From 8eb0892e179b4970a9835d29b5f57dd912ca4464 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Fri, 17 Apr 2020 01:06:20 +0100 Subject: IMPORTANT: software config directly under reproduce/software/config Until now the software configuration parameters were defined under the `reproduce/software/config/installation/' directory. This was because the configuration parameters of analysis software (for example Gnuastro's configurations) were placed under there too. But this was terribly confusing, because the run-time options of programs falls under the "analysis" phase of the project. With this commit, the Gnuastro configuration files have been moved under the new `reproduce/analysis/config/gnuastro' directory and the software configuration files are directly under `reproduce/software/config'. A clean build was done with this change and it didn't crash, but it may cause crashes in derived projects, so after merging with Maneage, please re-configure your project to see if anything has been missed. Please let us know if there is a problem. --- reproduce/software/config/LOCAL.conf.in | 17 ++ reproduce/software/config/TARGETS.conf | 42 ++++ reproduce/software/config/checksums.conf | 199 +++++++++++++++++++ .../software/config/gnuastro/astbuildprog.conf | 16 -- .../software/config/gnuastro/astconvertt.conf | 33 --- .../software/config/gnuastro/aststatistics.conf | 36 ---- reproduce/software/config/gnuastro/gnuastro.conf | 43 ---- .../software/config/installation/LOCAL.conf.in | 17 -- .../software/config/installation/TARGETS.conf | 42 ---- .../software/config/installation/checksums.conf | 199 ------------------- .../software/config/installation/numpy-scipy.cfg | 47 ----- .../config/installation/texlive-packages.conf | 24 --- .../software/config/installation/texlive.conf | 35 ---- .../software/config/installation/versions.conf | 221 --------------------- reproduce/software/config/numpy-scipy.cfg | 47 +++++ reproduce/software/config/texlive-packages.conf | 24 +++ reproduce/software/config/texlive.conf | 35 ++++ reproduce/software/config/versions.conf | 221 +++++++++++++++++++++ reproduce/software/make/basic.mk | 10 +- reproduce/software/make/high-level.mk | 16 +- reproduce/software/make/python.mk | 4 +- reproduce/software/shell/configure.sh | 14 +- 22 files changed, 607 insertions(+), 735 deletions(-) create mode 100644 reproduce/software/config/LOCAL.conf.in create mode 100644 reproduce/software/config/TARGETS.conf create mode 100644 reproduce/software/config/checksums.conf delete mode 100644 reproduce/software/config/gnuastro/astbuildprog.conf delete mode 100644 reproduce/software/config/gnuastro/astconvertt.conf delete mode 100644 reproduce/software/config/gnuastro/aststatistics.conf delete mode 100644 reproduce/software/config/gnuastro/gnuastro.conf delete mode 100644 reproduce/software/config/installation/LOCAL.conf.in delete mode 100644 reproduce/software/config/installation/TARGETS.conf delete mode 100644 reproduce/software/config/installation/checksums.conf delete mode 100644 reproduce/software/config/installation/numpy-scipy.cfg delete mode 100644 reproduce/software/config/installation/texlive-packages.conf delete mode 100644 reproduce/software/config/installation/texlive.conf delete mode 100644 reproduce/software/config/installation/versions.conf create mode 100644 reproduce/software/config/numpy-scipy.cfg create mode 100644 reproduce/software/config/texlive-packages.conf create mode 100644 reproduce/software/config/texlive.conf create mode 100644 reproduce/software/config/versions.conf (limited to 'reproduce/software') diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in new file mode 100644 index 0000000..0579218 --- /dev/null +++ b/reproduce/software/config/LOCAL.conf.in @@ -0,0 +1,17 @@ +# Local project configuration. +# +# This is just a template for the `./project configure' script to fill +# in. Please don't make any change to this file. +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# +# 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@ +DEPENDENCIES-DIR = @ddir@ +SYS_CPATH = @sys_cpath@ +DOWNLOADER = @downloader@ +GROUP-NAME = @groupname@ diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf new file mode 100644 index 0000000..84962f7 --- /dev/null +++ b/reproduce/software/config/TARGETS.conf @@ -0,0 +1,42 @@ +# Necessary high-level software to build in this project. +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# Copyright (C) 2019-2020 Raul Infante-Sainz +# +# 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. + + + + + +# AVAILABLE SOFTWARE +# ------------------ +# +# All software that are currently available for installation can be seen in +# the following