igwn-segments, respectively [1]. +# [1] https://github.com/ahnitz/ligo-segments/issues/1 +$(ipydir)/igwn-ligolw-$(igwn-ligolw-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=igwn-ligolw-$(igwn-ligolw-version).tar.lz + $(call import-source, $(igwn-ligolw-url), \ + $(igwn-ligolw-checksum)) + $(call pybuild, tar -xf, \ + igwn-ligolw-$(igwn-ligolw-version),,, \ + GPEP517) + echo "igwn-ligolw $(igwn-ligolw-version)" > $@ + +$(ipydir)/pyfftw-$(pyfftw-version): $(ipydir)/numpy-$(numpy-version) \ + $(ibidir)/fftw-$(fftw-version) + tarball=pyfftw-$(pyfftw-version).tar.lz + $(call import-source, $(pyfftw-url), $(pyfftw-checksum)) + $(call pybuild, tar -xf, pyfftw-$(pyfftw-version), , \ + Pyfftw $(pyfftw-version), GPEP517) + + +# Called 'fitsio' in pypi.org: https://pypi.org/project/fitsio +$(ipydir)/python3-fitsio-$(python3-fitsio-version): \ + $(ibidir)/patch-$(patch-version) \ + $(ipydir)/numpy-$(numpy-version) + tarball=python3-fitsio-$(python3-fitsio-version).tar.lz + $(call import-source, $(python3-fitsio-url), $(python3-fitsio-checksum)) + $(call pybuild, tar -xf, python3-fitsio-$(python3-fitsio-version), , \ + Python3 Fitsio $(python3-fitsio-version), GPEP517) + $(ipydir)/pythran-$(pythran-version): \ $(ipydir)/ply-$(ply-version) \ $(ipydir)/gast-$(gast-version) \ @@ -904,6 +1148,13 @@ $(ipydir)/pyyaml-$(pyyaml-version): \ $(call pybuild, tar -xf, pyyaml-$(pyyaml-version), , \ PyYAML $(pyyaml-version), GPEP517) +$(ipydir)/pytz-$(pytz-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=pytz-$(pytz-version).tar.lz + $(call import-source, $(pytz-url), $(pytz-checksum)) + $(call pybuild, tar -xf, pytz-$(pytz-version), , \ + Pytz $(pytz-version), GPEP517) + $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/certifi-$(certifi-version) \ @@ -914,41 +1165,39 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(call pybuild, tar -xf, requests-$(requests-version), , \ Requests $(requests-version)) -# 'pythran' is disabled in the build of Scipy because of complications it -# caused on some systems. We explicitly disable it using a preprocessor -# directive. 'Pythran' can in principle speed up compilation of scientific -# software [1][2]. +# Scipy building notes: +# +# 1. 'pythran' is disabled in the build of Scipy because of complications +# it caused on some systems. 'Pythran' can in principle speed up +# compilation of scientific software [1][2]. We explicitly disable it by +# modifying the source. Technically it should also be possible to pass +# the following option to the gpep517 build recipes with correct +# escaping of single and double quotes, but this has not tried as of +# 2025-02-25. +# --config-json='{"setup-args":"-Duse-pythran=false"}' +# +# 2. Scipy's MacOS builds using Xcode prior to 26.3 needed the following +# flags added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'. +# # [1] https://pythran.readthedocs.io/en/latest -# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html +# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran $(ipydir)/scipy-$(scipy-version): \ $(ipydir)/numpy-$(numpy-version) \ $(ipydir)/pybind11-$(pybind11-version) + +# Import the tarball. tarball=scipy-$(scipy-version).tar.lz $(call import-source, $(scipy-url), $(scipy-checksum)) - if [ x$(on_mac_os) = xyes ]; then - export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle" - else -# Same question as for 'numpy': why '-shared'? This obstructs -# the meson build. -# export LDFLAGS="$(LDFLAGS) -shared" - : - fi - conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" -# Disable pythran: see -# https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran -# export SCIPY_USE_PYTHRAN=0 # deprecated(?) -# Option 1: Hack the source: +# Disable pythran (see above). pyhook_before() { mv -iv meson.options meson.options.orig; \ sed -e 's/\(use-pythran.*value: *\)true/\1false/' \ meson.options.orig > meson.options } -# Option 2: pass the string -# --config-json='{"setup-args": "-Duse-pythran=false"}' -# to gpep517 with correct escaping of single and double quotes. -# Not tried as of 2025-02-25. +# Build Scipy. + conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" $(call pybuild, tar -xf, scipy-$(scipy-version),$$conf,, GPEP517) cp $(dtexdir)/scipy.tex $(ictdir)/ echo "Scipy $(scipy-version) \citep{scipy2020}" > $@ @@ -1003,6 +1252,26 @@ $(ipydir)/sip_tpv-$(sip_tpv-version): \ cp $(dtexdir)/sip_tpv.tex $(ictdir)/ echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@ +$(ipydir)/scikit-base-$(scikit-base-version): \ + $(ipydir)/gpep517-$(gpep517-version) \ + $(ipydir)/python-installer-$(python-installer-version) + tarball=scikit-base-$(scikit-base-version).tar.lz + $(call import-source, $(scikit-base-url), $(scikit-base-checksum)) + $(call pybuild, tar -xf, scikit-base-$(scikit-base-version), , \ + Scikit-base $(scikit-base-version), GPEP517) + echo "scikit-base $(scikit-base-version)" > $@ + +$(ipydir)/scikit-learn-$(scikit-learn-version): \ + $(ipydir)/joblib-$(joblib-version) \ + $(ipydir)/threadpoolctl-$(threadpoolctl-version) \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/scipy-$(scipy-version) + tarball=scikit-learn-$(scikit-learn-version).tar.lz + $(call import-source, $(scikit-learn-url), $(scikit-learn-checksum)) + $(call pybuild, tar -xf, scikit-learn-$(scikit-learn-version), , \ + Scikit-learn $(scikit-learn-version), GPEP517) + echo "scikit-learn $(scikit-learn-version)" > $@ + $(ipydir)/six-$(six-version): \ $(ipydir)/setuptools-$(setuptools-version) tarball=six-$(six-version).tar.lz @@ -1026,6 +1295,29 @@ $(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version) cp $(dtexdir)/sympy.tex $(ictdir)/ echo "SymPy $(sympy-version) \citep{sympy}" > $@ +$(ipydir)/threadpoolctl-$(threadpoolctl-version): \ + $(ipydir)/flit-core-$(flit-core-version) + tarball=threadpoolctl-$(threadpoolctl-version).tar.lz + $(call import-source, $(threadpoolctl-url), $(threadpoolctl-checksum)) + $(call pybuild, tar -xf, threadpoolctl-$(threadpoolctl-version), , \ + threadpoolctl $(threadpoolctl-version), GPEP517) + echo "threadpoolctl $(threadpoolctl-version)" > $@ + +$(ipydir)/tqdm-$(tqdm-version): \ + $(ipydir)/setuptools-scm-$(setuptools-scm-version) + tarball=tqdm-$(tqdm-version).tar.lz + $(call import-source, $(tqdm-url), $(tqdm-checksum)) + $(call pybuild, tar -xf, \ + tqdm-$(tqdm-version),, \ + Tqdm $(tqdm-version), GPEP517) + +$(ipydir)/trove-classifiers-$(trove-classifiers-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=trove-classifiers-$(trove-classifiers-version).tar.lz + $(call import-source, $(trove-classifiers-url), $(trove-classifiers-checksum)) + $(call pybuild, tar -xf, \ + trove-classifiers-$(trove-classifiers-version),,, GPEP517) + $(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version) tarball=uncertainties-$(uncertainties-version).tar.lz $(call import-source, $(uncertainties-url), $(uncertainties-checksum)) @@ -1040,6 +1332,13 @@ $(ipydir)/urllib3-$(urllib3-version): \ $(call pybuild, tar -xf, urllib3-$(urllib3-version), , \ Urllib3 $(urllib3-version)) +$(ipydir)/versioneer-$(versioneer-version): \ + $(ipydir)/setuptools-$(setuptools-version) + tarball=versioneer-$(versioneer-version).tar.lz + $(call import-source, $(versioneer-url), $(versioneer-checksum)) + $(call pybuild, tar -xf, versioneer-$(versioneer-version), , \ + Versioneer $(versioneer-version), GPEP517) + $(ipydir)/webencodings-$(webencodings-version): \ $(ipydir)/setuptools-$(setuptools-version) \ $(ipydir)/setuptools-scm-$(setuptools-scm-version) diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk index 7c86c23..7a09915 100644 --- a/reproduce/software/make/r-cran.mk +++ b/reproduce/software/make/r-cran.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2022-2025 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk index 864c32a..33847f3 100644 --- a/reproduce/software/make/xorg.mk +++ b/reproduce/software/make/xorg.mk @@ -14,8 +14,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -120,6 +120,7 @@ $(ibidir)/fontconfig-$(fontconfig-version): \ $(ibidir)/libxml2-$(libxml2-version) \ $(ibidir)/freetype-$(freetype-version) \ $(ibidir)/util-linux-$(util-linux-version) + # Import the source. tarball=fontconfig-$(fontconfig-version).tar.lz $(call import-source, $(fontconfig-url), $(fontconfig-checksum)) diff --git a/reproduce/software/containers/README-apptainer.md b/reproduce/software/shell/apptainer-README.md index 9608dc8..d2a14c8 100644 --- a/reproduce/software/containers/README-apptainer.md +++ b/reproduce/software/shell/apptainer-README.md @@ -1,7 +1,7 @@ # Maneage'd projects in Apptainer -Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>\ +Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es>\ See the end of the file for license conditions. For an introduction on containers, see the "Building in containers" section @@ -22,24 +22,22 @@ analysis files (data and PDF) on your host operating system. This enables you to keep the size of the image to a minimum (only containing the built software environment) to easily move it from one computer to another. - 1. Using your favorite text editor, create a `apptainer-local.sh` in your - project's top directory that contains the usage command shown at the - top of the 'apptainer.sh' script and take the following steps: - * Set the respective directories based on your own preferences. - * The `--software-dir` is optional (if you don't have the source - tarballs, Maneage will download them automatically. But that requires - internet (which may not always be available). If you regularly build - Maneage'd projects, you can clone the repository containing all the - tarballs at https://gitlab.cefca.es/maneage/tarballs-software - * Add an extra `--build-only` for the first run so it doesn't go onto - doing the analysis and just builds the image. After it has completed, - remove the `--build-only` and it will only run the analysis of your - project. - - 2. Once step one finishes, the build directory will contain two - Singularity Image Format (SIF) files listed below. You can move them to - any other (more permanent) positions in your filesystem or to other - computers as needed. + 1. Using your favorite text editor, create a `run.sh` in your top Maneage + directory (as described in the comments at the start of the + `apptainer.sh` script in this directory). Just add `--build-only` on + the first run so it doesn't go onto doing the analysis and just sets up + the software environment. Set the respective directory(s) based on your + filesystem (the software directory is optional). The `run.sh` file name + is already in `.gitignore` (because it contains local directories), so + Git will ignore it and it won't be committed by mistake. + + 2. Make the script executable with `chmod +x ./run.sh`, and run it with + `./run.sh`. + + 3. Once the build finishes, the build directory (on your host) will + contain two Singularity Image Format (SIF) files listed below. You can + move them to any other (more permanent) positions in your filesystem or + to other computers as needed. * `maneage-base.sif`: image containing the base operating system that was used to build your project. You can safely delete this unless you need to keep it for future builds without internet (you can give it @@ -49,6 +47,10 @@ software environment) to easily move it from one computer to another. project. This file is necessary for future runs of your project within the container. + 3. To execute your project remove the `--build-only` and use `./run.sh` to + execute it. If you want to enter your Maneage'd project shell, add the + `--project-shell` option to the call inside `./run.sh`. + diff --git a/reproduce/software/containers/apptainer.sh b/reproduce/software/shell/apptainer.sh index 52315f6..8760db6 100755 --- a/reproduce/software/containers/apptainer.sh +++ b/reproduce/software/shell/apptainer.sh @@ -9,39 +9,40 @@ # # Usage: # -# - When you are at the top Maneage'd project directory, you can run this -# script like the example below. Just set all the '/PATH/TO/...' -# directories. See the items below for optional values. +# - When you are at the top Maneage'd project directory, run this script +# like the example below. Just set the build directory location on your +# system. See the items below for optional values to optimize the +# process (avoid downloading for exmaple). # -# ./reproduce/software/containers/apptainer.sh \ -# --build-dir=/PATH/TO/BUILD/DIRECTORY \ -# --software-dir=/PATH/TO/SOFTWARE/TARBALLS +# ./reproduce/software/shell/apptainer.sh \ +# --build-dir=/PATH/TO/BUILD/DIRECTORY # -# - Non-mandatory options: +# - Non-mandatory options: # -# - If you already have the input data that is necessary for your -# project's, use the '--input-dir' option to specify its location -# on your host file system. Otherwise the necessary analysis -# files will be downloaded directly into the build -# directory. Note that this is only necessary when '--build-only' -# is not given. +# - If you already have the input data that is necessary for your +# project, use the '--input-dir' option to specify its location +# on your host file system. Otherwise the necessary analysis +# files will be downloaded directly into the build +# directory. Note that this is only necessary when '--build-only' +# is not given. # -# - The '--software-dir' is only useful if you want to build a -# container. Even in that case, it is not mandatory: if not -# given, the software tarballs will be downloaded (thus requiring -# internet). +# - If you already have the necessary software tarballs that are +# necessary for your project, use the '--software-dir' option to +# specify its location on your host file system only when +# building the container. No problem if you don't have them, they +# will be downloaded during the configuration phase. # -# - To avoid having to set them every time you want to start the -# apptainer environment, you can put this command (with the proper -# directories) into a 'run.sh' script in the top Maneage'd project -# source directory and simply execute that. The special name 'run.sh' -# is in Maneage's '.gitignore', so it will not be included in your -# git history by mistake. +# - To avoid having to set them every time you want to start the +# apptainer environment, you can put this command (with the proper +# directories) into a 'run.sh' script in the top Maneage'd project +# source directory and simply execute that. The special name 'run.sh' +# is in Maneage's '.gitignore', so it will not be included in your +# git history by mistake. # # Known problems: # -# Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es> +# Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -70,14 +71,14 @@ set -e # Default option values -jobs= +sif="" +jobs=0 quiet=0 source_dir= build_only= -base_name="" +base_sif="" shm_size=20gb scriptname="$0" -project_name="" project_shell=0 container_shell=0 base_os=debian:stable-slim @@ -96,16 +97,16 @@ Top-level script to build and run a Maneage'd project within Apptainer. --source-dir=STR Directory of source code (default: 'pwd -P'). Apptainer images + --sif=STR Project's apptainer image (a '.sif' file). --base-os=STR Base OS name (default: '$base_os'). - --base-name=STR Base OS apptainer image (a '.sif' file). - --project-name=STR Project's apptainer image (a '.sif' file). + --base-sif=STR Base OS apptainer image (a '.sif' file). Interactive shell --project-shell Open the project's shell within the container. --container-shell Open the container shell. Operating mode: - --quiet Do not print informative statements. + -q, --quiet Do not print informative statements. -?, --help Give this help list. -j, --jobs=INT Number of threads to use in each phase. --build-only Just build the container, don't run it. @@ -154,10 +155,12 @@ do --source-dir=*) source_dir="${1#*=}"; check_v "$1" "$source_dir"; shift;; # Container options. - --base-name) base_name="$2"; check_v "$1" "$base_name"; shift;shift;; - --base-name=*) base_name="${1#*=}"; check_v "$1" "$base_name"; shift;; - --project-name) project_name="$2"; check_v "$1" "$project_name"; shift;shift;; - --project-name=*) project_name="${1#*=}"; check_v "$1" "$project_name"; shift;; + --sif) sif="$2"; check_v "$1" "$sif"; shift;shift;; + --sif=*) sif="${1#*=}"; check_v "$1" "$sif"; shift;; + --base-os) base_os="$2"; check_v "$1" "$base_os"; shift;shift;; + --base-os=*) base_os="${1#*=}"; check_v "$1" "$base_os"; shift;; + --base-sif) base_sif="$2"; check_v "$1" "$base_sif"; shift;shift;; + --base-sif=*) base_sif="${1#*=}"; check_v "$1" "$base_sif"; shift;; # Interactive shell. --project-shell) project_shell=1; shift;; @@ -166,8 +169,8 @@ do --container_shell=*) on_off_option_error --container-shell;; # Operating mode - --quiet) quiet=1; shift;; - --quiet=*) on_off_option_error --quiet;; + -q|--quiet) quiet=1; shift;; + -q*|--quiet=*) on_off_option_error --quiet;; -j|--jobs) jobs="$2"; check_v "$1" "$jobs"; shift;shift;; -j=*|--jobs=*) jobs="${1#*=}"; check_v "$1" "$jobs"; shift;; -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v "$1" "$jobs"; shift;; @@ -192,21 +195,22 @@ done # # Make sure that the build directory is given and that it exists. if [ x$build_dir = x ]; then - printf "$scriptname: '--build-dir' not provided, this is the location " - printf "that all built analysis files will be kept on the host OS\n" + printf "$scriptname: '--build-dir' not provided, this is the " + printf "location that all built analysis files will be kept on " + printf "the host OS\n" exit 1; else if ! [ -d $build_dir ]; then - printf "$scriptname: '$build_dir' (value to '--build-dir') doesn't " - printf "exist\n" + printf "$scriptname: '$build_dir' (value to '--build-dir') " + printf "doesn't exist\n" exit 1; fi fi # Set the default project and base-OS image names (inside the build # directory). -if [ x"$base_name" = x ]; then base_name=$build_dir/maneage-base.sif; fi -if [ x"$project_name" = x ]; then project_name=$build_dir/maneaged.sif; fi +if [ x"$base_sif" = x ]; then base_sif=$build_dir/maneage-base.sif; fi +if [ x"$sif" = x ]; then sif=$build_dir/maneaged.sif; fi @@ -245,8 +249,22 @@ if ! [ x"$input_dir" = x ]; then fi # If no '--jobs' has been specified, use the maximum available jobs to the -# operating system. -if [ x$jobs = x ]; then jobs=$(nproc); fi +# operating system. Apptainer only works on GNU/Linux operating systems, so +# there is no need to account for reading the number of threads on macOS. +if [ x"$jobs" = x0 ]; then jobs=$(nproc); fi + +# Since the container is read-only and is run with the '--contain' option +# (which makes an empty '/tmp'), we need to make a dedicated directory for +# the container to be able to write to. This is necessary because some +# software (Biber in particular on the default branch) need to write there! +# See https://github.com/plk/biber/issues/494. We'll keep the directory on +# the host OS within the build directory, but as a hidden file (since it is +# not necessary in other types of build and ultimately only contains +# temporary files of programs that need it). +toptmp=$build_dir/.apptainer-tmp-$(whoami) +if ! [ -d $toptmp ]; then mkdir $toptmp; fi +chmod -R +w $toptmp/ # Some software remove writing flags on /tmp files. +if ! [ x"$( ls -A $toptmp )" = x ]; then rm -r "$toptmp"/*; fi # [APPTAINER-ONLY] Optional mounting option for the software directory. software_dir_mnt="" @@ -254,18 +272,6 @@ if ! [ x"$software_dir" = x ]; then software_dir_mnt="--mount type=bind,src=$software_dir,dst=/home/maneager/tarballs-software" fi -# [APPTAINER-ONLY] Since the container is read-only and is run with the -# '--contain' option (which makes an empty '/tmp'), we need to make a -# dedicated directory for the container to be able to write to. This is -# necessary because some software (Biber in particular on the default -# branch) need to write there! See https://github.com/plk/biber/issues/494. -# We'll keep the directory on the host OS within the build directory, but -# as a hidden file (since it is not necessary in other types of build and -# ultimately only contains temporary files of programs that need it). -toptmp=$build_dir/.apptainer-tmp-$(whoami) -if ! [ -d $toptmp ]; then mkdir $toptmp; fi -rm -rf $toptmp/* # So previous runs don't affect this run. - @@ -275,22 +281,24 @@ rm -rf $toptmp/* # So previous runs don't affect this run. # # Build the base operating system using Maneage's './project configure' # step. -if [ -f $project_name ]; then +if [ -f $sif ]; then if [ $quiet = 0 ]; then - printf "$scriptname: info: project's image ('$project_name') " + printf "$scriptname: info: project's image ('$sif') " printf "already exists and will be used. If you want to build a " printf "new project image, give a new name to '--project-name'. " printf "To remove this message run with '--quiet'\n" fi else - # Build the basic definition, with just Debian and gcc/g++ - if [ -f $base_name ]; then + # Build the basic definition, with just Debian-slim with minimal + # necessary tools. + if [ -f $base_sif ]; then if [ $quiet = 0 ]; then - printf "$scriptname: info: base OS docker image ('$base_name') " - printf "already exists and will be used. If you want to build a " - printf "new base OS image, give a new name to '--base-name'. " - printf "To remove this message run with '--quiet'\n" + printf "$scriptname: info: base OS apptainer image " + printf "('$base_sif') already exists and will be used. " + printf "If you want to build a new base OS image, give " + printf "a new name to '--base-sif'. To remove this " + printf "message run with '--quiet'\n" fi else @@ -300,11 +308,11 @@ Bootstrap: docker From: $base_os %post - apt-get update && apt-get install -y gcc g++ + apt-get update && apt-get install -y gcc g++ wget EOF # Build the base operating system container and delete the # temporary definition file. - apptainer build $base_name $base_def + apptainer build $base_sif $base_def rm $base_def fi @@ -321,10 +329,11 @@ EOF # software tarball directory, they will all be symbolic links that # aren't valid when the user runs the container (since we only # mount the software tarballs at build time). + intbuild=/home/maneager/build maneage_def=$build_dir/maneage.def cat <<EOF > $maneage_def Bootstrap: localimage -From: $base_name +From: $base_sif %setup mkdir -p \${APPTAINER_ROOTFS}/home/maneager/input @@ -336,24 +345,34 @@ From: $base_name cd /home/maneager/source ./project configure --jobs=$jobs \\ --input-dir=/home/maneager/input \\ - --build-dir=/home/maneager/build \\ + --build-dir=$intbuild \\ --software-dir=/home/maneager/tarballs-software rm /home/maneager/build/software/tarballs/* %runscript cd /home/maneager/source - if [ x"\$maneage_apptainer_stat" = xshell ]; then \\ - ./project shell; \\ - elif [ x"\$maneage_apptainer_stat" = xrun ]; then \\ - if [ x"\$maneage_jobs" = x ]; then \\ - ./project make; \\ + if ./project configure --build-dir=$intbuild \\ + --existing-conf --no-pause \\ + --offline --quiet; then \\ + if [ x"\$maneage_apptainer_stat" = xshell ]; then \\ + ./project shell --build-dir=$intbuild; \\ + elif [ x"\$maneage_apptainer_stat" = xrun ]; then \\ + if [ x"\$maneage_jobs" = x ]; then \\ + ./project make --build-dir=$intbuild; \\ + else \\ + ./project make --build-dir=$intbuild --jobs=\$maneage_jobs; \\ + fi; \\ else \\ - ./project make --jobs=\$maneage_jobs; \\ + printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ + printf "to 'maneage_apptainer_stat' environment variable) "; \\ + printf "is not recognized: should be either 'shell' or 'run'\n"; \\ + exit 1; \\ fi; \\ else \\ - printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ - printf "to 'maneage_apptainer_stat' environment variable) "; \\ - printf "is not recognized: should be either 'shell' or 'run'"; \\ + printf "$scriptname: configuration failed! This is probably "; \\ + printf "due to a mismatch between the software versions of "; \\ + printf "the container and the source that it is being "; \\ + printf "executed.\n"; \\ exit 1; \\ fi EOF @@ -369,7 +388,7 @@ EOF $software_dir_mnt \ --ignore-fakeroot-command \ \ - $project_name \ + $sif \ $maneage_def # Clean up. @@ -381,7 +400,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$project_name' image" + printf "successfully in the '$sif' image\n" fi exit 0 fi @@ -403,7 +422,7 @@ else fi # Build the hostname from the name of the SIF file of the project name. -hstname=$(echo "$project_name" \ +hstname=$(echo "$sif" \ | awk 'BEGIN{FS="/"}{print $NF}' \ | sed -e's|.sif$||') @@ -438,4 +457,4 @@ apptainer $aopt \ --hostname $hstname \ --cwd /home/maneager/source \ \ - $project_name + $sif diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh index 6bbd774..d88b84a 100755 --- a/reproduce/software/shell/bashrc.sh +++ b/reproduce/software/shell/bashrc.sh @@ -34,7 +34,7 @@ # shell'). # # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index e291f7b..3e0163e 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -2,9 +2,9 @@ # # Necessary preparations/configurations for the reproducible project. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -40,6 +40,14 @@ set -e # had the chance to implement it yet (please help if you can!). Until then, # please set them based on your project (if they differ from the core # branch). + +# If equals 1, a message will be printed, showing the nano-seconds since +# previous step: useful with '-e --offline --nopause --quiet' to find +# bottlenecks for speed optimization. Speed is important because this +# script is called automatically every time by the container scripts. +check_elapsed=0 + +# In case a fortran compiler is necessary to check. need_gfortran=0 @@ -52,14 +60,12 @@ need_gfortran=0 # These are defined to help make this script more readable. topdir="$(pwd)" optionaldir="/optional/path" -adir=reproduce/analysis/config cdir=reproduce/software/config -pconf=$cdir/LOCAL.conf -ptconf=$cdir/LOCAL_tmp.conf -poconf=$cdir/LOCAL_old.conf -depverfile=$cdir/versions.conf -depshafile=$cdir/checksums.conf + + + + @@ -73,14 +79,21 @@ depshafile=$cdir/checksums.conf # that their changes are not going to be permenant. create_file_with_notice () { - if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1" + if printf "# IMPORTANT: " > "$1" then - echo "#" >> "$1" - echo "# This file was created during configuration" >> "$1" - echo "# ('./project configure'). Therefore, it is not under" >> "$1" - echo "# version control and any manual changes to it will be" >> "$1" - echo "# over-written if the project re-configured." >> "$1" - echo "#" >> "$1" + # These commands may look messy, but the produced comments in the + # file are the main goal and they are readable. (without having to + # break our source-code line length). + printf "file can be RE-WRITTEN after './project " >> "$1" + printf "configure'.\n" >> "$1" + printf "#\n" >> "$1" + printf "# This file was created during configuration " >> "$1" + printf "('./project configure').\n" >> "$1" + printf "# Therefore, it is not under version control " >> "$1" + printf "and any manual changes\n" >> "$1" + printf "# to it will be over-written when the " >> "$1" + printf "project is re-configured.\n" >> "$1" + printf "#\n" >> "$1" else echo; echo "Can't write to $1"; echo; exit 1 @@ -102,7 +115,7 @@ absolute_dir () if stat "$address" 1> /dev/null; then echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")" else - exit 1; + echo "$optionaldir" fi } @@ -200,30 +213,113 @@ free_space_warning() -# See if we are on a Linux-based system -# -------------------------------------- +# Function to empty the temporary software building directory. This can +# either be a symbolic link (to RAM) or an actual directory, so we can't +# simply use 'rm -r' (because a symbolic link is not a directory for 'rm'). +empty_build_tmp() { + + # 'ls -A' does not print the '.' and '..' and the '-z' option of '[' + # checks if the string is empty or not. This allows us to only attempt + # deleting the directory's contents if it actually has anything inside + # of it. Otherwise, '*' will not expand and we'll get an 'rm' error + # complaining that '$tmpblddir/*' doesn't exist. We also don't want to + # use 'rm -rf $tmpblddir/*' because in case of a typo or while + # debugging (if '$tmpblddir' becomes an empty string), this can + # accidentally delete the whole root partition (or a least the '/home' + # partition of the user). + if ! [ x"$( ls -A $tmpblddir )" = x ]; then + rm -rf "$tmpblddir"/* + fi + rm -r "$tmpblddir" +} + + + + + +# Function to report the elapsed time between steps (if it was activated +# above with 'check_elapsed'). +elapsed_time_from_prev_step() { + if [ $check_elapsed = 1 ]; then + chel_now=$(date +"%N"); + chel_delta=$(echo $chel_prev $chel_now \ + | awk '{ delta=($2-$1)/1e6; \ + if(delta>0) d=delta; else d=0; \ + print d}') + chel_dsum=$(echo $chel_dsum $chel_delta | awk '{print $1+$2}') + echo $chel_counter $chel_delta "$1" \ + | awk '{ printf "Step %02d: %-6.2f [millisec]; %s\n", \ + $1, $2, $3}' + chel_counter=$((chel_counter+1)) + chel_prev=$(date +"%N") + fi +} + + + + + + + + + + +# In already-built container +# -------------------------- +# +# We need to run './project configure' at the start of every run of Maneage +# within a container (with 'shell' or 'make'). This is because we need to +# ensure the versions of all software are correct. However, the container +# filesystem (where the build/software directory is located) should be run +# as read-only when doing the analysis. So we will not be able to run some +# of the tests that require writing files or are generally not relevant +# when the container is already built (we want the configure command to be +# as fast as possible). +# +# The project source in Maneage'd containers is '/home/maneager/source'. +built_container=0 +if [ "$topdir" = /home/maneager/source ] \ + && [ -f .build/software/config/hardware-parameters.tex ]; then + built_container=1; +fi + +# Initialize the elapsed time measurement parameters. +if [ $check_elapsed = 1 ]; then + chel_dsum=0.00 + chel_counter=1 + chel_prev=$(date +"%N") + chel_start=$(date +"%N") +fi + + + + +# Identify the running OS +# ----------------------- # # Some features are tailored to GNU/Linux systems, while the BSD-based # behavior is different. Initially we only tested macOS (hence the name of # the variable), but as FreeBSD is also being inlucded in our tests. As # more systems get used, we need to tailor these kinds of things better. -kernelname=$(uname -s) -if [ x$kernelname = xLinux ]; then - on_mac_os=no - - # Don't forget to add the respective C++ compiler below (leave 'cc' in - # the end). - c_compiler_list="gcc clang cc" -elif [ x$kernelname = xDarwin ]; then - host_cc=1 - on_mac_os=yes - - # Don't forget to add the respective C++ compiler below (leave 'cc' in - # the end). - c_compiler_list="clang gcc cc" -else - on_mac_os=no - cat <<EOF +if [ $built_container = 0 ]; then + kernelname=$(uname -s) + if [ $pauseformsg = 1 ]; then pausesec=10; else pausesec=0; fi + if [ x$kernelname = xLinux ]; then + on_mac_os=no + + # Don't forget to add the respective C++ compiler below (leave 'cc' in + # the end). + c_compiler_list="gcc clang cc" + elif [ x$kernelname = xDarwin ]; then + host_cc=1 + on_mac_os=yes + + # Don't forget to add the respective C++ compiler below (leave 'cc' in + # the end). + c_compiler_list="clang gcc cc" + else + on_mac_os=no + cat <<EOF ______________________________________________________ !!!!!!! WARNING !!!!!!! @@ -234,17 +330,20 @@ web-form: https://savannah.nongnu.org/support/?func=additem&group=reproduce -The configuration will continue in 10 seconds... +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 10 + sleep $pausesec + fi + elapsed_time_from_prev_step os_identify fi - # Collect CPU information # ----------------------- # @@ -255,42 +354,47 @@ fi # later recorded as a LaTeX macro to be put in the final paper, but it # could be used in a more systematic way to optimize/revise project # workflow and build. -hw_class=$(uname -m) -if [ x$kernelname = xLinux ]; then - byte_order=$(lscpu \ - | grep 'Byte Order' \ - | awk '{ \ - for(i=3;i<NF;++i) \ - printf "%s ", $i; \ - printf "%s", $NF}') - address_sizes=$(lscpu \ - | grep 'Address sizes' \ - | awk '{ \ - for(i=3;i<NF;++i) \ - printf "%s ", $i; \ - printf "%s", $NF}') -elif [ x$on_mac_os = xyes ]; then - hw_byteorder=$(sysctl -n hw.byteorder) - if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian"; - elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian"; - fi - # On macOS, the way of obtaining the number of cores is different - # between Intel or Apple M1 CPUs. Here we disinguish between Apple M1 - # or others. - maccputype=$(sysctl -n machdep.cpu.brand_string) - if [ x"$maccputype" = x"Apple M1" ]; then - address_size_physical=$(sysctl -n machdep.cpu.thread_count) - address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) +if [ $built_container = 0 ]; then + if [ x$kernelname = xLinux ]; then + byte_order=$(lscpu \ + | grep 'Byte Order' \ + | awk '{ \ + for(i=3;i<NF;++i) \ + printf "%s ", $i; \ + printf "%s", $NF}') + address_sizes=$(lscpu \ + | grep 'Address sizes' \ + | awk '{ \ + for(i=3;i<NF;++i) \ + printf "%s ", $i; \ + printf "%s", $NF}') + elif [ x$on_mac_os = xyes ]; then + hw_byteorder=$(sysctl -n hw.byteorder) + if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian"; + elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian"; + fi + + # On macOS, the way of obtaining the number of cores is different + # between Intel or Apple M1 CPUs. Here we disinguish between Apple + # M1 or others. + maccputype=$(sysctl -n machdep.cpu.brand_string) + if [ x"$maccputype" = x"Apple M1" ] \ + || [ x"$maccputype" = x"Apple M2" ] \ + || [ x"$maccputype" = x"Apple M3" ] \ + || [ x"$maccputype" = x"Apple M4" ] \ + || [ x"$maccputype" = x"Apple M5" ] ; then + address_size_physical=$(sysctl -n machdep.cpu.thread_count) + address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) + else + address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) + address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) + fi + address_sizes="$address_size_physical bits physical, " + address_sizes+="$address_size_virtual bits virtual" else - address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) - address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) - fi - address_sizes="$address_size_physical bits physical, " - address_sizes+="$address_size_virtual bits virtual" -else - byte_order="unrecognized" - address_sizes="unrecognized" - cat <<EOF + byte_order="unrecognized" + address_sizes="unrecognized" + cat <<EOF ______________________________________________________ !!!!!!! WARNING !!!!!!! @@ -300,10 +404,15 @@ the necessary steps in the 'reproduce/software/shell/configure.sh' script https://savannah.nongnu.org/support/?func=additem&group=reproduce +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec + fi + elapsed_time_from_prev_step cpu-info fi @@ -318,7 +427,7 @@ fi # avoid these error it is highly recommended to install Xcode in the host # system. Here, it is checked that this is the case, and if not, warn the user # about not having Xcode already installed. -if [ x$on_mac_os = xyes ]; then +if [ $built_container = 0 ] && [ x$on_mac_os = xyes ]; then # 'which' isn't in POSIX, so we are using 'command -v' instead. xcode=$(command -v xcodebuild) @@ -341,12 +450,15 @@ web-form: https://savannah.nongnu.org/support/?func=additem&group=reproduce -The configuration will continue in 5 seconds ... +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec fi + elapsed_time_from_prev_step compiler-of-mac-os fi @@ -359,14 +471,15 @@ fi # To build the software, we'll need some basic tools (the C/C++ compilers # in particular) to be present. has_compilers=no -for c in $c_compiler_list; do +if [ $built_container = 0 ]; then + for c in $c_compiler_list; do - # Set the respective C++ compiler. - if [ x$c = xcc ]; then cplus=c++; - elif [ x$c = xgcc ]; then cplus=g++; - elif [ x$c = xclang ]; then cplus=clang++; - else - cat <<EOF + # Set the respective C++ compiler. + if [ x$c = xcc ]; then cplus=c++; + elif [ x$c = xgcc ]; then cplus=g++; + elif [ x$c = xclang ]; then cplus=clang++; + else + cat <<EOF ______________________________________________________ !!!!!!! BUG !!!!!!! @@ -379,21 +492,21 @@ script (just above this error message), or contact us with this web-form: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 - fi + exit 1 + fi - # Check if they exist. - if type $c > /dev/null 2>/dev/null; then - export CC=$c; - if type $cplus > /dev/null 2>/dev/null; then - export CXX=$cplus - has_compilers=yes - break + # Check if they exist. + if type $c > /dev/null 2>/dev/null; then + export CC=$c; + if type $cplus > /dev/null 2>/dev/null; then + export CXX=$cplus + has_compilers=yes + break + fi fi - fi -done -if [ x$has_compilers = xno ]; then - cat <<EOF + done + if [ x$has_compilers = xno ]; then + cat <<EOF ______________________________________________________ !!!!!!! C/C++ Compiler NOT FOUND !!!!!!! @@ -416,51 +529,52 @@ Xcode install are recommended. There are known problems with GCC on macOS. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 + exit 1 + fi + elapsed_time_from_prev_step compiler-present fi - -# Special directory for compiler testing -# -------------------------------------- -# -# This directory will be deleted when the compiler testing is finished. -compilertestdir=.compiler_test_dir_please_delete -if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi - - - - - # Check C compiler # ---------------- # -# Here we check if the C compiler works properly. About the "no warning" -# variable ('nowarnings'): -# -# -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and Xcode 12.4, -# hundreds of 'nullability-completeness' warnings are printed which can -# be very annoying and even hide important errors or warnings. It is -# also harmless for our test here, so it is generally added. -testprog=$compilertestdir/test +# We are checking the C compiler before asking for the directories to let +# the user fix lower-level problems before giving inputs. +compilertestdir=.compiler_test_dir_please_delete testsource=$compilertestdir/test.c -if [ x$on_mac_os = xyes ]; then - noccwarnings="-Wno-nullability-completeness" -fi -echo; echo; echo "Checking host C compiler ('$CC')..."; -cat > $testsource <<EOF +testprog=$compilertestdir/test +if [ $built_container = 0 ]; then + + # Here we check if the C compiler works properly. We'll start by + # making a directory to keep the products. + if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi + + # About the "no warning" variable ('nowarnings'): + # + # -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and + # Xcode 12.4, hundreds of 'nullability-completeness' warnings + # are printed which can be very annoying and even hide + # important errors or warnings. It is also harmless for our + # test here, so it is generally added. + if [ x$on_mac_os = xyes ]; then + noccwarnings="-Wno-nullability-completeness" + fi + if [ $quiet = 0 ]; then + echo; echo "Checking host C compiler ('$CC')..."; + fi + cat > $testsource <<EOF #include <stdio.h> #include <stdlib.h> -int main(void){printf("...C compiler works.\n"); - return EXIT_SUCCESS;} +int main(void){printf("Good!\n"); return EXIT_SUCCESS;} EOF -if $CC $noccwarnings $testsource -o$testprog && $testprog; then - rm $testsource $testprog -else - rm $testsource - cat <<EOF + if $CC $noccwarnings $testsource -o$testprog && $testprog > /dev/null; then + if [ $quiet = 0 ]; then echo "... yes"; fi + rm $testsource $testprog + else + rm $testsource + cat <<EOF ______________________________________________________ !!!!!!! C compiler doesn't work !!!!!!! @@ -479,13 +593,14 @@ https://savannah.nongnu.org/support/?func=additem&group=reproduce !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 + exit 1 + fi + elapsed_time_from_prev_step compiler-c-check fi - # See if we need the dynamic-linker (-ldl) # ---------------------------------------- # @@ -493,7 +608,8 @@ fi # GNU/Linux systems, we'll need the '-ldl' flag to link such programs. But # Mac OS doesn't need any explicit linking. So we'll check here to see if # it is present (thus necessary) or not. -cat > $testsource <<EOF +if [ $built_container = 0 ]; then + cat > $testsource <<EOF #include <stdio.h> #include <dlfcn.h> int @@ -502,17 +618,17 @@ main(void) { return 0; } EOF -if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then - needs_ldl=no; -else - needs_ldl=yes; + if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then + needs_ldl=no; + else + needs_ldl=yes; + fi + elapsed_time_from_prev_step compiler-needs-dynamic-linker fi - - # See if the C compiler can build static libraries # ------------------------------------------------ # @@ -528,32 +644,30 @@ fi # the library came from the system or our build. static_build=no - - - - # Print warning if the host CC is to be used. -if [ x$host_cc = x1 ]; then +if [ $built_container = 0 ] && [ x$host_cc = x1 ]; then cat <<EOF ______________________________________________________ !!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran -and etc) is currently not built on macOS systems for this project. To build -the project's necessary software on this system, we need to use your -system's C compiler. +and etc) is not going to be built for this project. Either it is a macOS, +or you have used '--host-cc'. -Project's configuration will continue in 5 seconds. -______________________________________________________ +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec fi + # Necessary C library element positions # ------------------------------------- # @@ -563,7 +677,7 @@ fi # similarly different location. sys_cpath="" sys_library_path="" -if [ x"$on_mac_os" != xyes ]; then +if [ $built_container = 0 ] && [ x"$on_mac_os" != xyes ]; then # Get the GCC target name of the compiler, when its given, special # C libraries and headers are in a sub-directory of the host. @@ -581,6 +695,7 @@ if [ x"$on_mac_os" != xyes ]; then # For a check: #echo "sys_library_path: $sys_library_path" #echo "sys_cpath: $sys_cpath" + elapsed_time_from_prev_step compiler-sys-cpath fi @@ -592,25 +707,28 @@ fi # # A static C library and the 'sys/cdefs.h' header are necessary for # building GCC. -if [ x"$host_cc" = x0 ]; then - echo; echo; echo "Checking if static C library is available..."; - cat > $testsource <<EOF +if [ $built_container = 0 ]; then + if [ x"$host_cc" = x0 ]; then + if [ $quiet = 0 ]; then + echo; echo "Checking if static C library is available..."; + fi + cat > $testsource <<EOF #include <stdio.h> #include <stdlib.h> #include <sys/cdefs.h> -int main(void){printf("...yes\n"); - return EXIT_SUCCESS;} +int main(void){printf("...yes\n"); return EXIT_SUCCESS;} EOF - cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc" - if $cc_call && $testprog; then - gccwarning=0 - rm $testsource $testprog - else - echo; echo "Compilation command:"; echo "$cc_call" - rm $testsource - gccwarning=1 - host_cc=1 - cat <<EOF + cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc" + if $cc_call && $testprog > /dev/null; then + gccwarning=0 + rm $testsource $testprog + if [ $quiet = 0 ]; then echo "... yes"; fi + else + echo; echo "Compilation command:"; echo "$cc_call" + rm $testsource + gccwarning=1 + host_cc=1 + cat <<EOF _______________________________________________________ !!!!!!!!!!!! Warning !!!!!!!!!!!! @@ -637,15 +755,14 @@ re-configure the project to fix this problem. $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS" $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS" - _______________________________________________________ EOF + fi fi -fi -# Print a warning if GCC is not meant to be built. -if [ x"$gccwarning" = x1 ]; then + # Print a warning if GCC is not meant to be built. + if [ x"$gccwarning" = x1 ]; then cat <<EOF PLEASE SEE THE WARNINGS ABOVE. @@ -655,16 +772,38 @@ seconds and use your system's C compiler (it won't build a custom GCC). But please consider installing the necessary package(s) to complete your C compiler, then re-run './project configure'. -Project's configuration will continue in 5 seconds. +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. EOF - sleep 5 + sleep $pausesec + fi + elapsed_time_from_prev_step compiler-linkable-static fi +# Older C standard versions +# ------------------------- +# +# Some basic packages require an old standard of C compilation; for their +# list, see the 'Not working with C23' list in '../config/versions.conf'. +# Here, we first try 'gnu17', but if that fails on the host compiler, we +# fall back to 'gnu99'. +if [ $built_container = 0 ]; then + printf "int main(void){; return 0;}\n" > $testsource + if gcc -std=gnu17 $testsource -o $testprog 2> /dev/null; then + std_c_old="gnu17" + else std_c_old="gnu99" + fi + rm $testsource $testprog +fi + + + + # Fortran compiler # ---------------- # @@ -672,7 +811,7 @@ fi # have a fortran compiler: we'll build it internally for high-level # programs with GCC. However, when the host C compiler is to be used, the # user needs to have a Fortran compiler available. -if [ $host_cc = 1 ]; then +if [ $built_container = 0 ] && [ $host_cc = 1 ]; then # If a Fortran compiler is necessary, see if 'gfortran' exists and can # be used. @@ -705,8 +844,9 @@ EOF # Then, see if the Fortran compiler works testsourcef=$compilertestdir/test.f echo; echo; echo "Checking host Fortran compiler..."; - echo " PRINT *, \"... Fortran Compiler works.\"" > $testsourcef - echo " END" >> $testsourcef + echo " PRINT *, \"... Fortran Compiler works.