From 3c4f1863d012ee4fefe64644c91b4a759a208e0f Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Fri, 3 Apr 2020 11:56:23 +0100 Subject: CMake updated to version 3.17.0 With this commit, CMake has been updated to its most recent version. This upgrade has been done because in the installation of XLSX I/O on macOS laptop, it crashes complaining about C compiler "not able to compile a simple test program". After a fast search, I found it could be possible to just use the most recent version of CMake to solve the problem. But it didn't work. In any case, it is good to have the most recent version of CMake included. --- .file-metadata | Bin 7813 -> 7874 bytes reproduce/software/config/installation/checksums.conf | 2 +- reproduce/software/config/installation/versions.conf | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.file-metadata b/.file-metadata index 0daa3df..9a732fa 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/config/installation/checksums.conf b/reproduce/software/config/installation/checksums.conf index 4a5d8aa..950880b 100644 --- a/reproduce/software/config/installation/checksums.conf +++ b/reproduce/software/config/installation/checksums.conf @@ -86,7 +86,7 @@ boost-checksum = 4378e20f18db9f186ac0f38ad98c522526e0fe48a8deb968c41325e3f69e733 cairo-checksum = 9eb27c4cf01c0b8b56f2e15e651f6d4e52c99d0005875546405b64f1132aed12fbf84727273f493d84056a13105e065009d89e94a8bfaf2be2649e232b82377f cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b743218cf62ab00eba0147abe82d9294223927f04b4cc3328620dfc9184a7049f8d515b29e4 cfitsio-checksum = c0502699e266928dd25abe57730dc4b357ccc9023789fe745324ae01aa688516aceaf37321ee578f0430111d9718f0fec0dc5b54c07f935529560f00b32ce1e3 -cmake-checksum = 7d0abf2f7c661c6b555a7e93a2fce5ab5610c653b0aa4949bed6e97bfbe6523fd0665f67115d3944d3729cbe07ae3aaf780ee673b06dd80f90018cec8a999658 +cmake-checksum = f09440681e0c414f5ca669f3aeba6666d09e0642f30a2e12c3199e7fb3da95a7dd17994fc54475c49638c37f0502ea0a2d8da0f9098805f11088ba7b299bf72a eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972 expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09 fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38 diff --git a/reproduce/software/config/installation/versions.conf b/reproduce/software/config/installation/versions.conf index 1b678ad..592d931 100644 --- a/reproduce/software/config/installation/versions.conf +++ b/reproduce/software/config/installation/versions.conf @@ -84,7 +84,7 @@ boost-version = 1.71.0 cairo-version = 1.16.0 cdsclient-version = 3.84 cfitsio-version = 3.47 -cmake-version = 3.15.3 +cmake-version = 3.17.0 eigen-version = 3.3.7 expat-version = 2.2.9 fftw-version = 3.3.8 -- cgit v1.2.1 From c2b36cc6b6c62b5f19745703c65df7cfa8b84cc4 Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Sun, 5 Apr 2020 17:03:16 +0100 Subject: Building Minizip 1.x instead of Minizip 2.x Minizip is a dependency of XLSX I/O and until now, I was just using the most recent version I found (2.9.2), but XLSX I/O is written for the Minizip 1.x series, not 2.x. Somehow it didn't cause a crash on my computer!!! I think XLSX I/O's CMake is instructed to look into system directories by default when it doesn't find the directories in the given places. And because I had installed Minizip on my operating system, it did't complain. Upon trying the build on their systems, Yahya, Raul and Zahra reported a failure in the build of XLSX I/O which was due the to the problem above (we were installing the wrong version of Minizip!). With this commit, this has been fixed by installing the 1.x series of Minizip (whish is actually installed within zlib!). This commit was original done by Mohammad Akhlaghi. --- .file-metadata | Bin 7874 -> 7946 bytes .../software/config/installation/checksums.conf | 2 +- .../software/config/installation/versions.conf | 5 +- reproduce/software/make/high-level.mk | 77 +++++++++++++++++---- 4 files changed, 67 insertions(+), 17 deletions(-) diff --git a/.file-metadata b/.file-metadata index 9a732fa..aa6d61e 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/config/installation/checksums.conf b/reproduce/software/config/installation/checksums.conf index 950880b..7531749 100644 --- a/reproduce/software/config/installation/checksums.conf +++ b/reproduce/software/config/installation/checksums.conf @@ -110,7 +110,6 @@ libpng-checksum = 59e8c1059013497ae616a14c3abbe239322d3873c6ded0912403fc62fb2605 libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a8e8c750202bc863fe27d0d1c577ab9de1710d15e9f6ed665aadbfd857525a81eea8 libtirpc-checksum = 392f391f9fc1bd68d81dc44e4058831a64b32790b5c8c37338b0ab416fad2ae4d16389e632596734dba09780347918cc65c6f134e0c1afd09e81ec250785ed23 libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810 -minizip-checksum = 56b5443f79d1a0a5f563a563f7b1c27b0b0fc5ba5b37248367b204a89a9373df7d12ea802c678f3f39c987d5f1766003eac3dd31b643773afa4463a3f6406628 missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795 netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6 openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0 @@ -129,6 +128,7 @@ tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3 wcslib-checksum = fed47771defb2a93fb50aa2e701c46f8ce35773dd3de91eeaed311b5a0474c096c7f9be6996fe95f82faa30b1d5c0aba892bca5da80bc32b15919dfaf551aeb7 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c yaml-checksum = 13d2197135946204323dbfccafa0ac7b3d05437e920545a56f46811fd7319c01419a58083090ce85fccd4d6901a620ceb9f1190078cc0830bc0ce769bb024f51 +zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae diff --git a/reproduce/software/config/installation/versions.conf b/reproduce/software/config/installation/versions.conf index 592d931..39642d4 100644 --- a/reproduce/software/config/installation/versions.conf +++ b/reproduce/software/config/installation/versions.conf @@ -107,7 +107,6 @@ libpng-version = 1.6.37 libtiff-version = 4.0.10 libtirpc-version = 1.1.4 libxml2-version = 2.9.9 -minizip-version = 2.9.2 missfits-version = 2.8.0 openblas-version = 0.3.5 openmpi-version = 4.0.1 @@ -216,3 +215,7 @@ 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/high-level.mk b/reproduce/software/make/high-level.mk index 274bcdf..43dfaa1 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -184,7 +184,6 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \ libpng-$(libpng-version).tar.xz \ libtirpc-$(libtirpc-version).tar.bz2 \ libxml2-$(libxml2-version).tar.gz \ - minizip-$(minizip-version).tar.gz \ missfits-$(missfits-version).tar.gz \ netpbm-$(netpbm-version).tar.gz \ openblas-$(openblas-version).tar.gz \ @@ -203,6 +202,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \ wcslib-$(wcslib-version).tar.bz2 \ xlsxio-$(xlsxio-version).tar.gz \ yaml-$(yaml-version).tar.gz \ + zlib-$(zlib-version).tar.gz \ , $(tdir)/$(t) ) $(tarballs): $(tdir)/%: | $(lockdir) @@ -282,10 +282,6 @@ $(tarballs): $(tdir)/%: | $(lockdir) w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz elif [ $$n = libtirpc ]; then c=$(libtirpc-checksum); w=https://downloads.sourceforge.net/libtirpc elif [ $$n = libxml ]; then c=$(libxml2-checksum); w=ftp://xmlsoft.org/libxml2 - elif [ $$n = minizip ]; then - mergenames=0 - c=$(minizip-checksum); - w=https://github.com/nmoinvaz/minizip/archive/$(minizip-version).tar.gz elif [ $$n = missfits ]; then c=$(missfits-checksum); w=https://www.astromatic.net/download/missfits elif [ $$n = netpbm ]; then c=$(netpbm-checksum); w=http://akhlaghi.org/reproduce-software elif [ $$n = openblas ]; then @@ -319,6 +315,7 @@ $(tarballs): $(tdir)/%: | $(lockdir) c=$(xlsxio-checksum); w=https://github.com/brechtsanders/xlsxio/archive/$(xlsxio-version).tar.gz elif [ $$n = yaml ]; then c=$(yaml-checksum); w=pyyaml.org/download/libyaml + elif [ $$n = zlib ]; then c=$(zlib-checksum); w=https://zlib.net else echo; echo; echo; echo "'$$n' not recognized as a software tarball name to download." @@ -927,8 +924,8 @@ $(ibidir)/ghostscript: $(ibidir)/libpng \ # First we need to make sure some necessary X11 libraries that we # don't yet install in this template are present on the host # system, see https://savannah.nongnu.org/task/?15481 . - # Adding `-L/opt/X11/lib' to LDFLAGS is necessary for macOS systems - # because X11 libraries used to be installed there. + # Adding `-L/opt/X11/lib' to LDFLAGS is necessary for macOS systems + # because X11 libraries used to be installed there. echo; echo "Template: testing necessary X11 libraries for ghostscript" echo "---------------------------------------------------------" @@ -1036,10 +1033,43 @@ $(ibidir)/imfit: $(ibidir)/gsl \ fi \ && echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ -$(ibidir)/minizip: $(ibidir)/cmake \ - | $(tdir)/minizip-$(minizip-version).tar.gz - $(call cbuild, minizip-$(minizip-version), static) \ - && echo "minizip $(minizip-version)" > $@ +# Minizip 1.x is actually distributed within zlib. It doesn't have its own +# independent tarball. So we need a custom build, which include the GNU +# Autotools (Autoconf and Automake). Note that Minizip 2.x isn't like this +# any more and has its own independent tarball, but currently the programs +# that depend on Minizip need Minizip 1.x. The instructions to build +# minizip were taken from ArchLinux. +# +# About deleting the final crypt.h file after installation, see +# https://bugzilla.redhat.com/show_bug.cgi?id=1424609 +$(ibidir)/minizip: $(ibidir)/automake \ + | $(tdir)/zlib-$(zlib-version).tar.gz + cd $(ddir) \ + && unpackdir=minizip-$(minizip-version) \ + && rm -rf $$unpackdir \ + && mkdir $$unpackdir \ + && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)) \ + -C$$unpackdir --strip-components=1; then \ + echo; echo "Tar error"; exit 1; \ + fi \ + && cd $$unpackdir\ + && ./configure --prefix=$(idir) \ + && make \ + && cd contrib/minizip \ + && cp Makefile Makefile.orig \ + && cp ../README.contrib readme.txt \ + && autoreconf --install \ + && ./configure --prefix=$(idir) \ + && make \ + && cd ../../ \ + && make test \ + && cd contrib/minizip \ + && make -f Makefile.orig test \ + && make install \ + && rm $(iidir)/minizip/crypt.h \ + && cd ../../.. \ + && rm -rf $$unpackdir \ + && echo "Minizip $(minizip)" > $@ $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz $(call gbuild, missfits-$(missfits-version), static) \ @@ -1152,11 +1182,29 @@ $(ibidir)/swig: | $(tdir)/swig-$(swig-version).tar.gz $(call gbuild, swig-$(swig-version), static, --without-pcre) \ && echo "Swig $(swig-version)" > $@ -$(ibidir)/xlsxio: $(ibidir)/expat \ +$(ibidir)/xlsxio: $(ibidir)/cmake \ + $(ibidir)/expat \ $(ibidir)/minizip \ | $(tdir)/xlsxio-$(xlsxio-version).tar.gz - export LDFLAGS="-lbz2 -lbsd"; \ - $(call cbuild, xlsxio-$(xlsxio-version), static) \ + if [ x$(on_mac_os) = xyes ]; then \ + export CC=clang; \ + export CXX=clang++; \ + export LDFLAGS="-lbz2"; \ + else \ + export LDFLAGS="-lbz2 -lbsd"; \ + fi; \ + $(call cbuild, xlsxio-$(xlsxio-version), static, \ + -DMINIZIP_DIR:PATH=$(idir) \ + -DMINIZIP_LIBRARIES=$(idir) \ + -DMINIZIP_INCLUDE_DIRS=$(iidir)) \ + && if [ "x$(on_mac_os)" != xyes ]; then \ + echo "Adding RPATH to the XLSX I/O executables..."; \ + for f in $(ibdir)/xlsxio_* $(ildir)/libxlsxio_*.so; do \ + patchelf --set-rpath $(ildir) $$f; \ + done; \ + fi \ + && echo "Deleting XLSX I/O example files..." \ + && rm $(ibdir)/example_xlsxio_* \ && echo "XLSX I/O $(xlsxio-version)" > $@ @@ -1166,7 +1214,6 @@ $(ibidir)/xlsxio: $(ibidir)/expat \ - # Since we want to avoid complicating the PATH, we are putting a symbolic # link of all the TeX Live executables in $(ibdir). But symbolic links are # hard to track for Make (as a target). Also, TeX in general is optional -- cgit v1.2.1 From 7201b0f0daf484ee326dcd13f3c1348b3f96f626 Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Sun, 5 Apr 2020 17:38:07 +0100 Subject: Including version number of Minizip in its installation target Until this commit, only the word `Minizip' was written into the Minizip installation target (without the version number of Minizip). With this commit, this minor bug has been fixed by using the appropiate Make variable: `$(minizip-version)'. --- .file-metadata | Bin 7946 -> 7946 bytes reproduce/software/make/high-level.mk | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/.file-metadata b/.file-metadata index aa6d61e..e0dba35 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 43dfaa1..916cb0a 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1069,7 +1069,7 @@ $(ibidir)/minizip: $(ibidir)/automake \ && rm $(iidir)/minizip/crypt.h \ && cd ../../.. \ && rm -rf $$unpackdir \ - && echo "Minizip $(minizip)" > $@ + && echo "Minizip $(minizip-version)" > $@ $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz $(call gbuild, missfits-$(missfits-version), static) \ -- cgit v1.2.1 From a4e2ec81d57eae3ec88c6f5af2f801f3b94bea24 Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Sun, 5 Apr 2020 17:54:39 +0100 Subject: The build of M4 and XLSX I/O on macOS has been fixed Until now, the M4 that was built on macOS had internal problems (as discussed in #1): it would simply print `Abort trap: 6' in the output and abort. After looking at the build of Homebrew, I noticed that they apply a patch (correct one line) to fix this problem. To be able to apply that patch on macOS systems, I had fully open up the build recipe of M4 and atleast on the testing system, it was built successfully. Also, after successfully building M4, and thus Autoconf and thus Minizip, we were able to build XLSX I/O on a macOS and found out that the internal library's full address wasn't being put in the libraries and executables. With this commit, we now use macOS's `install_name_tool' to correct the positions of the two `libxlsxio_*' libraries in all its executables. This commit was originally written by Mohammad Akhlaghi --- .file-metadata | Bin 7946 -> 7946 bytes reproduce/software/make/basic.mk | 28 ++++++++++++++++++++++++++-- reproduce/software/make/high-level.mk | 15 +++++++++++---- 3 files changed, 37 insertions(+), 6 deletions(-) diff --git a/.file-metadata b/.file-metadata index e0dba35..5b28e1d 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 212c738..47a01a3 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -1002,10 +1002,34 @@ $(ibidir)/libbsd: | $(ibidir)/coreutils \ $(call gbuild, libbsd-$(libbsd-version), static,,V=1) \ && echo "Libbsd $(libbsd-version)" > $@ -$(ibidir)/m4: | $(ibidir)/coreutils \ +# We need to apply a patch to the M4 source to be used properly on macOS. +# The patch [1] was inspired by Homebrew's build instructions [1]. +# +# [1] https://raw.githubusercontent.com/macports/macports-ports/edf0ee1e2cf/devel/m4/files/secure_snprintf.patch +# [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb +$(ibidir)/m4: | $(ibidir)/sed \ $(ibidir)/texinfo \ + $(ibidir)/coreutils \ $(tdir)/m4-$(m4-version).tar.gz - $(call gbuild, m4-$(m4-version), static,,V=1) \ + cd $(ddir); \ + unpackdir=m4-$(m4-version); \ + rm -rf $$unpackdir \ + && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \ + echo; echo "Tar error"; exit 1; \ + fi \ + && cd $$unpackdir \ + && if [ x$(on_mac_os) = xyes ]; then \ + sed -i -e's|if !