file. +# +# reproduce/software/config/versions.conf +# +# Please add any software that you need for your project in the respective +# part below (using its name in `versions.conf', but without the `-version' +# part). Just note that if a program/library is a dependency of another, +# you don't need to include it here (it will be installed before the +# higher-level software anyway). +# +# Note that many low-level software will be installed before those that are +# installed in this step. They are clearly distinguished from the +# higher-level (optional) software in `versions.conf'. These low-level +# software MUST NOT be added here. + + + + + +# Programs and libraries. +top-level-programs = gnuastro + +# Python libraries/modules. +top-level-python = astropy diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf new file mode 100644 index 0000000..37fe64d --- /dev/null +++ b/reproduce/software/config/checksums.conf @@ -0,0 +1,199 @@ +# sha512 checksums of all the necessary software tarballs. +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# +# 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 the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This Makefile is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# A copy of the GNU General Public License is available at +# . + + + + + +# Basic/low-level programs and libraires (installed in any case) +# -------------------------------------------------------------- +bash-checksum = a93f221fe800908e335584837f63d02a350d9c8b2711f1923e946980b960fb2d4a21e4321f722c70e5faf5554991a6b9ef6722d214a1921f71030896cf134639 +binutils-checksum = a5e1f77e985d7d66e3ec6ed62a51a61c82ed0964a5108a1f318bf717f3f2af4dcd018ec3a66c10d6dc7525bad801b118f468eca07b2502c836895f4091bbeed4 +bzip2-checksum = 00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 +cert-checksum = a81dfa59c70788126a395c576e54cb8f61c1ea34da69b5cd42e2d83ee6426c2a26941360c7302793774ea98ca16846deb6e683144cc7fb6da6ef87b70447e4c8 +coreutils-checksum = 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that are optional, The ones in +# `reproduce/software/config/TARGETS.conf' will be built as part of a +# project. To specify a software there, just remove the `-checksum' suffix +# from the list below. +apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b +apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706 +apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536 +astrometrynet-checksum = 35c268bf0a7068e01323b9bfccdf255c993df83c24b2e6026a00084c4ab87d031f1024205d0ed3aecc7e2a495d4bc0b0e67270d66679020b7cc2e4b2f30f5c4a +atlas-checksum = bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099fccdb5eaafe273c2682a41e41a3c6fabc8bbba4ce03180cffea40ede5df1d1f56e +autoconf-checksum = c25e834251bfc2befe822614caf1c80d7e1314a83e7173304abc235fd15a958b8db9fbc801e8ad98328dfd6d9dbc425bfbbefec500fa268992ae7bbf4fa5bc35 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So we'll set any specific configuration -# we want here, then import those. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. - -# To keep the program's compiled excutable file, comment this line. -deletecompiled 1 - -# Import the built configuration file -config .local/etc/astbuildprog.conf \ No newline at end of file diff --git a/reproduce/software/config/gnuastro/astconvertt.conf b/reproduce/software/config/gnuastro/astconvertt.conf deleted file mode 100644 index 770ac39..0000000 --- a/reproduce/software/config/gnuastro/astconvertt.conf +++ /dev/null @@ -1,33 +0,0 @@ -# Default parameters (System) for ConvertType. -# ConvertType is part of GNU Astronomy Utitlies. -# -# Use the long option name of each parameter followed by a value. The name -# and value should be separated by atleast one white-space character (for -# example ` '[space], or tab). Lines starting with `#' are ignored. -# -# For more information, please run these commands: -# -# $ astconvertt --help # Full list of options, short doc. -# $ astconvertt -P # Print all options and used values. -# $ info astconvertt # All options and input/output. -# $ info gnuastro "Configuration files" # How to use configuration files. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. - -# Input: - -# Output: - quality 100 - widthincm 10.0 - borderwidth 1 - output jpg - -# Flux: - invert 0 - -# Common options diff --git a/reproduce/software/config/gnuastro/aststatistics.conf b/reproduce/software/config/gnuastro/aststatistics.conf deleted file mode 100644 index 90f985d..0000000 --- a/reproduce/software/config/gnuastro/aststatistics.conf +++ /dev/null @@ -1,36 +0,0 @@ -# Default parameters (System) for Statistics. -# Statistics is part of GNU Astronomy Utitlies. -# -# Use the long option name of each parameter followed by a value. The name -# and value should be separated by atleast one white-space character (for -# example ` '[space], or tab). Lines starting with `#' are ignored. -# -# For more information, please run these commands: -# -# $ aststatistics --help # Full list of options, short doc. -# $ aststatistics -P # Print all options and used values. -# $ info aststatistics # All options and input/output. -# $ info gnuastro "Configuration files" # How to use configuration files. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. - -# Input image: - -# Sky and its STD settings - khdu 1 - meanmedqdiff 0.005 - outliersigma 10 - outliersclip 3,0.2 - smoothwidth 3 - sclipparams 3,0.1 - -# Histogram and CFP settings - numasciibins 70 - asciiheight 10 - numbins 100 - mirrordist 1.5 diff --git a/reproduce/software/config/gnuastro/gnuastro.conf b/reproduce/software/config/gnuastro/gnuastro.conf deleted file mode 100644 index 82cb100..0000000 --- a/reproduce/software/config/gnuastro/gnuastro.conf +++ /dev/null @@ -1,43 +0,0 @@ -# Default values for the common options to all the programs in GNU -# Astronomy Utitlies. -# -# IMPORTANT NOTE: The `lastconfig' option is very important in a -# reproducible environment. Because we don't want any of Gnuastro's -# programs to go into an un-controlled environment (user or system wide -# configuration files). -# -# The rest of this configuration file is taken from the default Gnuastro -# configuration from its source (`bin/gnuastro.conf'). -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. - -# Local project settings (`config' has to be before `lastconfig'). - config .gnuastro/gnuastro-local.conf - lastconfig 1 - -# Input: - hdu 1 - ignorecase 1 - searchin name - stdintimeout 100000 - -# Tessellation - tilesize 30,30 - numchannels 1,1 - remainderfrac 0.1 - workoverch 0 - interpmetric radial - interpnumngb 9 - interponlyblank 0 - -# Output: - tableformat fits-binary - -# Operating mode - quietmmap 0 - minmapsize 2000000000 diff --git a/reproduce/software/config/installation/LOCAL.conf.in b/reproduce/software/config/installation/LOCAL.conf.in deleted file mode 100644 index 0579218..0000000 --- a/reproduce/software/config/installation/LOCAL.conf.in +++ /dev/null @@ -1,17 +0,0 @@ -# Local project configuration. -# -# This is just a template for the `./project configure' script to fill -# in. Please don't make any change to this file. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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@ -DEPENDENCIES-DIR = @ddir@ -SYS_CPATH = @sys_cpath@ -DOWNLOADER = @downloader@ -GROUP-NAME = @groupname@ diff --git a/reproduce/software/config/installation/TARGETS.conf b/reproduce/software/config/installation/TARGETS.conf deleted file mode 100644 index d2d5e2c..0000000 --- a/reproduce/software/config/installation/TARGETS.conf +++ /dev/null @@ -1,42 +0,0 @@ -# Necessary high-level software to build in this project. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# Copyright (C) 2019-2020 Raul Infante-Sainz -# -# 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. - - - - - -# AVAILABLE SOFTWARE -# ------------------ -# -# All software that are currently available for installation can be seen in -# the following file. -# -# reproduce/software/config/installation/versions.conf -# -# Please add any software that you need for your project in the respective -# part below (using its name in `versions.conf', but without the `-version' -# part). Just note that if a program/library is a dependency of another, -# you don't need to include it here (it will be installed before the -# higher-level software anyway). -# -# Note that many low-level software will be installed before those that are -# installed in this step. They are clearly distinguished from the -# higher-level (optional) software in `versions.conf'. These low-level -# software MUST NOT be added here. - - - - - -# Programs and libraries. -top-level-programs = gnuastro - -# Python libraries/modules. -top-level-python = astropy diff --git a/reproduce/software/config/installation/checksums.conf b/reproduce/software/config/installation/checksums.conf deleted file mode 100644 index 7531749..0000000 --- a/reproduce/software/config/installation/checksums.conf +++ /dev/null @@ -1,199 +0,0 @@ -# sha512 checksums of all the necessary software tarballs. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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 the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This Makefile is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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Create a file like this -# called "site.cfg" next to your package's setup.py file and fill in the -# appropriate sections. Not all packages will use all sections so you -# should leave out sections that your package does not use. -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# Copyright (C) 2019-2020 Raul Infante-Sainz -# -# 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. - -# IMPORTANT NOTE -# -------------- -# -# The `ALL' grouping does't apply to ATLAS!!!!! - - [ALL] - library_dirs = @LIBDIR@ - include_dirs = @INCDIR@ - - -# FFT libraries -# ------------- -# There are two FFT libraries that we can configure here: FFTW (2 and 3) and djbfft. -# Note that these libraries are not used by numpy or scipy. -# -# http://fftw.org/ -# https://cr.yp.to/djbfft.html -# -# Given only this section, numpy.distutils will try to figure out which version -# of FFTW you are using. - -# Even with this section, Numpy apparently does not use fftw. But we will -# keep it here for the future (if a solution is found). -[fftw] -libraries = fftw3 -# -# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a . -#[djbfft] -#include_dirs = /usr/local/djbfft/include -#library_dirs = /usr/local/djbfft/lib diff --git a/reproduce/software/config/installation/texlive-packages.conf b/reproduce/software/config/installation/texlive-packages.conf deleted file mode 100644 index c53e170..0000000 --- a/reproduce/software/config/installation/texlive-packages.conf +++ /dev/null @@ -1,24 +0,0 @@ -# Necessary packages to install in TeX Live. -# -# If any extra TeX package is necessary to build your paper, just add its -# name to this variable (you can check in `ctan.org' to find the official -# name). -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. - - -# Note on `tex' and `fancyhdr': These two packages are installed along with -# the basic installation scheme that we used to install tlmgr, they will be -# ignored in the `tlmgr install' command, but will be used later when we -# want their versions. -texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xcolor \ - setspace caption footmisc datetime fmtcount titlesec \ - preprint ulem biblatex biber logreq pgf pgfplots fp \ - courier tex-gyre txfonts times csquotes kastrup \ - trimspaces pdftexcmds pdfescape letltxmacro bitset \ - mweights diff --git a/reproduce/software/config/installation/texlive.conf b/reproduce/software/config/installation/texlive.conf deleted file mode 100644 index b5075c6..0000000 --- a/reproduce/software/config/installation/texlive.conf +++ /dev/null @@ -1,35 +0,0 @@ -# Basic profile for build. Values to set: -# -# installdir: Install directory -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# -# 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. -selected_scheme scheme-basic -TEXDIR @installdir@/texlive/maneage -TEXMFCONFIG @installdir@/texlive-maneage/texmf-config -TEXMFLOCAL @installdir@/texlive/texmf-local -TEXMFSYSCONFIG @installdir@/texlive/maneage/texmf-config -TEXMFSYSVAR @installdir@/texlive/maneage/texmf-var -TEXMFVAR @installdir@/texlive-maneage/texmf-var -instopt_adjustpath 0 -instopt_adjustrepo 1 -instopt_letter 0 -instopt_portable 0 -instopt_write18_restricted 1 -tlpdbopt_autobackup 1 -tlpdbopt_backupdir @installdir@/texlive/maneage/backups -tlpdbopt_create_formats 1 -tlpdbopt_desktop_integration 1 -tlpdbopt_file_assocs 1 -tlpdbopt_generate_updmap 0 -tlpdbopt_install_docfiles 1 -tlpdbopt_install_srcfiles 1 -tlpdbopt_post_code 1 -tlpdbopt_sys_bin @installdir@/bin -tlpdbopt_sys_info @installdir@/share/info -tlpdbopt_sys_man @installdir@/share/man -tlpdbopt_w32_multi_user 1 diff --git a/reproduce/software/config/installation/versions.conf b/reproduce/software/config/installation/versions.conf deleted file mode 100644 index 39642d4..0000000 --- a/reproduce/software/config/installation/versions.conf +++ /dev/null @@ -1,221 +0,0 @@ -# Versions of the various dependencies -# -# Copyright (C) 2018-2020 Mohammad Akhlaghi -# Copyright (C) 2019-2020 Raul Infante-Sainz -# -# 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 the -# Free Software Foundation, either version 3 of the License, or (at your -# option) any later version. -# -# This Makefile is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General -# Public License for more details. -# -# A copy of the GNU General Public License is available at -# . - - - - - -# Basic/low-level programs and libraires (installed in any case) -# -------------------------------------------------------------- -bash-version = 5.0.11 -binutils-version = 2.32 -coreutils-version = 8.31 -curl-version = 7.65.3 -diffutils-version = 3.7 -file-version = 5.36 -findutils-version = 4.7.0 -gawk-version = 5.0.1 -gcc-version = 