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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2021-10-04 02:51:45 +0200
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2022-01-21 01:15:24 +0100
commit8463df97c6f26ec4d22cd5828bb0574fd5e450d2 (patch)
treedbaa2e7c2fc44856eb98555b79c6814f210a6c17 /reproduce/analysis/make/verify.mk
parent775fc036e0091f05ff56e41b855bc416b9ed36c8 (diff)
IMPORTANT: Updates to almost all software
This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2
Diffstat (limited to 'reproduce/analysis/make/verify.mk')
-rw-r--r--reproduce/analysis/make/verify.mk40
1 files changed, 20 insertions, 20 deletions
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 7e16add..d3f3282 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -94,7 +94,7 @@ verify-txt-no-comments-no-space = \
# (generated in various stages of the analysis.
#
# Since each analysis step's data files are already prerequisites of their
-# respective TeX macro file, its enough for `verify.tex' to depend on the
+# respective TeX macro file, its enough for 'verify.tex' to depend on the
# final TeX macro.
#
# USEFUL TIP: during the early phases of your research (when you are
@@ -103,40 +103,40 @@ verify-txt-no-comments-no-space = \
#
# Here is a description of the variables defined here.
#
-# verify-dep: The major step dependencies of `verify.tex', this includes
+# verify-dep: The major step dependencies of 'verify.tex', this includes
# all the steps that must be finished before it.
#
# verify-changes: The files whose contents are important. This is
-# essentially the same as `verify-dep', but it has removed
-# the `initialize' step (which is information about the
+# essentially the same as 'verify-dep', but it has removed
+# the 'initialize' step (which is information about the
# pipeline, not the results).
verify-dep = $(subst verify,,$(subst paper,,$(makesrc)))
verify-check = $(subst initialize,,$(verify-dep))
$(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
- # Make sure that verification is actually requested, the '@' at the
- # start of the recipe is added so Make doesn't print the commands
- # on the standard output because this recipe is run on every call
- # to the project and can be annoying (get mixed in the middle of
- # the analysis outputs or the LaTeX outputs).
+# Make sure that verification is actually requested, the '@' at the
+# start of the recipe is added so Make doesn't print the commands on
+# the standard output because this recipe is run on every call to the
+# project and can be annoying (get mixed in the middle of the
+# analysis outputs or the LaTeX outputs).
@if [ x"$(verify-outputs)" = xyes ]; then
- # Make sure the temporary output doesn't exist (because we want
- # to append to it). We are making a temporary output target so if
- # there is a crash in the middle, Make will not continue. If we
- # write in the final target progressively, the file will exist,
- # and its date will be more recent than all prerequisites, so
- # next time the project is run, Make will continue and ignore the
- # rest of the checks.
+# Make sure the temporary output doesn't exist (because we want to
+# append to it). We are making a temporary output target so if
+# there is a crash in the middle, Make will not continue. If we
+# write in the final target progressively, the file will exist, and
+# its date will be more recent than all prerequisites, so next time
+# the project is run, Make will continue and ignore the rest of the
+# checks.
rm -f $@.tmp
- # Verify the figure datasets.
+# Verify the figure datasets.
$(call verify-txt-no-comments-no-space, \
$(dm-squared), 6b6d3b0f9c351de53606507b59bca5d1, $@.tmp)
$(call verify-txt-no-comments-no-space, \
$(dm-img-histogram), b1f9c413f915a1ad96078fee8767b16c, $@.tmp)
- # Verify TeX macros (the values that go into the PDF text).
+# Verify TeX macros (the values that go into the PDF text).
for m in $(verify-check); do
file=$(mtexdir)/$$m.tex
if [ $$m == download ]; then s=49e4e9f049aa9da0453a67203d798587
@@ -146,7 +146,7 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
$(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
done
- # Move temporary file to final target.
+# Move temporary file to final target.
mv $@.tmp $@
else
echo "% Verification was DISABLED!" > $@