(((__GLIBC__ > 2|if !defined(__APPLE__) \&\& !(((__GLIBC__ > 2|' lib/vasnprintf.c; \ + fi \ + && sed -i -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \ + -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \ + configure \ + && ./configure --prefix=$(idir) SHELL=$(ibdir)/bash \ + LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" \ + && make SHELL=$(ibdir)/bash V=1 -j$(numthreads) \ + && make SHELL=$(ibdir)/bash V=1 install \ + && cd .. \ + && rm -rf $$unpackdir \ && echo "GNU M4 $(m4-version)" > $@ # Metastore is used (through a Git hook) to restore the source modification diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 916cb0a..603e710 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1069,7 +1069,7 @@ $(ibidir)/minizip: $(ibidir)/automake \ && rm $(iidir)/minizip/crypt.h \ && cd ../../.. \ && rm -rf $$unpackdir \ - && echo "Minizip $(minizip-version)" > $@ + && echo "Minizip $(minizip)" > $@ $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz $(call gbuild, missfits-$(missfits-version), static) \ @@ -1197,10 +1197,17 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \ -DMINIZIP_DIR:PATH=$(idir) \ -DMINIZIP_LIBRARIES=$(idir) \ -DMINIZIP_INCLUDE_DIRS=$(iidir)) \ - && if [ "x$(on_mac_os)" != xyes ]; then \ - echo "Adding RPATH to the XLSX I/O executables..."; \ + && echo "Correcting internal linking of XLSX I/O executables..." \ + && if [ "x$(on_mac_os)" = xyes ]; then \ + for f in $(ibdir)/xlsxio_* $(ildir)/libxlsxio_*.dylib; do \ + install_name_tool -change libxlsxio_read.dylib \ + $(ildir)/libxlsxio_read.dylib $$f; \ + install_name_tool -change libxlsxio_write.dylib \ + $(ildir)/libxlsxio_write.dylib $$f; \ + done; \ + else \ for f in $(ibdir)/xlsxio_* $(ildir)/libxlsxio_*.so; do \ - patchelf --set-rpath $(ildir) $$f; \ + patchelf --set-rpath $(ildir) $$f; \ done; \ fi \ && echo "Deleting XLSX I/O example files..." \ -- cgit v1.2.1 From 647ce436871b5b692fa07ff166b731f72dff8bf8 Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Sun, 5 Apr 2020 17:59:57 +0100 Subject: Commenting version numbers with an underscore for LaTeX Until now we would simply return the version numbers as they were written into the separate files and situations can happen where the version numbers contain an underscore (`_'). However, this character is a methematical character in LaTeX, causing LaTeX to complain and abort. With this commit, a step has been added at the end of the configure script to convert any possible `_' to `\_'. Once it is commented (a backslash is put behind it), the underscore will be printed as it is in the final PDF. This commit was originally written by Mohammad Akhlaghi --- .file-metadata | Bin 7946 -> 7946 bytes reproduce/software/shell/configure.sh | 4 +++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.file-metadata b/.file-metadata index 5b28e1d..0559dea 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index ca95a92..a0fc228 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1320,9 +1320,11 @@ prepare_name_version () | .local/bin/sed '/^\s*$/d' \ | .local/bin/wc -l) - # Put them all in one paragraph. + # Put them all in one paragraph, while sorting them, commenting any + # possible underscores and removing blank lines. .local/bin/cat $@ \ | .local/bin/sort \ + | .local/bin/sed -e's|_|\\_|' \ | .local/bin/awk 'NF>0 { \ c++; \ if(c==1) \ -- cgit v1.2.1 From d0a51f78d4705c2496c42a02c49b0bc70e931cf7 Mon Sep 17 00:00:00 2001 From: Raul Infante-Sainz Date: Mon, 6 Apr 2020 09:12:47 +0100 Subject: Astropy now depending on the Expat library to fix internal conflict Until now, Astropy was instructed to build its own internal copy of the Expat library. However, with the recent commits before, Maneage now includes an installation of Expat and Astropy can't keep the two (its internal version and the project's version) separate, so they conflict and don't let Astropy get built. With this commit, the problem is fixed by setting the Expat library as an explicit dependency of Astropy and asking Astropy to ignore its internal copy. While doing this, I recognized that it is much easier and elegant to add steps in various stages of the `pybuild' function through hooks instead of variables. So the fifth argument of the `pybuild' function