9.2.0 -git-version = 2.23.0 -gmp-version = 6.1.2 -grep-version = 3.3 -gzip-version = 1.10 -isl-version = 0.18 -libbsd-version = 0.9.1 -libiconv-version = 1.16 -libtool-version = 2.4.6 -lzip-version= 1.20 -m4-version = 1.4.18 -make-version = 4.3 -metastore-version = 1.1.2-23-fa9170b -mpc-version = 1.1.0 -mpfr-version = 4.0.2 -ncurses-version = 6.1 -openssl-version = 1.1.1a -patchelf-version = 0.10 -perl-version = 5.30.0 -pkgconfig-version = 0.29.2 -readline-version = 8.0 -sed-version = 4.7 -tar-version = 1.32 -texinfo-version = 6.6 -unzip-version = 6.0 -wget-version = 1.20.3 -which-version = 2.21 -xz-version = 5.2.4 -zip-version = 3.0 -zlib-version = 1.2.11 - - - - - -# Optional/high-level programs and libraries -# ------------------------------------------ -# -# These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.conf' will be built as -# part of a project. To specify a software there, just remove the -# `-version' suffix from the list below. -apachelog4cxx-version = 0.10.0-603-014954db -apr-version = 1.7.0 -apr-util-version = 1.6.1 -astrometrynet-version = 0.77 -atlas-version = 3.10.3 -autoconf-version = 2.69.200-babc -automake-version = 1.16.1 -bison-version = 3.4.2 -boost-version = 1.71.0 -cairo-version = 1.16.0 -cdsclient-version = 3.84 -cfitsio-version = 3.47 -cmake-version = 3.17.0 -eigen-version = 3.3.7 -expat-version = 2.2.9 -fftw-version = 3.3.8 -flex-version = 2.6.4 -flock-version = 0.2.3 -freetype-version = 2.9 -gdb-version = 8.3 -ghostscript-version = 9.50 -gnuastro-version = 0.11 -gsl-version = 2.6 -hdf5-version = 1.10.5 -healpix-version = 3.50 -help2man-version = 1.47.11 -imagemagick-version = 7.0.8-67 -imfit-version = 1.6.1 -libffi-version = 3.2.1 -libjpeg-version = v9b -libnsl-version = 1.2.0-4a062cf -libpng-version = 1.6.37 -libtiff-version = 4.0.10 -libtirpc-version = 1.1.4 -libxml2-version = 2.9.9 -missfits-version = 2.8.0 -openblas-version = 0.3.5 -openmpi-version = 4.0.1 -openssh-version = 8.0p1 -pixman-version = 0.38.0 -python-version = 3.7.4 -R-version = 3.6.2 -rpcsvc-proto-version = 1.4 -scamp-version = 2.6.7 -scons-version = 3.0.5 -sextractor-version = 2.25.0 -swarp-version = 2.38.0 -swig-version = 3.0.12 -tides-version = 2.0 -xlsxio-version = 0.2.21 -yaml-version = 0.2.2 - - - - - -# Python packages -# --------------- -# -# Similar to optional programs and libraries above. -# -# IMPORTANT: If you intend to change the version of any of the Python -# modules/libraries below, please fix the hash strings of the respective -# URL in `reproduce/software/make/python.mk'. -asn1crypto-version = 0.24.0 -asteval-version = 0.9.16 -astropy-version = 4.0 -astroquery-version = 0.4 -beautifulsoup4-version = 4.7.1 -certifi-version = 2018.11.29 -cffi-version = 1.12.2 -chardet-version = 3.0.4 -corner-version = 2.0.1 -cryptography-version = 2.6.1 -cycler-version = 0.10.0 -cython-version = 0.29.6 -eigency-version = 1.77 -emcee-version = 3.0.1 -entrypoints-version = 0.3 -esutil-version = 0.6.4 -flake8-version = 3.7.8 -future-version = 0.18.1 -galsim-version = 2.2.1 -h5py-version = 2.9.0 -healpy-version = installed-with-healpix -html5lib-version = 1.0.1 -idna-version = 2.8 -jeepney-version = 0.4 -keyring-version = 18.0.0 -kiwisolver-version = 1.0.1 -lmfit-version = 0.9.14 -lsstdesccoord-version = 1.2.0 -matplotlib-version = 3.1.1 -mpi4py-version = 3.0.2 -mpmath-version = 1.1.0 -numpy-version = 1.17.2 -pexpect-version = 4.7.0 -pip-version = 19.0.2 -pycodestyle-version = 2.5.0 -pycparser-version = 2.19 -pyflakes-version = 2.1.1 -pybind11-version = 2.4.3 -pyparsing-version = 2.3.1 -pypkgconfig-version = 1.5.1 -python-dateutil-version = 2.8.0 -pyyaml-version = 5.1 -requests-version = 2.21.0 -scipy-version = 1.3.1 -secretstorage-version = 3.1.1 -setuptools-version = 41.6.0 -setuptools_scm-version = 3.3.3 -sip_tpv-version = 1.1 -six-version = 1.12.0 -soupsieve-version = 1.8 -sympy-version = 1.4 -uncertainties-version = 3.1.2 -urllib3-version = 1.24.1 -virtualenv-version = 16.4.0 -webencodings-version = 0.5.1 - - - - - -# Special programs and libraries -# ------------------------------ -# -# When updating the version of these libraries, please look into the build -# rule first: In one way or another, the version string becomes necessary -# during their build and must be accounted for. -# -# Special notes: -# - `netpbm' questions in the configure steps maybe change with different -# or new versions. - -# Basic/low-level -bzip2-version = 1.0.6 - -# Optional/high-level -lapack-version = 3.8.0 -libgit2-version = 0.28.2 -netpbm-version = 10.86.99 -wcslib-version = 6.4 - -# Minizip is installed as a part of `zlib', and they have the same version. -zlib-version = 1.2.11 -minizip-version = $(zlib-version) diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg new file mode 100644 index 0000000..82cc1e1 --- /dev/null +++ b/reproduce/software/config/numpy-scipy.cfg @@ -0,0 +1,47 @@ +# THIS IS A COPY OF NUMPY'S site.cfg.example, CUSTOMIZED FOR THIS TEMPLATE +# ------------------------------------------------------------------------ + +# This file provides configuration information about non-Python +# dependencies for numpy.distutils-using packages. Create a file like this +# called "site.cfg" next to your package's setup.py file and fill in the +# appropriate sections. Not all packages will use all sections so you +# should leave out sections that your package does not use. +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# Copyright (C) 2019-2020 Raul Infante-Sainz +# +# 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. + +# IMPORTANT NOTE +# -------------- +# +# The `ALL' grouping does't apply to ATLAS!!!!! + + [ALL] + library_dirs = @LIBDIR@ + include_dirs = @INCDIR@ + + +# FFT libraries +# ------------- +# There are two FFT libraries that we can configure here: FFTW (2 and 3) and djbfft. +# Note that these libraries are not used by numpy or scipy. +# +# http://fftw.org/ +# https://cr.yp.to/djbfft.html +# +# Given only this section, numpy.distutils will try to figure out which version +# of FFTW you are using. + +# Even with this section, Numpy apparently does not use fftw. But we will +# keep it here for the future (if a solution is found). +[fftw] +libraries = fftw3 +# +# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a . +#[djbfft] +#include_dirs = /usr/local/djbfft/include +#library_dirs = /usr/local/djbfft/lib diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf new file mode 100644 index 0000000..c53e170 --- /dev/null +++ b/reproduce/software/config/texlive-packages.conf @@ -0,0 +1,24 @@ +# Necessary packages to install in TeX Live. +# +# If any extra TeX package is necessary to build your paper, just add its +# name to this variable (you can check in `ctan.org' to find the official +# name). +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# +# 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. + + +# Note on `tex' and `fancyhdr': These two packages are installed along with +# the basic installation scheme that we used to install tlmgr, they will be +# ignored in the `tlmgr install' command, but will be used later when we +# want their versions. +texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xcolor \ + setspace caption footmisc datetime fmtcount titlesec \ + preprint ulem biblatex biber logreq pgf pgfplots fp \ + courier tex-gyre txfonts times csquotes kastrup \ + trimspaces pdftexcmds pdfescape letltxmacro bitset \ + mweights diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf new file mode 100644 index 0000000..b5075c6 --- /dev/null +++ b/reproduce/software/config/texlive.conf @@ -0,0 +1,35 @@ +# Basic profile for build. Values to set: +# +# installdir: Install directory +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# +# 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. +selected_scheme scheme-basic +TEXDIR @installdir@/texlive/maneage +TEXMFCONFIG @installdir@/texlive-maneage/texmf-config +TEXMFLOCAL @installdir@/texlive/texmf-local +TEXMFSYSCONFIG @installdir@/texlive/maneage/texmf-config +TEXMFSYSVAR @installdir@/texlive/maneage/texmf-var +TEXMFVAR @installdir@/texlive-maneage/texmf-var +instopt_adjustpath 0 +instopt_adjustrepo 1 +instopt_letter 0 +instopt_portable 0 +instopt_write18_restricted 1 +tlpdbopt_autobackup 1 +tlpdbopt_backupdir @installdir@/texlive/maneage/backups +tlpdbopt_create_formats 1 +tlpdbopt_desktop_integration 1 +tlpdbopt_file_assocs 1 +tlpdbopt_generate_updmap 0 +tlpdbopt_install_docfiles 1 +tlpdbopt_install_srcfiles 1 +tlpdbopt_post_code 1 +tlpdbopt_sys_bin @installdir@/bin +tlpdbopt_sys_info @installdir@/share/info +tlpdbopt_sys_man @installdir@/share/man +tlpdbopt_w32_multi_user 1 diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf new file mode 100644 index 0000000..0c2cd0b --- /dev/null +++ b/reproduce/software/config/versions.conf @@ -0,0 +1,221 @@ +# Versions of the various dependencies +# +# Copyright (C) 2018-2020 Mohammad Akhlaghi +# Copyright (C) 2019-2020 Raul Infante-Sainz +# +# 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 the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This Makefile is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# A copy of the GNU General Public License is available at +# . + + + + + +# Basic/low-level programs and libraires (installed in any case) +# -------------------------------------------------------------- +bash-version = 5.0.11 +binutils-version = 2.32 +coreutils-version = 8.31 +curl-version = 7.65.3 +diffutils-version = 3.7 +file-version = 5.36 +findutils-version = 4.7.0 +gawk-version = 5.0.1 +gcc-version = 9.2.0 +git-version = 2.23.0 +gmp-version = 6.1.2 +grep-version = 3.3 +gzip-version = 1.10 +isl-version = 0.18 +libbsd-version = 0.9.1 +libiconv-version = 1.16 +libtool-version = 2.4.6 +lzip-version= 1.20 +m4-version = 1.4.18 +make-version = 4.3 +metastore-version = 1.1.2-23-fa9170b +mpc-version = 1.1.0 +mpfr-version = 4.0.2 +ncurses-version = 6.1 +openssl-version = 1.1.1a +patchelf-version = 0.10 +perl-version = 5.30.0 +pkgconfig-version = 0.29.2 +readline-version = 8.0 +sed-version = 4.7 +tar-version = 1.32 +texinfo-version = 6.6 +unzip-version = 6.0 +wget-version = 1.20.3 +which-version = 2.21 +xz-version = 5.2.4 +zip-version = 3.0 +zlib-version = 1.2.11 + + + + + +# Optional/high-level programs and libraries +# ------------------------------------------ +# +# These are programs and libraries that are optional, The ones in +# `reproduce/software/config/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-version' suffix from the list below. +apachelog4cxx-version = 0.10.0-603-014954db +apr-version = 1.7.0 +apr-util-version = 1.6.1 +astrometrynet-version = 0.77 +atlas-version = 3.10.3 +autoconf-version = 2.69.200-babc +automake-version = 1.16.1 +bison-version = 3.4.2 +boost-version = 1.71.0 +cairo-version = 1.16.0 +cdsclient-version = 3.84 +cfitsio-version = 3.47 +cmake-version = 3.17.0 +eigen-version = 3.3.7 +expat-version = 2.2.9 +fftw-version = 3.3.8 +flex-version = 2.6.4 +flock-version = 0.2.3 +freetype-version = 2.9 +gdb-version = 8.3 +ghostscript-version = 9.50 +gnuastro-version = 0.11 +gsl-version = 2.6 +hdf5-version = 1.10.5 +healpix-version = 3.50 +help2man-version = 1.47.11 +imagemagick-version = 7.0.8-67 +imfit-version = 1.6.1 +libffi-version = 3.2.1 +libjpeg-version = v9b +libnsl-version = 1.2.0-4a062cf +libpng-version = 1.6.37 +libtiff-version = 4.0.10 +libtirpc-version = 1.1.4 +libxml2-version = 2.9.9 +missfits-version = 2.8.0 +openblas-version = 0.3.5 +openmpi-version = 4.0.1 +openssh-version = 8.0p1 +pixman-version = 0.38.0 +python-version = 3.7.4 +R-version = 3.6.2 +rpcsvc-proto-version = 1.4 +scamp-version = 2.6.7 +scons-version = 3.0.5 +sextractor-version = 2.25.0 +swarp-version = 2.38.0 +swig-version = 3.0.12 +tides-version = 2.0 +xlsxio-version = 0.2.21 +yaml-version = 0.2.2 + + + + + +# Python packages +# --------------- +# +# Similar to optional programs and libraries above. +# +# IMPORTANT: If you intend to change the version of any of the Python +# modules/libraries below, please fix the hash strings of the respective +# URL in `reproduce/software/make/python.mk'. +asn1crypto-version = 0.24.0 +asteval-version = 0.9.16 +astropy-version = 4.0 +astroquery-version = 0.4 +beautifulsoup4-version = 4.7.1 +certifi-version = 2018.11.29 +cffi-version = 1.12.2 +chardet-version = 3.0.4 +corner-version = 2.0.1 +cryptography-version = 2.6.1 +cycler-version = 0.10.0 +cython-version = 0.29.6 +eigency-version = 1.77 +emcee-version = 3.0.1 +entrypoints-version = 0.3 +esutil-version = 0.6.4 +flake8-version = 3.7.8 +future-version = 0.18.1 +galsim-version = 2.2.1 +h5py-version = 2.9.0 +healpy-version = installed-with-healpix +html5lib-version = 1.0.1 +idna-version = 2.8 +jeepney-version = 0.4 +keyring-version = 18.0.0 +kiwisolver-version = 1.0.1 +lmfit-version = 0.9.14 +lsstdesccoord-version = 1.2.0 +matplotlib-version = 3.1.1 +mpi4py-version = 3.0.2 +mpmath-version = 1.1.0 +numpy-version = 1.17.2 +pexpect-version = 4.7.0 +pip-version = 19.0.2 +pycodestyle-version = 2.5.0 +pycparser-version = 2.19 +pyflakes-version = 2.1.1 +pybind11-version = 2.4.3 +pyparsing-version = 2.3.1 +pypkgconfig-version = 1.5.1 +python-dateutil-version = 2.8.0 +pyyaml-version = 5.1 +requests-version = 2.21.0 +scipy-version = 1.3.1 +secretstorage-version = 3.1.1 +setuptools-version = 41.6.0 +setuptools_scm-version = 3.3.3 +sip_tpv-version = 1.1 +six-version = 1.12.0 +soupsieve-version = 1.8 +sympy-version = 1.4 +uncertainties-version = 3.1.2 +urllib3-version = 1.24.1 +virtualenv-version = 16.4.0 +webencodings-version = 0.5.1 + + + + + +# Special programs and libraries +# ------------------------------ +# +# When updating the version of these libraries, please look into the build +# rule first: In one way or another, the version string becomes necessary +# during their build and must be accounted for. +# +# Special notes: +# - `netpbm' questions in the configure steps maybe change with different +# or new versions. + +# Basic/low-level +bzip2-version = 1.0.6 + +# Optional/high-level +lapack-version = 3.8.0 +libgit2-version = 0.28.2 +netpbm-version = 10.86.99 +wcslib-version = 6.4 + +# Minizip is installed as a part of `zlib', and they have the same version. +zlib-version = 1.2.11 +minizip-version = $(zlib-version) diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 47a01a3..17bb47a 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -33,10 +33,10 @@ # Top level environment +include reproduce/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.conf -include reproduce/software/config/installation/versions.conf -include reproduce/software/config/installation/checksums.conf +include reproduce/software/config/versions.conf +include reproduce/software/config/checksums.