\"" \ + > $testsourcef + echo " END" >> $testsourcef if gfortran $testsourcef -o$testprog && $testprog; then rm $testsourcef $testprog else @@ -732,6 +872,41 @@ EOF exit 1 fi fi + elapsed_time_from_prev_step compiler-fortran +fi + + + + + + + + + + +# Paths needed by the host compiler (only for 'basic.mk') +# ------------------------------------------------------- +# +# At the end of the basic build, we need to build GCC. But GCC will build +# in multiple phases, making its own simple compiler in order to build +# itself completely. The intermediate/simple compiler doesn't recognize +# some system specific locations like '/usr/lib/ARCHITECTURE' that some +# operating systems use. We thus need to tell the intermediate compiler +# where its necessary libraries and headers are. +if [ $built_container = 0 ]; then + if [ x"$sys_library_path" != x ]; then + if [ x"$LIBRARY_PATH" = x ]; then + export LIBRARY_PATH="$sys_library_path" + else + export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path" + fi + if [ x"$CPATH" = x ]; then + export CPATH="$sys_cpath" + else + export CPATH="$CPATH:$sys_cpath" + fi + fi + elapsed_time_from_prev_step compiler-paths fi @@ -743,7 +918,8 @@ fi # # Print some basic information so the user gets a feeling of what is going # on and is prepared on what will happen next. -cat <<EOF +if [ $quiet = 0 ]; then + cat <<EOF ----------------------------- Project's local configuration @@ -758,33 +934,29 @@ components from pre-defined webpages). It is STRONGLY recommended to read the description above each question before answering it. EOF +fi - -# What to do with possibly existing configuration file -# ---------------------------------------------------- +# Previous configuration +# ---------------------- # -# 'LOCAL.conf' is the top-most local configuration for the project. If it -# already exists when this script is run, we'll make a copy of it as backup -# (for example the user might have ran './project configure' by mistake). -printnotice=yes -rewritepconfig=yes -if [ -f $pconf ]; then +# 'LOCAL.conf' is the top-most local configuration for the project. At this +# point, if a LOCAL.conf exists within the '.build' symlink, we use it +# (instead of asking the user to interactively specify it). +rewritelconfig=yes +lconf=.build/software/config/LOCAL.conf +if [ -f $lconf ]; then if [ $existing_conf = 1 ]; then - printnotice=no - if [ -f $pconf ]; then rewritepconfig=no; fi + rewritelconfig=no; fi fi - - - # Make sure the group permissions satisfy the previous configuration (if it # exists and we don't want to re-write it). -if [ $rewritepconfig = no ]; then - oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf) +if [ $rewritelconfig = no ]; then + oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $lconf) if [ "x$oldgroupname" = "x$maneage_group_name" ]; then just_a_place_holder_to_avoid_not_equal_test=1; else @@ -805,65 +977,9 @@ if [ $rewritepconfig = no ]; then echo " $confcommand"; echo exit 1 fi -fi - - - - - -# Identify the downloader tool -# ---------------------------- -# -# After this script finishes, we will have both Wget and cURL for -# downloading any necessary dataset during the processing. However, to -# complete the configuration, we may also need to download the source code -# of some necessary software packages (including the downloaders). So we -# need to check the host's available tool for downloading at this step. -if [ $rewritepconfig = yes ]; then - if type wget > /dev/null 2>/dev/null; then - - # 'which' isn't in POSIX, so we are using 'command -v' instead. - name=$(command -v wget) - - # See if the host wget has the '--no-use-server-timestamps' option - # (for example wget 1.12 doesn't have it). If not, we'll have to - # remove it. This won't affect the analysis of Maneage in anyway, - # its just to avoid re-downloading if the server timestamps are - # bad; at the worst case, it will just cause a re-download of an - # input software source code (for data inputs, we will use our own - # wget that has this option). - tsname="no-use-server-timestamps" - tscheck=$(wget --help | grep $tsname || true) - if [ x"$tscheck" = x ]; then wgetts="" - else wgetts="--$tsname"; - fi - # By default Wget keeps the remote file's timestamp, so we'll have - # to disable it manually. - downloader="$name $wgetts -O"; - elif type curl > /dev/null 2>/dev/null; then - name=$(command -v curl) - - # - cURL doesn't keep the remote file's timestamp by default. - # - With the '-L' option, we tell cURL to follow redirects. - downloader="$name -L -o" - else - cat <<EOF - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -Couldn't find GNU Wget, or cURL on this system. These programs are used for -downloading necessary programs and data if they aren't already present (in -directories that you can specify with this configure script). Therefore if -the necessary files are not present, the project will crash. - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - downloader="no-downloader-found" - fi; + # Report timing of this step if necessary. + elapsed_time_from_prev_step LOCAL-and-group-check fi @@ -873,7 +989,7 @@ fi # Build directory # --------------- currentdir="$(pwd)" -if [ $rewritepconfig = yes ]; then +if [ $rewritelconfig = yes ]; then cat <<EOF =============== @@ -901,12 +1017,18 @@ Do not choose any directory under the top source directory (this directory). The build directory cannot be a subdirectory of the source. --------------- +Build directory: + - Must be writable by running user. + - Not a sub-directory of the source directory. + - No meta-characters in name: SPACE ! ' @ # $ % ^ & * ( ) + ; + EOF bdir= junkname=pure-junk-974adfkj38 while [ x"$bdir" = x ] do - # Ask the user (if not already set on the command-line). + # Ask the user (if not already set on the command-line: 'build_dir' + # comes from the 'project' script). if [ x"$build_dir" = x ]; then if read -p"Please enter the top build directory: " build_dir; then @@ -948,9 +1070,11 @@ EOF # If it was newly created, it will be empty, so delete it. if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi - # Inform the user that this is not acceptable and reset 'bdir'. + # Inform the user that this is not acceptable and reset + # 'bdir'. bdir= - echo " ** The build-directory cannot be under the source-directory." + printf " ** The build-directory cannot be under the " + printf "source-directory." fi fi @@ -959,7 +1083,8 @@ EOF # building. if ! [ x"$bdir" = x ]; then hasmeta=0; - case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac + case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; + esac if [ $hasmeta = 1 ]; then # If it was newly created, it will be empty, so delete it. @@ -967,9 +1092,10 @@ EOF # Inform the user and set 'bdir' to empty again. bdir= - echo " ** Build directory should not contain meta-characters" - echo " ** (like SPACE, %, \$, !, ;, or parenthesis, among " - echo " ** others): they can interrup the build for some software." + printf " ** Build directory should not contain " + printf "meta-characters (like SPACE, %, \$, !, ;, or " + printf "parenthesis, among others): they can interrup " + printf "the build for some software." fi fi @@ -980,16 +1106,29 @@ EOF if ! $(check_permission "$bdir"); then # Unable to handle permissions well bdir= - echo " ** File permissions can't be modified in this directory" + printf " ** File permissions can not be modified in " + printf "this directory" else # Able to handle permissions, now check for 5GB free space # in the given partition (note that the number is in units # of 1024 bytes). If this is not the case, print a warning. if $(free_space_warning 5000000 "$bdir"); then - echo " !! LESS THAN 5GB FREE SPACE IN: $bdir" - echo " !! We recommend choosing another partition." - echo " !! Build will continue in 5 seconds..." - sleep 5 + cat <<EOF + +_______________________________________________________ +!!!!!!!!!!!! Warning !!!!!!!!!!!! + +Less than 5GB free space in '$bdir'. We recommend choosing another +partition. Note that the software environment alone will take roughly +4.5GB, so if your datasets are large, it will fill up very soon. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec fi fi fi @@ -1003,9 +1142,42 @@ EOF echo " ** Please select another directory." echo "" else + # Set the '.build' and '.local' symbolic links (and delete + # possibly existing symbolic links). These commands are also + # present in the top-level 'project' script, but they are only + # invoked when '--build-dir' is called. When it is not called + # (the user wants to insert the directories interactively: the + # scenario here), the links need to be created from + # scratch. Furthermore, in case the given directory to + # '--build-dir' has problems (fails to pass the sanity checks + # above), the symbolic links also need to be recreated. + rm -f .build .local + ln -s $bdir .build + ln -s $bdir/software/installed .local + + # Inform the user echo " -- Build directory set to ($instring): '$bdir'" fi done + + # Report timing if necessary + elapsed_time_from_prev_step build-dir + +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode. +else + + # Read the build directory from existing configuration file. It is + # assumed that 'LOCAL.conf' is created by this script (above the + # 'else') and that all the sanity checks there have already been + # applied. We'll just check if it is empty or not. + bdir=$(awk '$1=="BDIR" {print $3}' $lconf) + if [ x"$bdir" = x ]; then + printf "$scriptname: no value to 'BDIR' of '$lconf'. Please run " + printf "the project configuration again, but without " + printf "'--existing-conf' (or '-e')" + exit 1 + fi fi @@ -1014,13 +1186,10 @@ fi # Input directory # --------------- -if [ x"$input_dir" = x ]; then - indir="$optionaldir" -else - indir="$input_dir" +if [ x"$input_dir" = x ]; then indir="$optionaldir" +else indir="$input_dir" fi -noninteractive_sleep=2 -if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then +if [ $rewritelconfig = yes ]; then cat <<EOF ---------------------------------- @@ -1047,35 +1216,61 @@ don't want to make duplicates, you can create symbolic links to them and put those symbolic links in the given top-level directory. EOF - # Read the input directory if interactive mode is enabled. - if read -p"(OPTIONAL) Input datasets directory ($indir): " inindir; then - just_a_place_holder_to_avoid_not_equal_test=1; - else - echo "WARNING: interactive-mode seems to be disabled!" - echo "If you have a local copy of the inputs, use '--input-dir'." - echo "... project configuration will continue in $noninteractive_sleep sec ..." - sleep $noninteractive_sleep + # In case an input directory is not given, ask the user interactively. + if [ x"$input_dir" = x ]; then + + # Read the input directory if interactive mode is enabled. + if read -p"(OPTIONAL) Input datasets directory ($indir): " \ + inindir; then + just_a_place_holder_to_avoid_not_equal_test=1; + else + cat <<EOF +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! + +WARNING: interactive-mode seems to be disabled! If you have a local copy of +the inputs, use '--input-dir'. Otherwise, all the data will be downloaded. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec + fi + else # An input directory was given. + inindir="$input_dir" fi - # In case an input-directory is given, write it in 'indir'. + # If the given string is not empty, write it in 'indir'. if [ x$inindir != x ]; then indir="$(absolute_dir "$inindir")" echo " -- Using '$indir'" fi + + # Report timing if necessary. + elapsed_time_from_prev_step input-dir + +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode; similar to 'bdir' above. +else + indir=$(awk '$1=="INDIR" {print $3}' $lconf) fi + # Dependency tarball directory # ---------------------------- -if [ x"$software_dir" = x ]; then - ddir=$optionaldir -else - ddir=$software_dir +if [ x"$software_dir" = x ]; then ddir=$optionaldir +else ddir=$software_dir fi -if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then +if [ $rewritelconfig = yes ]; then + + # Print information. cat <<EOF --------------------------------------- @@ -1091,14 +1286,32 @@ of a dependency, it is necessary to have an internet connection because the project will download the tarballs it needs automatically. EOF - # Read the software directory if interactive mode is enabled. - if read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir; then - just_a_place_holder_to_avoid_not_equal_test=1; + + # Ask the user for the software directory if it is not given as an + # option. + if [ x"$software_dir" = x ]; then + if read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " \ + tmpddir; then + just_a_place_holder_to_avoid_not_equal_test=1; + else + cat <<EOF +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! + +WARNING: interactive-mode seems to be disabled! If you have a local copy of +the software source tarballs, use '--software-dir'. Otherwise, all the +necessary tarballs will be downloaded. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec + fi else - echo "WARNING: interactive-mode seems to be disabled!" - echo "If you have a local copy of the software source, use '--software-dir'." - echo "... project configuration will continue in $noninteractive_sleep sec ..." - sleep $noninteractive_sleep + tmpddir="$software_dir" fi # If given, write the software directory. @@ -1106,105 +1319,165 @@ EOF ddir="$(absolute_dir "$tmpddir")" echo " -- Using '$ddir'" fi -fi - +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode; similar to 'bdir' above. +else + indir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $lconf) +fi +elapsed_time_from_prev_step software-dir -# Write the parameters into the local configuration file. -if [ $rewritepconfig = yes ]; then - # Add commented notice. - create_file_with_notice $pconf - # Write the values. - sed -e's|@bdir[@]|'"$bdir"'|' \ - -e's|@indir[@]|'"$indir"'|' \ - -e's|@ddir[@]|'"$ddir"'|' \ - -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ - -e's|@downloader[@]|'"$downloader"'|' \ - -e's|@groupname[@]|'"$maneage_group_name"'|' \ - $pconf.in >> $pconf -else - # Read the values from existing configuration file. Note that the build - # directory may have space characters. Even though we currently check - # against it, we hope to be able to remove this condition in the - # future. - inbdir=$(awk '$1=="BDIR" { for(i=3; i<NF; i++) \ - printf "%s ", $i; \ - printf "%s", $NF }' $pconf) - - # Read the software directory (same as 'inbdir' above about space). - ddir=$(awk '$1=="DEPENDENCIES-DIR" { for(i=3; i<NF; i++) \ - printf "%s ", $i; \ - printf "%s", $NF}' $pconf) - - # The downloader command may contain multiple elements, so we'll just - # change the (in memory) first and second tokens to empty space and - # write the full line (the original file is unchanged). - downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf) - - # Make sure all necessary variables have a value - err=0 - verr=0 - novalue="" - if [ x"$inbdir" = x ]; then novalue="BDIR, "; fi - if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER; fi - if [ x"$novalue" != x ]; then verr=1; err=1; fi - - # Make sure 'bdir' is an absolute path and it exists. - berr=0 - ierr=0 - bdir="$(absolute_dir "$inbdir")" - - if ! [ -d "$bdir" ]; then if ! mkdir "$bdir"; then berr=1; err=1; fi; fi - if [ $err = 1 ]; then - cat <<EOF +# Downloader +# ---------- +# +# After this script finishes, we will have both Wget and cURL for +# downloading any necessary dataset during the processing. However, to +# complete the configuration, we may also need to download the source code +# of some necessary software packages (including the downloaders). So we +# need to check the host's available tool for downloading at this step. +if [ $rewritelconfig = yes ]; then + if type wget > /dev/null 2>/dev/null; then -################################################################# -######## ERORR reading existing configuration file ############ -################################################################# -EOF - if [ $verr = 1 ]; then - cat <<EOF + # 'which' isn't in POSIX, so we are using 'command -v' instead. + name=$(command -v wget) -These variables have no value: $novalue. -EOF + # See if the host wget has the '--no-use-server-timestamps' option + # (for example wget 1.12 doesn't have it). If not, we'll have to + # remove it. This won't affect the analysis of Maneage in anyway, + # its just to avoid re-downloading if the server timestamps are + # bad; at the worst case, it will just cause a re-download of an + # input software source code (for data inputs, we will use our own + # wget that has this option). + tsname="no-use-server-timestamps" + tscheck=$(wget --help | grep $tsname || true) + if [ x"$tscheck" = x ]; then wgetts="" + else wgetts="--$tsname"; fi - if [ $berr = 1 ]; then - cat <<EOF -Couldn't create the build directory '$bdir' (value to 'BDIR') in -'$pconf'. -EOF - fi + # By default Wget keeps the remote file's timestamp, so we'll have + # to disable it manually. + downloader="$name $wgetts -O"; + elif type curl > /dev/null 2>/dev/null; then + name=$(command -v curl) + # - cURL doesn't keep the remote file's timestamp by default. + # - With the '-L' option, we tell cURL to follow redirects. + downloader="$name -L -o" + else cat <<EOF -Please run the configure script again (accepting to re-write existing -configuration file) so all the values can be filled and checked. -################################################################# +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +Couldn't find GNU Wget, or cURL on this system. These programs are used for +downloading necessary programs and data if they aren't already present (in +directories that you can specify with this configure script). Therefore if +the necessary files are not present, the project will crash. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + EOF + downloader="no-downloader-found" + fi; + +# The downloader should be extracted from the existing LOCAL.conf. +else + # The value will be a command (including white spaces), so we will read + # all the "fields" from the third to the end. + downloader=$(awk '$1=="DOWNLOADER" { for(i=3; i<NF; i++) \ + printf "%s ", $i; \ + printf "%s", $NF }' $lconf) + + if [ x"$downloader" = x ]; then + printf "$scriptname: no value to 'DOWNLOADER' of '$lconf'. " + printf "Please run the project configuration again, but " + printf "without '--existing-conf' (or '-e')" + exit 1 fi fi +elapsed_time_from_prev_step downloader -# Delete final configuration target -# --------------------------------- +# Libraries necessary for the system's shell +# ------------------------------------------ # -# We only want to start running the project later if this script has -# completed successfully. To make sure it hasn't crashed in the middle -# (without the user noticing), in the end of this script we make a file and -# we'll delete it here (at the start). Therefore if the script crashed in -# the middle that file won't exist. -sdir="$bdir"/software -finaltarget="$sdir"/configuration-done.txt -if ! [ -d "$sdir" ]; then mkdir "$sdir"; fi -rm -f "$finaltarget" +# In some cases (mostly the programs that Maneage doesn't yet build by +# itself), the programs may call the system's shell, not Maneage's +# shell. After we close-off the system environment from Maneage, this will +# cause a crash! To avoid such cases, we need to find the locations of the +# libraries that the shell needs and temporarily add them to the library +# search path. +# +# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some +# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] +# that is different to the formats that are assumed, prior to this commit, +# by the algorithm in 'configure.sh' when evaluating the variable +# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) +# 'ncurses', because the option using 'sys_library_sh_path' contains an +# unquoted RAM address in parentheses. Even if the address were quoted, it +# would still be incorrect. This 'grep' command excludes candidate host +# path strings that look like RAM addresses to address the problem. +# +# [1] https://savannah.nongnu.org/bugs/index.php?66847 +# [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program +# [3] man vdso +if [ $built_container = 0 ]; then + if [ x"$on_mac_os" = xyes ]; then + sys_library_sh_path=$(otool -L /bin/sh \ + | awk '/\/lib/{print $1}' \ + | sed 's#/[^/]*$##' \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + else + sys_library_sh_path=$(ldd /bin/sh \ + | awk '{if($3!="") print $3}' \ + | sed 's#/[^/]*$##' \ + | grep -v "(0x[^)]*)" \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + fi + elapsed_time_from_prev_step sys-library-sh-path +fi + + + + + +# When no local configuration existed, write the parameters into the local +# configuration file. +sdir=$bdir/software +sconfdir=$sdir/config +if ! [ -d "$sdir" ]; then mkdir "$sdir"; fi +if ! [ -d "$sconfdir" ]; then mkdir "$sconfdir"; fi +if [ $rewritelconfig = yes ]; then + + # Put the basic comments at the top of the file. + create_file_with_notice $lconf + + # Write the values. + lconfin=$cdir/LOCAL.conf.in + sed -e's|@bdir[@]|'"$bdir"'|' \ + -e's|@indir[@]|'"$indir"'|' \ + -e's|@ddir[@]|'"$ddir"'|' \ + -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ + -e's|@downloader[@]|'"$downloader"'|' \ + -e's|@groupname[@]|'"$maneage_group_name"'|' \ + -e's|@sys_library_sh_path[@]|'"$sys_library_sh_path"'|' \ + $lconfin >> $lconf +fi +elapsed_time_from_prev_step LOCAL-write @@ -1217,98 +1490,92 @@ rm -f "$finaltarget" # avoid too many directory dependencies throughout the software and # analysis Makefiles (thus making them hard to read), we are just building # them here -# Software tarballs tardir="$sdir"/tarballs -if ! [ -d "$tardir" ]; then mkdir "$tardir"; fi - -# Installed software instdir="$sdir"/installed -if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi +tmpblddir="$sdir"/build-tmp -# To record software versions and citation. +# Second-level directories. +instlibdir="$instdir"/lib +instbindir="$instdir"/bin verdir="$instdir"/version-info -if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi -# Program and library versions and citation. -ibidir="$verdir"/proglib -if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi - -# Python module versions and citation. +# Sub-directories of version-info +itidir="$verdir"/tex +ictdir="$verdir"/cite ipydir="$verdir"/python -if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi - -# R module versions and citation. +ibidir="$verdir"/proglib ircrandir="$verdir"/r-cran -if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi - -# Used software BibTeX entries. -ictdir="$verdir"/cite -if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi - -# TeXLive versions. -itidir="$verdir"/tex -if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi - -# Some software install their libraries in '$(idir)/lib64'. But all other -# libraries are in '$(idir)/lib'. Since Maneage's build is only for a -# single architecture, we can set the '$(idir)/lib64' as a symbolic link to -# '$(idir)/lib' so all the libraries are always available in the same -# place. -instlibdir="$instdir"/lib -if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi -ln -fs "$instlibdir" "$instdir"/lib64 - -# Wrapper over Make as a single command so it does not default to '/bin/sh' -# during installation (needed by some programs like CMake). -instbindir=$instdir/bin -if ! [ -d $instbindir ]; then mkdir $instbindir; fi -makewshell="$instbindir/make-with-shell" -echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell -chmod +x $makewshell - +if [ $built_container = 0 ]; then + + # Top-level directories. + if ! [ -d "$tardir" ]; then mkdir "$tardir"; fi + if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi + + # Second-level directories. + if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi + if ! [ -d "$instbindir" ]; then mkdir "$instbindir"; fi + + # Sub-directories of version-info + if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi + if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi + if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi + if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi + if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi + + # Some software install their libraries in '$(idir)/lib64'. But all + # other libraries are in '$(idir)/lib'. Since Maneage's build is only + # for a single architecture, we can set the '$(idir)/lib64' as a + # symbolic link to '$(idir)/lib' so all the libraries are always + # available in the same place. + if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi + ln -fs "$instlibdir" "$instdir"/lib64 + + # Wrapper over Make as a single command so it does not default to + # '/bin/sh' during installation (needed by some programs like CMake). + makewshell="$instbindir/make-with-shell" + if ! [ -f "$makewshell" ]; then + echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell + chmod +x $makewshell + fi + # Report the execution time of this step. + elapsed_time_from_prev_step subdirectories-of-build +fi -# Project's top-level built analysis directories -# ---------------------------------------------- -# Top-level LaTeX. -texdir="$sdir"/tex -if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi - -# If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete -# them and we can continue. However, when the project is being built from -# the tarball, these two are not symbolic links but actual directories with -# the necessary built-components to build the PDF in them. In this case, -# because 'tex/build' is a directory, 'rm -f' will fail, so we'll just -# rename the two directories (as backup) and let the project build the -# proper symbolic links afterwards. -if rm -f tex/build; then - rm -f tex/tikz -else - mv tex/tikz tex/tikz-from-tarball - mv tex/build tex/build-from-tarball -fi -# Set the symbolic links for easy access to the top project build -# directories. Note that these are put in each user's source/cloned -# directory, not in the build directory (which can be shared between many -# users and thus may already exist). +# See if the linker accepts -Wl,-rpath-link +# ----------------------------------------- # -# Note: if we don't delete them first, it can happen that an extra link -# will be created in each directory that points to its parent. So to be -# safe, we are deleting all the links on each re-configure of the -# project. Note that at this stage, we are using the host's 'ln', not our -# own, so its best not to assume anything (like 'ln -sf'). -rm -f .build .local - -ln -s "$bdir" .build -ln -s "$instdir" .local - -# --------- Delete for no Gnuastro --------- -rm -f .gnuastro -# ------------------------------------------ +# '-rpath-link' is used to write the information of the linked shared +# library into the shared object (library or program). But some versions of +# LLVM's linker don't accept it an can cause problems. +# +# IMPORTANT NOTE: This test has to be done **AFTER** the definition of +# 'instdir'. Otherwise, the rpath-link value set within rpath_command in +# the case of a successful test compile (if $CC ...) will be "/lib", +# i.e. the host system root /lib directory, instead of the maneage library +# directory. +if [ $built_container = 0 ]; then + cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +int main(void) {return EXIT_SUCCESS;} +EOF + if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \ + > /dev/null; then + export rpath_command="-Wl,-rpath-link=$instdir/lib" + else + export rpath_command="" + fi + + # Delete the temporary directory for compiler checking. + rm -f $testprog $testsource + rm -r $compilertestdir + elapsed_time_from_prev_step compiler-rpath +fi @@ -1322,120 +1589,116 @@ rm -f .gnuastro # HDDs/SSDs and improve speed, it is therefore better to build them in the # RAM when possible. The RAM of most systems today (>8GB) is large enough # for the parallel building of the software. - +# # Set the top-level shared memory location. Currently there is only one # standard location (for GNU/Linux OSs), so doing this check here and the # main job below may seem redundant. However, it is written separately from # the main code below because later, we expect to add more possible # mounting locations (for other OSs). -if [ -d /dev/shm ]; then shmdir=/dev/shm -else shmdir="" -fi +if [ $built_container = 0 ]; then + if [ -d /dev/shm ]; then shmdir=/dev/shm + else shmdir="" + fi -# If a shared memory mounted directory exists and has the necessary -# conditions, set that directory to build software. -if [ x"$shmdir" != x ]; then - - # Make sure it has enough space. - needed_space=2000000 - available_space=$(df "$shmdir" | awk 'NR==2{print $4}') - if [ $available_space -gt $needed_space ]; then - - # Set the Maneage-specific directory within the shared - # memory. We'll use the names of the two parent directories to the - # current/running directory, separated by a '-' instead of - # '/'. We'll then appended that with the user's name (in case - # multiple users may be working on similar project names). - # - # Maybe later, we can use something like 'mktemp' to add random - # characters to this name and make it unique to every run (even for - # a single user). - dirname=$(pwd | sed -e's/\// /g' \ - | awk '{l=NF-1; printf("%s-%s", $l, $NF)}') - tbshmdir="$shmdir"/"$dirname"-$(whoami) - - # Try to make the directory if it does not yet exist. A failed - # directory creation will be tested for a few lines later, when - # testing for the existence and executability of a test file. - if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi - - # Some systems may protect '/dev/shm' against the right to execute - # programs by ordinary users. We thus need to check that the device - # allows execution within this directory by this user. - shmexecfile="$tbshmdir"/shm-execution-check.sh - rm -f $shmexecfile # We also don't want any existing flags. - - # Create the file to be executed, but do not fail fatally if it - # cannot be created. We will check a few lines later if the file - # really exists. - (cat > "$shmexecfile" <<EOF || true) + # If a shared memory mounted directory exists and has the necessary + # conditions, set that directory to build software. + if [ x"$shmdir" != x ]; then + + # Make sure it has enough space. + needed_space=2000000 + available_space=$(df "$shmdir" | awk 'NR==2{print $4}') + if [ $available_space -gt $needed_space ]; then + + # Set the Maneage-specific directory within the shared + # memory. We'll use the names of the two parent directories to + # the current/running directory, separated by a '-' instead of + # '/'. We'll then appended that with the user's name (in case + # multiple users may be working on similar project names). + # + # Maybe later, we can use something like 'mktemp' to add random + # characters to this name and make it unique to every run (even + # for a single user). + dirname=$(pwd | sed -e's/\// /g' \ + | awk '{l=NF-1; printf("%s-%s", $l, $NF)}') + tbshmdir="$shmdir"/"$dirname"-$(whoami) + + # Try to make the directory if it does not yet exist. A failed + # directory creation will be tested for a few lines later, when + # testing for the existence and executability of a test file. + if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi + + # Some systems may protect '/dev/shm' against the right to + # execute programs by ordinary users. We thus need to check + # that the device allows execution within this directory by + # this user. + shmexecfile="$tbshmdir"/shm-execution-check.sh + rm -f $shmexecfile # We also don't want any existing flags. + + # Create the file to be executed, but do not fail fatally if it + # cannot be created. We will check a few lines later if the + # file really exists. + (cat > "$shmexecfile" <<EOF || true) #!