was removed and now it actually checks if hooks are defined as functions and if so, they will be called. The `pyhook_after' function was also implemented in the installation of `pybind11' (which needed it, given that the 5th argument of `pybuild' was removed) and after doing a test-build, I noticed that two lines were not ending with a `\' in `boost' (a dependency of `pybind11'). Commit written originally by Mohammad Akghlaghi --- .file-metadata | Bin 7946 -> 7874 bytes reproduce/software/make/high-level.mk | 6 +++--- reproduce/software/make/python.mk | 30 +++++++++++++++++++++++------- 3 files changed, 26 insertions(+), 10 deletions(-) diff --git a/.file-metadata b/.file-metadata index 0559dea..1cea790 100644 Binary files a/.file-metadata and b/.file-metadata differ diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 603e710..7d2577a 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -520,8 +520,8 @@ $(ibidir)/boost: $(ibidir)/openmpi \ vstr=$$(echo $(boost-version) | sed -e's/\./_/g') rm -rf $(ddir)/boost_$$vstr topdir=$(pwd); cd $(ddir); - tar xf $(word 1,$(filter $(tdir)/%,$|)) - && cd boost_$$vstr + tar xf $(word 1,$(filter $(tdir)/%,$|)) \ + && cd boost_$$vstr \ && ./bootstrap.sh --prefix=$(idir) --with-libraries=all \ --with-python=python3 \ && echo "using mpi ;" > project-config.jam \ @@ -1069,7 +1069,7 @@ $(ibidir)/minizip: $(ibidir)/automake \ && rm $(iidir)/minizip/crypt.h \ && cd ../../.. \ && rm -rf $$unpackdir \ - && echo "Minizip $(minizip)" > $@ + && echo "Minizip $(minizip-version)" > $@ $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz $(call gbuild, missfits-$(missfits-version), static) \ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index fef1605..9c79abc 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -335,7 +335,10 @@ $(ibidir)/python: $(ibidir)/libffi \ # 2) Unpacked directory name after unpacking the tarball # 3) site.cfg file (optional). # 4) Official software name (for paper). -# 5) Manual step after installation. +# +# Hooks: +# pyhook_before: optional steps before running `python setup.py build' +# pyhook_after: optional steps after running `python setup.py install' pybuild = cd $(ddir); rm -rf $(2); \ if ! $(1) $(word 1,$(filter $(tdir)/%,$|)); then \ echo; echo "Tar error"; exit 1; \ @@ -346,11 +349,10 @@ pybuild = cd $(ddir); rm -rf $(2); \ -e 's|@INCDIR[@]|'"$(idir)/include"'|' \ $(3) > site.cfg; \ fi; \ - if [ x"$(5)" = x ]; then after="echo no after"; \ - else after="$(5)"; fi \ + if type pyhook_before &>/dev/null; then pyhook_before; fi \ && python setup.py build \ && python setup.py install \ - && $$after \ + && if type pyhook_after &>/dev/null; then pyhook_after; fi \ && cd .. \ && rm -rf $(2) \ && echo "$(4)" > $@ @@ -381,12 +383,24 @@ $(ipydir)/astroquery: $(ipydir)/astropy \ Astroquery $(astroquery-version)) $(ipydir)/astropy: $(ipydir)/h5py \ + $(ibidir)/expat \ $(ipydir)/scipy \ $(ipydir)/numpy \ $(ipydir)/pyyaml \ $(ipydir)/html5lib \ $(ipydir)/beautifulsoup4 \ | $(tdir)/astropy-$(astropy-version).tar.gz + # Currently, when the Expat library is already built in a project + # (for example as a dependency of another program), Astropy's + # internal building of Expat will conflict with the project's. So + # we have added Expat as a dependency of Astropy (so it is always + # built before it, and we tell Astropy to use the project's + # libexpat. + pyhook_before () { + echo "" >> setup.cfg + echo "[build]" >> setup.cfg + echo "use_system_expat=1" >> setup.cfg + } $(call pybuild, tar xf, astropy-$(astropy-version)) \ && cp $(dtexdir)/astropy.tex $(ictdir)/ \ && echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@ @@ -474,7 +488,7 @@ $(ipydir)/galsim: $(ipydir)/future \ $(ipydir)/pybind11 \ $(ipydir)/lsstdesccoord \ | $(tdir)/galsim-$(galsim-version).tar.gz - $(call pybuild, tar xf, GalSim-$(galsim-version), ,) \ + $(call pybuild, tar xf, GalSim-$(galsim-version)) \ && cp $(dtexdir)/galsim.tex $(ictdir)/ \ && echo "Galsim $(galsim-version) \citep{galsim}" > $@ @@ -610,9 +624,11 @@ $(ipydir)/pybind11: $(ibidir)/eigen \ $(ibidir)/boost \ $(ipydir)/setuptools \ | $(tdir)/pybind11-$(pybind11-version).tar.gz + pyhook_after() { + cp -r include/pybind11 $(iidir)/python$(python-major-version)m/ + } $(call pybuild, tar xf, pybind11-$(pybind11-version), ,\ - pybind11 $(pybind11-version), - cp -r include/pybind11 $(iidir)/python$(python-major-version)m/) + pybind11 $(pybind11-version)) $(ipydir)/pycparser: $(ipydir)/setuptools \ | $(tdir)/pycparser-$(pycparser-version).tar.gz -- cgit v1.2.1 From fb041fe844074d2556cfc350b52f5742bfb866b3 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Sun, 12 Apr 2020 15:26:37 +0100 Subject: Configure (numpy): added --std=c99 to CFLAGS to fix error Elham Saremi recently reported the following errors when building Numpy in numpy/core/src/npysort/radixsort.c.src: "error: 'for' loop initial declarations are only allowed in C99 or C11 mode". After some searching, I found Issue 14147[1] on Numpy's main repository about the same problem. As described there, apparently Numpy needs C99 compiler, but doesn't check for it or set it manually (for some strange reason, leaving it to the packagers to check if they want!!!). Any way, after a check with Elham, we were able to fix it by adding the `--std=c99' to CFLAGS of Numpy's build and with this commit, it is now being implemented in the core Maneage to not cause a problem in any other project. [1] https://github.com/numpy/numpy/issues/14147 --- reproduce/software/make/python.mk | 1 + 1 file changed, 1 insertion(+) diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 9c79abc..a15841c 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -599,6 +599,7 @@ $(ipydir)/numpy: $(ibidir)/unzip \ else \ export LDFLAGS="$(LDFLAGS) -shared"; \ fi; \ + export CFLAGS="--std=c99 $$CFLAGS"; \ conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \ $(call pybuild, unzip, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version)) \ -- cgit v1.2.1 From 7523206bf425829865179375120773cfa23716bf Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 13 Apr 2020 21:39:55 +0100 Subject: Configure (TeXLive): Year of distribution no longer in directory It is this time of year again: TeXLive has transitioned to its 2020 release and the year is imprinted into the installation directory of TeXLive. Until now, we have had to manually change this year and it caused complications and was very annoying. With this commit, the explicit year has been removed from TeXLive's installation and we now simply put a `maneage' instead of the year. I tried this on another system and it worked nicely. Until the time that we can fully install LaTeX packages from source tarballs, this is the best thing we could do for now. --- reproduce/analysis/make/initialize.mk | 2 +- reproduce/software/config/installation/texlive.conf | 12 ++++++------ reproduce/software/make/high-level.mk | 10 ++++------ 3 files changed, 11 insertions(+), 13 deletions(-) diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 79f9266..3af0012 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -323,7 +323,7 @@ $(packagecontents): paper.pdf | $(texdir) # file. TIP: you can use the same strategy for other LaTeX packages # that may cause problems on the arXiv server. cp tex/build/build/paper.bbl $$dir/ - tltopdir=.local/texlive/2019/texmf-dist/tex/latex + tltopdir=.local/texlive/maneage/texmf-dist/tex/latex find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \ | xargs -0 cp -t $$dir diff --git a/reproduce/software/config/installation/texlive.conf b/reproduce/software/config/installation/texlive.conf index 2e86ac4..b5075c6 100644 --- a/reproduce/software/config/installation/texlive.conf +++ b/reproduce/software/config/installation/texlive.conf @@ -9,19 +9,19 @@ # this notice are preserved. This file is offered as-is, without any # warranty. selected_scheme scheme-basic -TEXDIR @installdir@/texlive/2019 -TEXMFCONFIG @installdir@/texlive2019/texmf-config +TEXDIR @installdir@/texlive/maneage +TEXMFCONFIG @installdir@/texlive-maneage/texmf-config TEXMFLOCAL @installdir@/texlive/texmf-local -TEXMFSYSCONFIG @installdir@/texlive/2019/texmf-config -TEXMFSYSVAR @installdir@/texlive/2019/texmf-var -TEXMFVAR @installdir@/texlive2019/texmf-var +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/2019/backups +tlpdbopt_backupdir @installdir@/texlive/maneage/backups tlpdbopt_create_formats 1 tlpdbopt_desktop_integration 1 tlpdbopt_file_assocs 1 diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 7d2577a..46b79ca 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1259,12 +1259,10 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co # don't want the configure script to fail if it can't run. if ./install-tl --profile=texlive.conf -repository $(tlmirror); then - # Put a symbolic link of the TeX Live executables in `ibdir'. The - # main problem is that the year and build system (for example - # `x86_64-linux') are also in the directory names, making it hard - # to be generic. We are using wildcards here, but only in this - # Makefile, not in any other. - ln -fs $(idir)/texlive/20*/bin/*/* $(ibdir)/ + # Put a symbolic link of the TeX Live executables in `ibdir' to + # avoid all the complexities of its sub-directories and additions + # to PATH. + ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/ # Register that the build was successful. echo "TeX Live is ready." > $@ -- cgit v1.2.1 From e0a57efde9206c0c7420e03e5fb2a354d568c3ad Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 13 Apr 2020 21:48:59 +0100 Subject: Configure (TeXLive): year correction also in high-level packages In the previous commit, I removed the year from the basic installation of TeXLive packages, but I forgot to correct this in the high-level TeXLive packages! This is corrected with this commit. --- reproduce/software/make/high-level.mk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 46b79ca..6e01354 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1322,7 +1322,7 @@ $(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf # Make a symbolic link of all the TeX Live executables in the bin # directory so we don't have to modify `PATH'. - ln -fs $(idir)/texlive/20*/bin/*/* $(ibdir)/ + ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/ # Get all the necessary versions. texlive=$$(pdflatex --version | awk 'NR==1' | sed 's/.