diff options
Diffstat (limited to 'reproduce/software')
| -rw-r--r-- | reproduce/software/config/LOCAL.conf.in (renamed from reproduce/software/config/installation/LOCAL.conf.in) | 0 | ||||
| -rw-r--r-- | reproduce/software/config/TARGETS.conf (renamed from reproduce/software/config/installation/TARGETS.conf) | 2 | ||||
| -rw-r--r-- | reproduce/software/config/checksums.conf (renamed from reproduce/software/config/installation/checksums.conf) | 8 | ||||
| -rw-r--r-- | reproduce/software/config/gnuastro/astbuildprog.conf | 16 | ||||
| -rw-r--r-- | reproduce/software/config/gnuastro/astconvertt.conf | 33 | ||||
| -rw-r--r-- | reproduce/software/config/gnuastro/aststatistics.conf | 36 | ||||
| -rw-r--r-- | reproduce/software/config/gnuastro/gnuastro.conf | 43 | ||||
| -rw-r--r-- | reproduce/software/config/numpy-scipy.cfg (renamed from reproduce/software/config/installation/numpy-scipy.cfg) | 0 | ||||
| -rw-r--r-- | reproduce/software/config/texlive-packages.conf (renamed from reproduce/software/config/installation/texlive-packages.conf) | 0 | ||||
| -rw-r--r-- | reproduce/software/config/texlive.conf (renamed from reproduce/software/config/installation/texlive.conf) | 0 | ||||
| -rw-r--r-- | reproduce/software/config/versions.conf (renamed from reproduce/software/config/installation/versions.conf) | 6 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 10 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 19 | ||||
| -rw-r--r-- | reproduce/software/make/python.mk | 7 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 14 |
15 files changed, 33 insertions, 161 deletions
diff --git a/reproduce/software/config/installation/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index 0579218..0579218 100644 --- a/reproduce/software/config/installation/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in diff --git a/reproduce/software/config/installation/TARGETS.conf b/reproduce/software/config/TARGETS.conf index bb402be..00ce387 100644 --- a/reproduce/software/config/installation/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -18,7 +18,7 @@ # All software that are currently available for installation can be seen in # the following file. # -# reproduce/software/config/installation/versions.conf +# 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' diff --git a/reproduce/software/config/installation/checksums.conf b/reproduce/software/config/checksums.conf index 04327aa..37fe64d 100644 --- a/reproduce/software/config/installation/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff # ------------------------------------------ # # 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 -# `-checksum' suffix from the list below. +# `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 @@ -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/gnuastro/astbuildprog.conf b/reproduce/software/config/gnuastro/astbuildprog.conf deleted file mode 100644 index 7adb4d1..0000000 --- a/reproduce/software/config/gnuastro/astbuildprog.conf +++ /dev/null @@ -1,16 +0,0 @@ -# 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 <mohammad@akhlaghi.org> -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice and -# this notice are preserved. This file is offered as-is, without any -# warranty. - -# 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 <mohammad@akhlaghi.org> -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice and -# this notice are preserved. This file is offered as-is, without any -# warranty. - -# 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 <mohammad@akhlaghi.org> -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice and -# this notice are preserved. This file is offered as-is, without any -# warranty. - -# 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 <mohammad@akhlaghi.org> -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice and -# this notice are preserved. This file is offered as-is, without any -# warranty. - -# 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/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg index 82cc1e1..82cc1e1 100644 --- a/reproduce/software/config/installation/numpy-scipy.cfg +++ b/reproduce/software/config/numpy-scipy.cfg diff --git a/reproduce/software/config/installation/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index 6760eba..6760eba 100644 --- a/reproduce/software/config/installation/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf diff --git a/reproduce/software/config/installation/texlive.conf b/reproduce/software/config/texlive.conf index b5075c6..b5075c6 100644 --- a/reproduce/software/config/installation/texlive.conf +++ b/reproduce/software/config/texlive.conf diff --git a/reproduce/software/config/installation/versions.conf b/reproduce/software/config/versions.conf index e61bcb5..0c2cd0b 100644 --- a/reproduce/software/config/installation/versions.conf +++ b/reproduce/software/config/versions.conf @@ -69,7 +69,7 @@ zlib-version = 1.2.11 # ------------------------------------------ # # These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.conf' will be built as +# `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 @@ -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 @@ -218,4 +218,4 @@ 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)
\ No newline at end of file +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 b0847a9..ef4dd4c 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 @@ -1069,7 +1069,7 @@ $(ibidir)/minizip: $(ibidir)/automake \ && rm $(iidir)/minizip/crypt.h \ && cd ../../.. \ && rm -rf $$unpackdir \ - && echo "Minizip $(minizip)" > $@ + && echo "Minizip $(minizip-version)" > $@ $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz $(call gbuild, missfits-$(missfits-version), static) \ @@ -1222,7 +1222,6 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \ - # Since we want to avoid complicating the PATH, we are putting a symbolic # link of all the TeX Live executables in $(ibdir). But symbolic links are # hard to track for Make (as a target). Also, TeX in general is optional @@ -1242,7 +1241,7 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \ tlmirror=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet # The core TeX Live system. -$(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.conf \ +$(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf \ | $(tdir)/install-tl-unx.tar.gz # Unpack, enter the directory, and install based on the given @@ -1253,7 +1252,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co tar xf $(tdir)/install-tl-unx.tar.gz cd install-tl-* sed -e's|@installdir[@]|$(idir)|g' \ - $$topdir/reproduce/software/config/installation/texlive.conf \ + $$topdir/reproduce/software/config/texlive.conf \ > texlive.conf # TeX Live's installation may fail due to any reason. But TeX Live @@ -1294,7 +1293,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co #else #forbiber = $(ibidir)/libnsl #endif -$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \ +$(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr \ $(forbiber) diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index a1d198d..1ef1bf2 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -393,7 +393,7 @@ $(ipydir)/astropy: $(ipydir)/h5py \ # Currently, when the Expat library is already built in a project # (for example as a dependency of another program), Astropy's # internal building of Expat will conflict with the project's. So - # we have added Expat as a dependency of astropy (so it is always + # we have added Expat as a dependency of Astropy (so it is always # built before it, and we tell Astropy to use the project's # libexpat. pyhook_before () { @@ -599,7 +599,8 @@ $(ipydir)/numpy: $(ibidir)/unzip \ else \ export LDFLAGS="$(LDFLAGS) -shared"; \ fi; \ - conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \ + export CFLAGS="--std=c99 $$CFLAGS"; \ + conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \ $(call pybuild, unzip, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version)) \ && cp $(dtexdir)/numpy.tex $(ictdir)/ \ @@ -678,7 +679,7 @@ $(ipydir)/scipy: $(ipydir)/numpy \ else \ export LDFLAGS="$(LDFLAGS) -shared"; \ fi; \ - conf="$$(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}" > $@ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index cf2ef5d..4eefe7b 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -36,15 +36,13 @@ optionaldir="/optional/path" adir=reproduce/analysis/config cdir=reproduce/software/config -sbdir=$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 # ------------------------------------------ |