/bin/sh -echo "This file successfully executed." +a=b EOF - # If the file was successfully created, then make the file - # executable and see if it runs. If not, set 'tbshmdir' to an empty - # string so it is not used in later steps. In any case, delete the - # temporary file afterwards. - # - # We aren't adding '&> /dev/null' after the execution command - # because it can produce false failures randomly on some systems. - if [ -e "$shmexecfile" ]; then - - # Add the executable flag. - chmod +x "$shmexecfile" - - # The following line tries to execute the file. - if "$shmexecfile"; then - # Successful execution. The colon is a "no-op" (no - # operation) shell command. - : + # If the file was successfully created, then make the file + # executable and see if it runs. If not, set 'tbshmdir' to an + # empty string so it is not used in later steps. In any case, + # delete the temporary file afterwards. + # + # We aren't adding '&> /dev/null' after the execution command + # because it can produce false failures randomly on some + # systems. + if [ -e "$shmexecfile" ]; then + + # Add the executable flag. + chmod +x "$shmexecfile" + + # The following line tries to execute the file. + if "$shmexecfile"; then + # Successful execution. The colon is a "no-op" (no + # operation) shell command. + : + else + tbshmdir="" + fi + rm "$shmexecfile" else tbshmdir="" fi - rm "$shmexecfile" - else - tbshmdir="" fi + else + tbshmdir="" fi -else - tbshmdir="" -fi - - - + # If a shared memory directory was created, set the software building + # directory to be a symbolic link to it. Otherwise, just build the + # temporary build directory under the project's build directory. + # + # If it is a link, we need to empty its contents first, then itself. + if [ -d "$tmpblddir" ]; then empty_build_tmp; fi + + # Now that we are sure it doesn't exist, we'll make it (either as a + # directory or as a symbolic link). + if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir"; + else ln -s "$tbshmdir" "$tmpblddir"; + fi -# If a shared memory directory was created, set the software building -# directory to be a symbolic link to it. Otherwise, just build the -# temporary build directory under the project's build directory. -tmpblddir="$sdir"/build-tmp -rm -rf "$tmpblddir"/* "$tmpblddir" # If it is a link, we need to empty - # its contents first, then itself. -if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir"; -else ln -s "$tbshmdir" "$tmpblddir"; + # Report the time this step took. + elapsed_time_from_prev_step temporary-software-building-dir fi -# Make sure the temporary build directory is empty (un-finished -# source/build files from previous builds can remain there during debugging -# or software updates). -rm -rf $tmpblddir/* - - - - - # Inform the user that the build process is starting # ------------------------------------------------- # # Everything is ready, let the user know that the building is going to # start. -if [ $printnotice = yes ]; then - tsec=10 +if [ $quiet = 0 ]; then cat <<EOF ------------------------- @@ -1450,20 +1713,20 @@ NOTE: the built software will NOT BE INSTALLED in standard places of your OS (so no root access is required). They are only for local usage by this project. -**TIP**: you can see which software are being installed at every moment -with the following command. See "Inspecting status" section of -'README-hacking.md' for more. In short, run it while the project is being -configured (in another terminal, but in this same directory: -'$currentdir'): +TIP: you can see which software are being installed at every moment with +the following command. See "Inspecting status" section of +'README-hacking.md' for more. In short, run it in another terminal while +the project is being configured. $ ./project --check-config -Project's configuration will continue in $tsec seconds. +Project's configuration will continue in $tsec seconds. To avoid the pause +on such messages use the '--no-pause' option. ------------------------- EOF - sleep $tsec + sleep $pausesec fi @@ -1479,123 +1742,20 @@ fi # - On BSD-based systems (for example FreeBSD and macOS), we have a # 'hw.ncpu' in the output of 'sysctl'. # - When none of the above work, just set the number of threads to 1. -if [ $jobs = 0 ]; then - if type nproc > /dev/null 2> /dev/null; then - numthreads=$(nproc --all); - else - numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') - if [ x"$numthreads" = x ]; then numthreads=1; fi - fi -else - numthreads=$jobs -fi - - - - - -# See if the linker accepts -Wl,-rpath-link -# ----------------------------------------- # -# '-rpath-link' is used to write the information of the linked shared -# library into the shared object (library or program). But some versions of -# LLVM's linker don't accept it an can cause problems. -# -# IMPORTANT NOTE: This test has to be done **AFTER** the definition of -# 'instdir', otherwise, it is going to be used as an empty string. -cat > $testsource <<EOF -#include <stdio.h> -#include <stdlib.h> -int main(void) {return EXIT_SUCCESS;} -EOF -if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then - export rpath_command="-Wl,-rpath-link=$instdir/lib" -else - export rpath_command="" -fi - - - - - -# Delete the compiler testing directory -# ------------------------------------- -# -# This directory was made above to make sure the necessary compilers can be -# run. -rm -f $testprog $testsource -rm -rf $compilertestdir - - - - - -# Paths needed by the host compiler (only for 'basic.mk') -# ------------------------------------------------------- -# -# At the end of the basic build, we need to build GCC. But GCC will build -# in multiple phases, making its own simple compiler in order to build -# itself completely. The intermediate/simple compiler doesn't recognize -# some system specific locations like '/usr/lib/ARCHITECTURE' that some -# operating systems use. We thus need to tell the intermediate compiler -# where its necessary libraries and headers are. -if [ x"$sys_library_path" != x ]; then - if [ x"$LIBRARY_PATH" = x ]; then - export LIBRARY_PATH="$sys_library_path" - else - export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path" - fi - if [ x"$CPATH" = x ]; then - export CPATH="$sys_cpath" +# This check is also used in 'reproduce/software/shell/docker.sh'. +if [ $built_container = 0 ]; then + if [ $jobs = 0 ]; then + if type nproc > /dev/null 2> /dev/null; then + numthreads=$(nproc --all); + else + numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') + if [ x"$numthreads" = x ]; then numthreads=1; fi + fi else - export CPATH="$CPATH:$sys_cpath" + numthreads=$jobs fi -fi - - - - - -# Libraries necessary for the system's shell -# ------------------------------------------ -# -# In some cases (mostly the programs that Maneage doesn't yet build by -# itself), the programs may call the system's shell, not Maneage's -# shell. After we close-off the system environment from Maneage, this will -# cause a crash! To avoid such cases, we need to find the locations of the -# libraries that the shell needs and temporarily add them to the library -# search path. -# -# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some -# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] -# that is different to the formats that are assumed, prior to this commit, -# by the algorithm in 'configure.sh' when evaluating the variable -# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) -# 'ncurses', because the option using 'sys_library_sh_path' contains an -# unquoted RAM address in parentheses. Even if the address were quoted, it -# would still be incorrect. This 'grep command excludes candidate host path -# strings that look like RAM addresses to address the problem. -# -# [1] https://savannah.nongnu.org/bugs/index.php?66847 -# [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program -# [3] man vdso -if [ x"$on_mac_os" = xyes ]; then - sys_library_sh_path=$(otool -L /bin/sh \ - | awk '/\/lib/{print $1}' \ - | sed 's#/[^/]*$##' \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') -else - sys_library_sh_path=$(ldd /bin/sh \ - | awk '{if($3!="") print $3}' \ - | sed 's#/[^/]*$##' \ - | grep -v "(0x[^)]*)" \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') + elapsed_time_from_prev_step num-threads fi @@ -1619,42 +1779,32 @@ fi # which will download the DOI-resolved webpage, and extract the Zenodo-URL # of the most recent version from there (using the 'coreutils' tarball as # an example, the directory part of the URL for all the other software are -# the same). This is not done if the options '--debug' or `--offline` are used. +# the same). This is not done if the options '--debug' or `--offline` are +# used. zenodourl="" user_backup_urls="" -zenodocheck=.build/software/zenodo-check.html -if [ x$debug = x ] && [ x$offline = x ]; then - if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then - zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ - | sed -n -e'/http/p' \ - | tr ' ' '\n' \ - | grep http \ - | sed -e 's/href="//' -e 's|/coreutils| |' \ - | awk 'NR==1{print $1}') - fi +zenodocheck="$bdir"/software/zenodo-check.html +if [ $built_container = 0 ]; then + if [ x$debug = x ] && [ x$offline = x ]; then + if $downloader $zenodocheck \ + https://doi.org/10.5281/zenodo.3883409; then + zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ + | sed -n -e'/http/p' \ + | tr ' ' '\n' \ + | grep http \ + | sed -e 's/href="//' -e 's|/coreutils| |' \ + | awk 'NR==1{print $1}') + fi + fi + rm -f $zenodocheck + + # Add the Zenodo URL to the user's given back software URLs. Since the + # user can specify 'user_backup_urls' (not yet implemented as an option + # in './project'), we'll give preference to their specified servers, + # then add the Zenodo URL afterwards. + user_backup_urls="$user_backup_urls $zenodourl" + elapsed_time_from_prev_step zenodo-url fi -rm -f $zenodocheck - -# Add the Zenodo URL to the user's given back software URLs. Since the user -# can specify 'user_backup_urls' (not yet implemented as an option in -# './project'), we'll give preference to their specified servers, then add -# the Zenodo URL afterwards. -user_backup_urls="$user_backup_urls $zenodourl" - - - - - -# Build core tools for project -# ---------------------------- -# -# Here we build the core tools that 'basic.mk' depends on: Lzip -# (compression program), GNU Make (that 'basic.mk' is written in), Dash -# (minimal Bash-like shell) and Flock (to lock files and enable serial -# download). -export on_mac_os -./reproduce/software/shell/pre-make-build.sh \ - "$bdir" "$ddir" "$downloader" "$user_backup_urls" @@ -1682,13 +1832,29 @@ fi -# Build other basic tools our own GNU Make -# ---------------------------------------- +# Core software +# ------------- # -# When building these software we don't have our own un-packing software, -# Bash, Make, or AWK. In this step, we'll install such low-level basic -# tools, but we have to be very portable (and use minimal features in all). -echo; echo "Building necessary software (if necessary)..." +# Here we build the core tools that 'basic.mk' depends on: Lzip +# (compression program), GNU Make (that 'basic.mk' is written in), Dash +# (minimal Bash-like shell) and Flock (to lock files and enable serial +# operations where necessary: mostly in download). +export on_mac_os +if [ $quiet = 0 ]; then echo "Building/validating software: pre-make"; fi +./reproduce/software/shell/pre-make-build.sh \ + "$bdir" "$ddir" "$downloader" "$user_backup_urls" +elapsed_time_from_prev_step make-software-pre-make + + + + + +# Basic software +# -------------- +# +# Having built the core tools, we are now ready to build GCC and all its +# dependencies (the "basic" software). +if [ $quiet = 0 ]; then echo "Building/validating software: basic"; fi .local/bin/make $keepgoing -f reproduce/software/make/basic.mk \ sys_library_sh_path=$sys_library_sh_path \ user_backup_urls="$user_backup_urls" \ @@ -1698,25 +1864,22 @@ echo; echo "Building necessary software (if necessary)..." numthreads=$numthreads \ needs_ldl=$needs_ldl \ on_mac_os=$on_mac_os \ + std_c_old=$std_c_old \ host_cc=$host_cc \ -j$numthreads +elapsed_time_from_prev_step make-software-basic -# All other software -# ------------------ +# High-level software +# ------------------- # -# We will be making all the dependencies before running the top-level -# Makefile. To make the job easier, we'll do it in a Makefile, not a -# script. Bash and Make were the tools we need to run Makefiles, so we had -# to build them in this script. But after this, we can rely on Makefiles. -if [ $jobs = 0 ]; then - numthreads=$(.local/bin/nproc --all) -else - numthreads=$jobs -fi +# Having our custom GCC in place, we can now build the high-level (science) +# software: we are using our custom-built 'env' to ensure that nothing from +# the host environment leaks into the high-level software environment. +if [ $quiet = 0 ]; then echo "Building/validating software: high-level"; fi .local/bin/env -i HOME=$bdir \ .local/bin/make $keepgoing \ -f reproduce/software/make/high-level.mk \ @@ -1732,16 +1895,7 @@ fi host_cc=$host_cc \ offline=$offline \ -j$numthreads - - - - - -# Delete the temporary Make wrapper -# --------------------------------- -# -# See above for its description. -rm $makewshell +elapsed_time_from_prev_step make-software-high-level @@ -1756,22 +1910,23 @@ rm $makewshell # will just stop at the stage when all the processing is complete and it is # only necessary to build the PDF. So we don't want to stop the project's # configuration and building if its not present. -if [ -f $itidir/texlive-ready-tlmgr ]; then - texlive_result=$(cat $itidir/texlive-ready-tlmgr) -else - texlive_result="NOT!" -fi -if [ x"$texlive_result" = x"NOT!" ]; then - cat <<EOF +if [ $built_container = 0 ]; then + if [ -f $itidir/texlive-ready-tlmgr ]; then + texlive_result=$(cat $itidir/texlive-ready-tlmgr) + else + texlive_result="NOT!" + fi + if [ x"$texlive_result" = x"NOT!" ]; then + cat <<EOF -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! TeX Live couldn't be installed during the configuration (probably because -there were downloading problems). TeX Live is only necessary in making the -final PDF (which is only done after all the analysis has been complete). It -is not used at all during the analysis. +there were downloading problems, or you used the '--offline' option). TeX +Live is only necessary in making the final PDF (which is only done after +all the analysis has been complete). It is not used at all during the +analysis. Therefore, if you don't need the final PDF, and just want to do the analysis, you can safely ignore this warning and continue. @@ -1786,18 +1941,23 @@ and re-run configure: ./project configure -e -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +The configuration will continue in $pausesec seconds. To avoid the pause on +such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 10 # increase the chance that an interactive user reads this message + sleep $pausesec + fi + elapsed_time_from_prev_step check-tex-installation fi -# Citation of installed software +# Software information the paper +# ------------------------------ # # After everything is installed, we'll put all the names and versions in a # human-readable paragraph and also prepare the BibTeX citation for the @@ -1839,101 +1999,101 @@ prepare_name_version () fi } -# Import the context/sentences for placing between the list of software -# names during their acknowledgment. -. $cdir/software_acknowledge_context.sh - -# Report the different software in separate contexts (separating Python and -# TeX packages from the C/C++ programs and libraries). -proglibs=$(prepare_name_version $verdir/proglib/*) -pymodules=$(prepare_name_version $verdir/python/*) -texpkg=$(prepare_name_version $verdir/tex/texlive) - -# Acknowledge these software packages in a LaTeX paragraph. -pkgver=$texdir/dependencies.tex - -# Add the text to the ${pkgver} file. -.local/bin/echo "$thank_software_introduce " > $pkgver -.local/bin/echo "$thank_progs_libs $proglibs. " >> $pkgver -if [ x"$pymodules" != x ]; then - .local/bin/echo "$thank_python $pymodules. " >> $pkgver -fi -.local/bin/echo "$thank_latex $texpkg. " >> $pkgver -.local/bin/echo "$thank_software_conclude" >> $pkgver - -# Prepare the BibTeX entries for the used software (if there are any). -hasentry=0 -bibfiles="$ictdir/*" -for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done; - -# Make sure we start with an empty output file. -pkgbib=$texdir/dependencies-bib.tex -echo "" > $pkgbib - -# Fill it in with all the BibTeX entries in this directory. We'll just -# avoid writing any comments (usually copyright notices) and also put an -# empty line after each file's contents to make the output more readable. -if [ $hasentry = 1 ]; then - for f in $bibfiles; do - awk '!