*(\(.*\))/\1/' \ -- cgit v1.2.1 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. --- README-hacking.md | 59 +++--- .../analysis/config/gnuastro/astbuildprog.conf | 16 ++ .../analysis/config/gnuastro/astconvertt.conf | 33 +++ .../analysis/config/gnuastro/aststatistics.conf | 36 ++++ reproduce/analysis/config/gnuastro/gnuastro.conf | 43 ++++ reproduce/analysis/make/initialize.mk | 4 +- reproduce/analysis/make/top-make.mk | 2 +- reproduce/analysis/make/top-prepare.mk | 2 +- 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 +- 30 files changed, 768 insertions(+), 769 deletions(-) create mode 100644 reproduce/analysis/config/gnuastro/astbuildprog.conf create mode 100644 reproduce/analysis/config/gnuastro/astconvertt.conf create mode 100644 reproduce/analysis/config/gnuastro/aststatistics.conf create mode 100644 reproduce/analysis/config/gnuastro/gnuastro.conf 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 diff --git a/README-hacking.md b/README-hacking.md index 82b40e3..c1efccc 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -321,17 +321,17 @@ variables/configurations) and _workhorse-Makefiles_ (Makefiles that actually contain analysis/processing rules). The configuration-Makefiles are those that satisfy these two wildcards: -`reproduce/software/config/installation/*.conf` (for building the necessary -software when you run `./project configure`) and -`reproduce/analysis/config/*.conf` (for the high-level analysis, when you -run `./project make`). These Makefiles don't actually have any rules, they -just have values for various free parameters throughout the configuration -or analysis. Open a few of them to see for yourself. These Makefiles must -only contain raw Make variables (project configurations). By "raw" we mean -that the Make variables in these files must not depend on variables in any -other configuration-Makefile. This is because we don't want to assume any -order in reading them. It is also very important to *not* define any rule, -or other Make construct, in these configuration-Makefiles. +`reproduce/software/config/*.conf` (for building the necessary software +when you run `./project configure`) and `reproduce/analysis/config/*.conf` +(for the high-level analysis, when you run `./project make`). These +Makefiles don't actually have any rules, they just have values for various +free parameters throughout the configuration or analysis. Open a few of +them to see for yourself. These Makefiles must only contain raw Make +variables (project configurations). By "raw" we mean that the Make +variables in these files must not depend on variables in any other +configuration-Makefile. This is because we don't want to assume any order +in reading them. It is also very important to *not* define any rule, or +other Make construct, in these configuration-Makefiles. Following this rule-of-thumb enables you to set these configure-Makefiles as a prerequisite to any target that depends on their variable @@ -372,9 +372,8 @@ Let's see how this design is implemented. Please open and inspect `top-make.mk` it as we go along here. The first step (un-commented line) is to import the local configuration (your answers to the questions of `./project configure`). They are defined in the configuration-Makefile -`reproduce/software/config/installation/LOCAL.conf` which was also built by -`./project configure` (based on the `LOCAL.conf.in` template of the same -directory). +`reproduce/software/config/LOCAL.conf` which was also built by `./project +configure` (based on the `LOCAL.conf.in` template of the same directory). The next non-commented set of the top `Makefile` defines the ultimate target of the whole project (`paper.pdf`). But to avoid mistakes, a sanity @@ -767,21 +766,21 @@ Other basic customizations - **High-level software**: The template installs all the software that your project needs. You can specify which software your project needs - in `reproduce/software/config/installation/TARGETS.conf`. The - necessary software are classified into two classes: 1) programs or - libraries (usually written in C/C++) which are run directly by the - operating system. 