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs @@ -1334,12 +1334,14 @@ $(ibidir)/gcc: | $(ibidir)/binutils \ && cd ../.. \ && tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy \ && if [ "x$(on_mac_os)" != xyes ]; then \ - patchelf --add-needed $(ildir)/libiconv.so $(ildir)/libstdc++.so; \ for f in $$(find $(idir)/libexec/gcc) $(ildir)/libstdc++*; do \ isdynamic=$$(file $$f | grep "dynamically linked"); \ if [ x"$$isdynamic" != x ]; then \ cp $$f $$tempname; \ patchelf --set-rpath $(ildir) $$tempname; \ + if [ "$$f" = $(ildir)/libstdc++.so ]; then \ + patchelf --add-needed $(ildir)/libiconv.so $$tempname; \ + fi; \ mv $$tempname $$f; echo "corrected"; \ fi; \ done; \ diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 6e01354..e62f02f 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -27,12 +27,12 @@ # Top level environment +include reproduce/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.conf -include reproduce/software/config/installation/TARGETS.conf -include reproduce/software/config/installation/versions.conf -include reproduce/software/config/installation/checksums.conf -include reproduce/software/config/installation/texlive-packages.conf +include reproduce/software/config/TARGETS.conf +include reproduce/software/config/versions.conf +include reproduce/software/config/checksums.conf +include reproduce/software/config/texlive-packages.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs @@ -1240,7 +1240,7 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \ tlmirror=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet # The core TeX Live system. -$(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.conf \ +$(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf \ | $(tdir)/install-tl-unx.tar.gz # Unpack, enter the directory, and install based on the given @@ -1251,7 +1251,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co tar xf $(tdir)/install-tl-unx.tar.gz cd install-tl-* sed -e's|@installdir[@]|$(idir)|g' \ - $$topdir/reproduce/software/config/installation/texlive.conf \ + $$topdir/reproduce/software/config/texlive.conf \ > texlive.conf # TeX Live's installation may fail due to any reason. But TeX Live @@ -1292,7 +1292,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co #else #forbiber = $(ibidir)/libnsl #endif -$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \ +$(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr \ $(forbiber) diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index a15841c..1ef1bf2 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -600,7 +600,7 @@ $(ipydir)/numpy: $(ibidir)/unzip \ export LDFLAGS="$(LDFLAGS) -shared"; \ fi; \ export CFLAGS="--std=c99 $$CFLAGS"; \ - conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \ + conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \ $(call pybuild, unzip, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version)) \ && cp $(dtexdir)/numpy.tex $(ictdir)/ \ @@ -679,7 +679,7 @@ $(ipydir)/scipy: $(ipydir)/numpy \ else \ export LDFLAGS="$(LDFLAGS) -shared"; \ fi; \ - conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \ + conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \ $(call pybuild, tar xf, scipy-$(scipy-version),$$conf) \ && cp $(dtexdir)/scipy.tex $(ictdir)/ \ && echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index a0fc228..919acde 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -36,15 +36,13 @@ optionaldir="/optional/path" adir=reproduce/analysis/config cdir=reproduce/software/config -sbdir=$cdir/installation - -pconf=$sbdir/LOCAL.conf -ptconf=$sbdir/LOCAL_tmp.conf -poconf=$sbdir/LOCAL_old.conf -depverfile=$cdir/installation/versions.conf -depshafile=$cdir/installation/checksums.conf +pconf=$cdir/LOCAL.conf +ptconf=$cdir/LOCAL_tmp.conf +poconf=$cdir/LOCAL_old.conf +depverfile=$cdir/versions.conf +depshafile=$cdir/checksums.conf # --------- Delete for no Gnuastro --------- -glconf=$cdir/gnuastro/gnuastro-local.conf +glconf=$adir/gnuastro/gnuastro-local.conf # ------------------------------------------ -- cgit v1.2.1