/^%/{print} END{print ""}' $f >> $pkgbib - done -fi - +# Relevant files +pkgver=$sconfdir/dependencies.tex +pkgbib=$sconfdir/dependencies-bib.tex +# Build the software LaTeX source but only when not in a container. +if [ $built_container = 0 ]; then + # Import the context/sentences for placing between the list of software + # names during their acknowledgment. + . $cdir/software_acknowledge_context.sh + # Report the different software in separate contexts (separating Python + # and TeX packages from the C/C++ programs and libraries). + proglibs=$(prepare_name_version $verdir/proglib/*) + pymodules=$(prepare_name_version $verdir/python/*) + texpkg=$(prepare_name_version $verdir/tex/texlive) -# Report machine architecture -# --------------------------- -# -# Report hardware -hwparam="$texdir/hardware-parameters.tex" + # Acknowledge these software packages in a LaTeX paragraph. + .local/bin/echo "$thank_software_introduce " > $pkgver + .local/bin/echo "$thank_progs_libs $proglibs. " >> $pkgver + if [ x"$pymodules" != x ]; then + .local/bin/echo "$thank_python $pymodules. " >> $pkgver + fi + .local/bin/echo "$thank_latex $texpkg. " >> $pkgver + .local/bin/echo "$thank_software_conclude" >> $pkgver + + # Prepare the BibTeX entries for the used software (if there are any). + hasentry=0 + bibfiles="$ictdir/*" + for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done; + + # Fill it in with all the BibTeX entries in this directory. We'll just + # avoid writing any comments (usually copyright notices) and also put an + # empty line after each file's contents to make the output more readable. + echo "" > $pkgbib # We don't want to inherit any pre-existing content. + if [ $hasentry = 1 ]; then + for f in $bibfiles; do + awk '!/^%/{print} END{print ""}' $f >> $pkgbib + done + fi -# Add the text to the ${hwparam} file. Since harware class might include -# underscore, it must be replaced with '\_', otherwise pdftex would -# complain and break the build process when doing ./project make. -hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')" -.local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" > $hwparam -.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam -.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam + # Report the time that this operation took. + elapsed_time_from_prev_step tex-macros +fi -# Clean the temporary build directory -# --------------------------------- +# Report machine architecture (has to be final created file) +# ---------------------------------------------------------- # -# By the time the script reaches here the temporary software build -# directory should be empty, so just delete it. Note 'tmpblddir' may be a -# symbolic link to shared memory. So, to work in any scenario, first delete -# the contents of the directory (if it has any), then delete 'tmpblddir'. -.local/bin/rm -rf $tmpblddir/* $tmpblddir - - - - - -# Register successful completion -# ------------------------------ -echo `.local/bin/date` > $finaltarget - +# This is the final file that is created in the configuration phase: it is +# used by the high-level project script to verify that configuration has +# been completed. If any other files should be created in the final statges +# of configuration, be sure to add them before this. +# +# Since harware class might include underscore, it must be replaced with +# '\_', otherwise pdftex would complain and break the build process when +# doing ./project make. +if [ $built_container = 0 ]; then + hw_class=$(uname -m) + hwparam="$sconfdir/hardware-parameters.tex" + hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')" + .local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" \ + > $hwparam + .local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" \ + >> $hwparam + .local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" \ + >> $hwparam + elapsed_time_from_prev_step hardware-params +fi -# Final notice -# ------------ +# Clean up and final notice +# ------------------------- # -# The configuration is now complete, we can inform the user on the next -# step(s) to take. -if [ x$maneage_group_name = x ]; then - buildcommand="./project make -j8" -else - buildcommand="./project make --group=$maneage_group_name -j8" -fi -cat <<EOF +# The configuration is now complete. We just need to delete the temporary +# build directory and inform the user (if '--quiet' wasn't called) on the +# next step(s). +if [ -d $tmpblddir ]; then empty_build_tmp; fi +if [ $quiet = 0 ]; then + + # Suggest the command to use. + if [ x$maneage_group_name = x ]; then + buildcommand="./project make -j8" + else + buildcommand="./project make --group=$maneage_group_name -j8" + fi + + # Print the message. + cat <<EOF ---------------- The project and its environment are configured with no errors. @@ -1951,3 +2111,10 @@ Please run the following command to start the project. $buildcommand EOF +fi + + +# Total time +if [ $check_elapsed = 1 ]; then + echo $chel_dsum | awk '{printf "Total: %-6.2f [millisec]\n", $1}' +fi diff --git a/reproduce/software/containers/README-docker.md b/reproduce/software/shell/docker-README.md index f86dceb..dd46f4f 100644 --- a/reproduce/software/containers/README-docker.md +++ b/reproduce/software/shell/docker-README.md @@ -1,6 +1,6 @@ # Maneage'd projects in Docker -Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. For an introduction on containers, see the "Building in containers" section @@ -35,25 +35,25 @@ software environment) to easily move it from one computer to another. systemctl start docker ``` - 2. Using your favorite text editor, create a `docker-local.sh` in your top - Maneage directory (as described in the comments at the start of the - `docker.sh` script in this directory). Just activate `--build-only` on - the first run so it doesn't go onto doing the analysis and just sets up - the software environment. - - 3. After the setup is complete, run the following command to confirm that - the `maneage-base` (the OS of the container) and `maneaged` (your - project's full Maneage'd environment) images are available. If you want - different names for these images, add the `--project-name` and - `--base-name` options to the `docker.sh` call. + 2. At the start of the `docker.sh` script in this directory, you can see + the necessary command to run. Just activate `--build-only` on the first + run so it doesn't go onto doing the analysis (that can be done at any + later time). Set the respective directory(s) based on your filesystem + (the software directory is optional). You can put the command in a + `run.sh` at the top of the project (it is already in `.gitignore`: + because it contains local directories). + + 3. After the setup is complete, remove the `--build-only` and run the + command below to confirm that `maneage-base` (the OS of the container) + and `maneaged` (your project's full Maneage'd environment) images are + available. If you want different names for these images, add the + `--project-name` and `--base-name` options to the `docker.sh` call. You + can see the list of available images with this command: ```shell docker image list ``` - 4. You are now ready to do your analysis by removing the `--build-only` - option. - @@ -85,6 +85,24 @@ image into it. Below are some useful Docker usage scenarios that have proved to be relevant for us in Maneage'd projects. +### Saving and loading an image as a file + +Docker keeps its images in hard to access (by humans) location on the +operating system. Very much like Git, but with much less elegance: the +place is shared by all users and projects of the system. So they are not +easy to archive for usage on another system at a low-level. But it does +have an interface (`docker save`) to copy all the relevant files within an +image into a tar ball that you can archive externally. There is also a +separate interface to load the tarball back into docker (`docker load`). + +Both of these have been implemented as the `--image-file` option of the +`docker.sh` script. If you want to save your Maneage'd image into an image, +simply give the tarball name to this option. Alternatively, if you already +have a tarball and want to load it into Docker, give it to this option once +(until you "clean up", as explained below). In fact, docker images take a +lot of space and it is better to "clean up" regularly. And the only way you +can clean up safely is through saving your needed images as a file. + ### Cleaning up Docker has stored many large files in your operating system that can drain diff --git a/reproduce/software/containers/docker.sh b/reproduce/software/shell/docker.sh index d5b5682..5cd8f11 100755 --- a/reproduce/software/containers/docker.sh +++ b/reproduce/software/shell/docker.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/usr/bin/env bash # # Create a Docker container from an existing image of the built software # environment, but with the source, data and build (analysis) directories @@ -9,35 +9,35 @@ # # Usage: # -# - When you are at the top Maneage'd project directory, you can run this -# script like the example below. Just set all the '/PATH/TO/...' -# directories (see below for '--tmp-dir'). See the items below for -# optional values. +# - When you are at the top Maneage'd project directory, run this script +# like the example below. Just set the build directory location on your +# system. See the items below for optional values to optimize the +# process (avoid downloading for exmaple). # -# ./reproduce/software/containers/docker.sh --shm-size=15gb \ -# --software-dir=/PATH/TO/SOFTWARE/TARBALLS \ -# --build-dir=/PATH/TO/BUILD/DIRECTORY +# ./reproduce/software/shell/docker.sh --shm-size=20gb \ +# --build-dir=/PATH/TO/BUILD/DIRECTORY # -# - Non-mandatory options: +# - Non-mandatory options: # -# - If you already have the input data that is necessary for your -# project's, use the '--input-dir' option to specify its location -# on your host file system. Otherwise the necessary analysis -# files will be downloaded directly into the build -# directory. Note that this is only necessary when '--build-only' -# is not given. +# - If you already have the input data that is necessary for your +# project, use the '--input-dir' option to specify its location +# on your host file system. Otherwise the necessary analysis +# files will be downloaded directly into the build +# directory. Note that this is only necessary when '--build-only' +# is not given. # -# - The '--software-dir' is only useful if you want to build a -# container. Even in that case, it is not mandatory: if not -# given, the software tarballs will be downloaded (thus requiring -# internet). +# - If you already have the necessary software tarballs that are +# necessary for your project, use the '--software-dir' option to +# specify its location on your host file system only when +# building the container. No problem if you don't have them, they +# will be downloaded during the configuration phase. # -# - To avoid having to set the directory(s) every time you want to -# start the docker environment, you can put this command (with the -# proper directories) into a 'run.sh' script in the top Maneage'd -# project source directory and simply execute that. The special name -# 'run.sh' is in Maneage's '.gitignore', so it will not be included -# in your git history by mistake. +# - To avoid having to set them every time you want to start the +# apptainer environment, you can put this command (with the proper +# directories) into a 'run.sh' script in the top Maneage'd project +# source directory and simply execute that. The special name 'run.sh' +# is in Maneage's '.gitignore', so it will not be included in your +# git history by mistake. # # Known problems: # @@ -47,7 +47,7 @@ # clipped, log limit 2MiB reached]" message. We need to find a way to # fix this (so nothing gets clipped: useful for debugging). # -# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -76,7 +76,7 @@ set -e # Default option values -jobs= +jobs=0 quiet=0 source_dir= build_only= @@ -116,7 +116,7 @@ Top-level script to build and run a Maneage'd project within Docker. --container-shell Open the container shell. Operating mode: - --quiet Do not print informative statements. + -q, --quiet Do not print informative statements. -?, --help Give this help list. --shm-size=STR Passed to 'docker build' (default: $shm_size). -j, --jobs=INT Number of threads to use in each phase. @@ -168,6 +168,8 @@ do # Container options. --base-name) base_name="$2"; check_v "$1" "$base_name"; shift;shift;; --base-name=*) base_name="${1#*=}"; check_v "$1" "$base_name"; shift;; + --project-name) project_name="$2"; check_v "$1" "$project_name"; shift;shift;; + --project-name=*) project_name="${1#*=}"; check_v "$1" "$project_name"; shift;; # Interactive shell. --project-shell) project_shell=1; shift;; @@ -176,8 +178,8 @@ do --container_shell=*) on_off_option_error --container-shell;; # Operating mode - --quiet) quiet=1; shift;; - --quiet=*) on_off_option_error --quiet;; + -q|--quiet) quiet=1; shift;; + -q*|--quiet=*) on_off_option_error --quiet;; -j|--jobs) jobs="$2"; check_v "$1" "$jobs"; shift;shift;; -j=*|--jobs=*) jobs="${1#*=}"; check_v "$1" "$jobs"; shift;; -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v "$1" "$jobs"; shift;; @@ -250,17 +252,43 @@ if ! [ x"$input_dir" = x ]; then input_dir_mnt="-v $input_dir:/home/maneager/input" fi -# If no '--jobs' has been specified, use the maximum available jobs to the -# operating system. -if [ x$jobs = x ]; then jobs=$(nproc); fi +# Number of threads to build software (taken from 'configure.sh'). +if [ x"$jobs" = x0 ]; then + if type nproc > /dev/null 2> /dev/null; then + numthreads=$(nproc --all); + else + numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') + if [ x"$numthreads" = x ]; then numthreads=1; fi + fi +else + numthreads=$jobs +fi -# [DOCKER-ONLY] Make sure the user is a member of the 'docker' group: -glist=$(groups $(whoami) | awk '/docker/') -if [ x"$glist" = x ]; then - printf "$scriptname: you are not a member of the 'docker' group " - printf "You can run the following command as root to fix this: " - printf "'usermod -aG docker $(whoami)'\n" - exit 1 +# Since the container is read-only and is run with the '--contain' option +# (which makes an empty '/tmp'), we need to make a dedicated directory for +# the container to be able to write to. This is necessary because some +# software (Biber in particular on the default branch or Ghostscript) need +# to write there! See https://github.com/plk/biber/issues/494. We'll keep +# the directory on the host OS within the build directory, but as a hidden +# file (since it is not necessary in other types of build and ultimately +# only contains temporary files of programs that need it). +toptmp=$build_dir/.docker-tmp-$(whoami) +if ! [ -d $toptmp ]; then mkdir $toptmp; fi +chmod -R +w $toptmp/ # Some software remove writing flags on /tmp files. +if ! [ x"$( ls -A $toptmp )" = x ]; then rm -r "$toptmp"/*; fi + +# [DOCKER-ONLY] Make sure the user is a member of the 'docker' group. This +# is needed only for Linux, given that other systems uses other strategies. +# (See: https://stackoverflow.com/a/70385997) +kernelname=$(uname -s) +if [ x$kernelname = xLinux ]; then + glist=$(groups $(whoami) | awk '/docker/') + if [ x"$glist" = x ]; then + printf "$scriptname: you are not a member of the 'docker' group " + printf "You can run the following command as root to fix this: " + printf "'usermod -aG docker $(whoami)'\n" + exit 1 + fi fi # [DOCKER-ONLY] Function to check the temporary directory for building the @@ -341,6 +369,7 @@ fi # # Having the base operating system in place, we can now construct the # project's docker file. +intbuild=/home/maneager/build if docker image list | grep $project_name &> /dev/null; then if [ $quiet = 0 ]; then printf "$scriptname: info: project's image ('$project_name') " @@ -380,22 +409,25 @@ else # that the user gave there. mkdir $tmp_dir/$tsdir cp -r "$software_dir"/* $tmp_dir/$tsdir/ - printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" >> $df + printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" \ + >> $df fi # Construct the rest of the 'RUN' command. printf " cp -r $dsr /home/maneager/source; \x5C\n" >> $df printf " cd /home/maneager/source; \x5C\n" >> $df - printf " ./project configure --jobs=$jobs \x5C\n" >> $df - printf " --build-dir=/home/maneager/build \x5C\n" >> $df + printf " ./project configure \x5C\n" >> $df + printf " --no-pause \x5C\n" >> $df + printf " --jobs=$jobs \x5C\n" >> $df + printf " --build-dir=$intbuild \x5C\n" >> $df printf " --input-dir=/home/maneager/input \x5C\n" >> $df - printf " --software-dir=$dts; \x5C\n" >> $df + printf " --software-dir=$dts; \x5C\n" >> $df - # We are deleting the '.build/software/tarballs' directory because this - # directory is not relevant for the analysis of the project. But in - # case any tarball was downloaded, it will consume space within the - # container. - printf " rm -rf .build/software/tarballs; \x5C\n" >> $df + # We are deleting the contents of the '.build/software/tarballs' + # directory (tarballs of the sources of the software) because they are + # not relevant to the execution of the project and will consume space + # within the container. + printf " rm -rf .build/software/tarballs/*; \x5C\n" >> $df # We are deleting the source directory becaues later (at 'docker run' # time), the 'source' will be mounted directly from the host operating @@ -403,12 +435,9 @@ else printf " cd /home/maneager; \x5C\n" >> $df printf " rm -rf source\n" >> $df - # Build the Maneage container and delete the temporary directory. The - # '--progress plain' option is for Docker to print all the outputs - # (otherwise, it will only print a very small part!). + # Build the Maneage container and delete the temporary directory. cd $tmp_dir docker build ./ -t $project_name \ - --progress=plain \ --shm-size=$shm_size \ --no-cache \ 2>&1 | tee build.log @@ -424,14 +453,15 @@ if ! [ x"$image_file" = x ] && ! [ -f "$image_file" ]; then # Save the image into a tarball tarname=$(echo $image_file | sed -e's|.gz$||') if [ $quiet = 0 ]; then - printf "$scriptname: info: saving docker image to '$tarname'" + printf "$scriptname: info: saving docker image to '$tarname'\n" fi docker save -o $tarname $project_name # Compress the saved image if [ $quiet = 0 ]; then printf "$scriptname: info: compressing to '$image_file' (can " - printf "take +10 minutes, but volume decreases by more than half!)" + printf "take +10 minutes, but volume decreases by more than " + printf "half!)\n" fi gzip --best $tarname fi @@ -441,7 +471,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$project_name' image" + printf "successfully in the '$project_name' image\n" fi exit 0 fi @@ -456,29 +486,33 @@ fi # The startup command of the container is managed though the 'shellopt' # variable that starts here. shellopt="" +sobase="/bin/bash -c 'cd source; " +sobase="$sobase ./project configure --build-dir=$intbuild " +sobase="$sobase --existing-conf --no-pause --offline --quiet && " +sobase="$sobase ./project MODE --build-dir=$intbuild" if [ $container_shell = 1 ] || [ $project_shell = 1 ]; then - # If the user wants to start the project shell within the container, - # add the necessary command. + # The interactive flag is necessary for both these scenarios. + interactiveopt="-it" + + # With '--project-shell' we need 'shellopt', the MODE just needs to be + # set to 'shell'. if [ $project_shell = 1 ]; then - shellopt="/bin/bash -c 'cd source; ./project shell;'" + shellopt="$(echo $sobase | sed -e's|MODE|shell|');'" fi - # Finish the 'shellop' string with a single quote (necessary in any - # case) and run Docker. - interactiveopt="-it" - # No interactive shell requested, just run the project. else interactiveopt="" - shellopt="/bin/bash -c 'cd source; ./project make --jobs=$jobs;'" + shellopt="$(echo $sobase | sed -e's|MODE|make|') --jobs=$jobs;'" fi # Execute Docker. The 'eval' is because the 'shellopt' variable contains a # single-quote that the shell should "evaluate". -eval docker run \ +eval docker run --read-only \ -v "$analysis_dir":/home/maneager/build/analysis \ -v "$source_dir":/home/maneager/source \ + -v $toptmp:/tmp \ $input_dir_mnt \ $shm_mnt \ $interactiveopt \ diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout index 7b521a3..7bf747a 100755 --- a/reproduce/software/shell/git-post-checkout +++ b/reproduce/software/shell/git-post-checkout @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is taken from the 'examples/hooks/pre-commit' file of the # 'metastore' package (installed within the project, with an MIT license diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit index 7b98ad0..e570346 100755 --- a/reproduce/software/shell/git-pre-commit +++ b/reproduce/software/shell/git-pre-commit @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # WARNING: # diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 28b7385..8236247 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -2,7 +2,7 @@ # # Very basic tools necessary to start Maneage's default building. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -135,16 +135,6 @@ download_tarball() { else mv "$ucname" "$maneagetar" fi fi - - # If the tarball is newer than the (possibly existing) program (the - # version has changed), then delete the program. When the LaTeX name is - # not given here, the software is re-built later (close to the end of - # 'basic.mk') and the name is properly placed there. - if [ -f "$ibidir/$progname" ]; then - if [ "$maneagetar" -nt "$ibidir/$progname" ]; then - rm "$ibidir/$progname" - fi - fi } @@ -159,6 +149,9 @@ build_program() { # Options configoptions=$1 + # Inform the user. + echo; echo "Pre-make building of $progname"; echo + # Go into the temporary building directory. cd "$tmpblddir" unpackdir="$progname"-"$version" @@ -183,7 +176,8 @@ build_program() { # build the project, either with Make and either without it. if [ x$progname = xlzip ]; then - ./configure --build --check --installdir="$instdir/bin" $configoptions + ./configure --build --check --installdir="$instdir/bin" \ + $configoptions else # All others accept the configure script. ./configure --prefix="$instdir" $configoptions @@ -196,7 +190,10 @@ build_program() { case $on_mac_os in yes) sed -e's/\%1u/\%d/' src/flock.c > src/flock-new.c;; no) sed -e's/\%1u/\%ld/' src/flock.c > src/flock-new.c;; - *) echo "pre-make-build.sh: '$on_mac_os' unrecognized value for on_mac_os";; + *) + printf "pre-make-build.sh: '$on_mac_os' " + printf "unrecognized value for on_mac_os" + exit 1;; esac mv src/flock-new.c src/flock.c fi @@ -218,9 +215,9 @@ build_program() { cd "$topdir" rm -rf "$tmpblddir/$unpackdir" if [ x"$progname_tex" = x ]; then - echo "" > "$ibidir/$progname" + echo "" > "$texfile" else - echo "$progname_tex $version" > "$ibidir/$progname" + echo "$progname_tex $version" > "$texfile" fi fi } @@ -238,12 +235,12 @@ build_program() { # (without compression it is just ~400Kb). So we use its '.tar' file and # won't rely on the host's compression tools at all. progname="lzip" -progname_tex="" # Lzip re-built after GCC (empty string to avoid repetition) +progname_tex="" # Lzip is re-built after GCC (empty to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile") tarball=$progname-$version.tar -download_tarball -build_program +texfile="$ibidir/$progname-$version-pre-make" +if ! [ -f $texfile ]; then download_tarball; build_program; fi @@ -268,8 +265,11 @@ progname_tex="" # Make re-built after GCC (empty string to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program "--disable-dependency-tracking --without-guile" +texfile="$ibidir/$progname-$version-pre-make" +if ! [ -f $texfile ]; then + download_tarball + build_program "--disable-dependency-tracking --without-guile" +fi @@ -286,13 +286,11 @@ progname_tex="Dash" url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program +texfile="$ibidir/$progname-$version" +if ! [ -f $texfile ]; then download_tarball; build_program; fi # If the 'sh' symbolic link isn't set yet, set it to point to Dash. -if [ -f $bindir/sh ]; then just_a_place_holder=1 -else ln -sf $bindir/dash $bindir/sh; -fi +if ! [ -f $bindir/sh ]; then ln -sf $bindir/dash $bindir/sh; fi @@ -315,12 +313,5 @@ progname_tex="Discoteq flock" url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program - - - - - -# Finish this script successfully -exit 0 +texfile="$ibidir/$progname-$version" +if ! [ -f $texfile ]; then download_tarball; build_program; fi diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh index dcdc472..2959255 100755 --- a/reproduce/software/shell/prep-source.sh +++ b/reproduce/software/shell/prep-source.sh @@ -7,7 +7,7 @@ # directory that it is run in ): # ./prep-source.sh /FULL/ADDRESS/TO/DESIRED/BIN # -# Copyright (C) 2024-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2024-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -47,17 +47,18 @@ fi -# Find all the files that contain the '/bin/sh' string and correct them to -# Maneage's own Bash. We are using 'while read' to read the file names line -# by line. This is necessary to account file names that include the 'SPACE' -# character (happens in CMake for example!). +# Find all the files that contain the '/bin/sh' or '/bin/bash' strings and +# correct them to Maneage's own shell (Dash or Bash). We are using 'while +# read' to read the file names line by line. This is necessary to account +# file names that include the 'SPACE' character (happens in CMake for +# example!). # # Note that dates are important in the source directory (files depend on # each other), so we should read the original date and after making. We are # also not using GNU SED's '-i' ('--in-place') option because the host OS # may not have GNU SED. # -# Actual situation which prompted the addition of this step: a Maneage'd +# The situation which prompted the addition of this step: a Maneage'd # project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a # system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The # newer version of Bash needed the newer Readline library function(s) that @@ -74,18 +75,35 @@ fi # hard-coded in the source code of almost all programs (their build # scripts); and in special programs like GNU Make, GNU M4 or CMake it is # actually hardcoded in the source code (not just build scripts). -if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash +bashpath="$bindir"/bash +if [ -f "$bindir/bash" ]; then shpath="$bashpath" else shpath="$bindir"/dash fi -grep -I -r -e'/bin/sh' $(pwd)/* \ + +# On MacOS the syntax for 'stat' is a bit different, so if we are using the +# system one on mac we need a specific syntax. The one installed by maneage +# instead uses the ordinary Linux syntax. +if [ -f "$bindir/stat" ] || [ x"$on_mac_os" = xno ]; then + format="--format %a" +else + format="-f %OLp" +fi + +# On MacOS 'touch' wants the time expressed according to ISO8601 with a +# precision up to the seconds. We then use 'sed' to remove the information +# regarding the timezone, as the format is not accepted by 'touch'. +# LCTYPE and LANG are also required on macos systems by sed. +grep -I -r -e'/bin/sh' -e'/bin/bash' $(pwd)/* \ | sed -e's|:|\t|' \ | awk 'BEGIN{FS="\t"}{print $1}' \ | sort \ | uniq \ | while read filename; do \ tmp="$filename".tmp; \ - origtime="$(date -R -r "$filename")"; \ - origperm=$(stat -c '%a' "$filename"); \ + origtimex="$(date -Iseconds -r "$filename")"; \ + origtime=$(echo $origtimex | sed 's/.\{6\}$//'); \ + origperm=$(stat $format "$filename"); \ + LC_CTYPE=C; LANG=C; \ sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \ mv "$tmp" "$filename"; \ chmod $origperm "$filename"; \ diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in index 053f5f3..21c347f 100755 --- a/reproduce/software/shell/run-parts.in +++ b/reproduce/software/shell/run-parts.in @@ -10,8 +10,8 @@ # However, it didn't have a copyright statement. So one is being added # here. # -# Copyright (C) 2025 Authors mentioned above. -# Copyright (C) 2025-2024 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2026 Authors mentioned above. +# Copyright (C) 2026-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh index 8e30931..ed1cfd0 100755 --- a/reproduce/software/shell/tarball-prepare.sh +++ b/reproduce/software/shell/tarball-prepare.sh @@ -15,9 +15,9 @@ # # Discussion: https://savannah.nongnu.org/task/?15699 # -# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> -# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es> +# Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the @@ -51,6 +51,9 @@ basedir=$PWD scriptname=$0 + + + # The --help output print_help() { cat <<EOF |