2) Python modules/libraries that are run within - Python. By default `TARGETS.conf` only has GNU Astronomy Utilities - (Gnuastro) as one scientific program and Astropy as one scientific - Python module. Both have many dependencies which will be installed - into your project during the configuration step. To see a list of - software that are currently ready to be built in the template, see - `reproduce/software/config/installation/versions.conf` (which has - their versions also), the comments in `TARGETS.conf` describe how to use - the software name from `versions.conf`. Currently the raw pipeline just - uses Gnuastro to make the demonstration plots. Therefore if you don't - need Gnuastro, go through the analysis steps in `reproduce/analysis` - and remove all its use cases (clearly marked). + in `reproduce/software/config/TARGETS.conf`. The necessary software + are classified into two classes: 1) programs or libraries (usually + written in C/C++) which are run directly by the operating system. 2) + Python modules/libraries that are run within Python. By default + `TARGETS.conf` only has GNU Astronomy Utilities (Gnuastro) as one + scientific program and Astropy as one scientific Python module. Both + have many dependencies which will be installed into your project + during the configuration step. To see a list of software that are + currently ready to be built in the template, see + `reproduce/software/config/versions.conf` (which has their versions + also), the comments in `TARGETS.conf` describe how to use the software + name from `versions.conf`. Currently the raw pipeline just uses + Gnuastro to make the demonstration plots. Therefore if you don't need + Gnuastro, go through the analysis steps in `reproduce/analysis` and + remove all its use cases (clearly marked). - **Input dataset**: The input datasets are managed through the `reproduce/analysis/config/INPUTS.conf` file. It is best to gather all @@ -856,7 +855,7 @@ Other basic customizations TeXLive comes (once every year), if you would like to build the paper, its necessary to update it in your project (otherwise the configure script will crash). To do that, just modify the years in - `reproduce/software/config/installation/texlive.conf`, then delete + `reproduce/software/config/texlive.conf`, then delete `.build/software/tarballs/install-tl-unx.tar.gz`. The next time you run `./project configure`, the new TeXLive will be installed and used. diff --git a/reproduce/analysis/config/gnuastro/astbuildprog.conf b/reproduce/analysis/config/gnuastro/astbuildprog.conf new file mode 100644 index 0000000..7adb4d1 --- /dev/null +++ b/reproduce/analysis/config/gnuastro/astbuildprog.conf @@ -0,0 +1,16 @@ +# BuildProgram's configuration file depends on the build and is installed +# along with the rest of Gnuastro. 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/analysis/config/gnuastro/astconvertt.conf b/reproduce/analysis/config/gnuastro/astconvertt.conf new file mode 100644 index 0000000..770ac39 --- /dev/null +++ b/reproduce/analysis/config/gnuastro/astconvertt.conf @@ -0,0 +1,33 @@ +# 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/analysis/config/gnuastro/aststatistics.conf b/reproduce/analysis/config/gnuastro/aststatistics.conf new file mode 100644 index 0000000..90f985d --- /dev/null +++ b/reproduce/analysis/config/gnuastro/aststatistics.conf @@ -0,0 +1,36 @@ +# 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/analysis/config/gnuastro/gnuastro.conf b/reproduce/analysis/config/gnuastro/gnuastro.conf new file mode 100644 index 0000000..82cb100 --- /dev/null +++ b/reproduce/analysis/config/gnuastro/gnuastro.conf @@ -0,0 +1,43 @@ +# 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/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 3af0012..d8a8b73 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -308,8 +308,8 @@ $(packagecontents): paper.pdf | $(texdir) # have this machine's local settings and are irrelevant for anyone # else. rm -rf $$dir/tex/build/build* - rm $$dir/reproduce/software/config/installation/LOCAL.conf - rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf + rm $$dir/reproduce/software/config/LOCAL.conf + rm $$dir/reproduce/analysis/config/gnuastro/gnuastro-local.conf # 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' diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 6c940b8..43e88b2 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -21,7 +21,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/LOCAL.conf diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 1778c6b..be7482c 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -25,7 +25,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/LOCAL.conf 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. 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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