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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2020-04-17 04:02:28 +0100
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2020-04-17 04:02:28 +0100
commit9ed594ec27405e38548d6efd6fe28a4dabf0fb41 (patch)
treec1fdf80bd1b65056d5216b9cdda2e3fccc958c1a /reproduce
parentf4d998a36d6777164147b848b0ac4747c38067cf (diff)
parent8eb0892e179b4970a9835d29b5f57dd912ca4464 (diff)
Imported recent work in Maneage, minor conflicts fixed
A few minor conflicts came up that were easily fixed.
Diffstat (limited to 'reproduce')
-rw-r--r--reproduce/analysis/config/gnuastro/astbuildprog.conf (renamed from reproduce/software/config/gnuastro/astbuildprog.conf)0
-rw-r--r--reproduce/analysis/config/gnuastro/astconvertt.conf (renamed from reproduce/software/config/gnuastro/astconvertt.conf)0
-rw-r--r--reproduce/analysis/config/gnuastro/aststatistics.conf (renamed from reproduce/software/config/gnuastro/aststatistics.conf)0
-rw-r--r--reproduce/analysis/config/gnuastro/gnuastro.conf (renamed from reproduce/software/config/gnuastro/gnuastro.conf)0
-rw-r--r--reproduce/analysis/make/initialize.mk4
-rw-r--r--reproduce/analysis/make/top-make.mk2
-rw-r--r--reproduce/analysis/make/top-prepare.mk2
-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/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.mk10
-rw-r--r--reproduce/software/make/high-level.mk19
-rw-r--r--reproduce/software/make/python.mk7
-rwxr-xr-xreproduce/software/shell/configure.sh14
18 files changed, 37 insertions, 37 deletions
diff --git a/reproduce/software/config/gnuastro/astbuildprog.conf b/reproduce/analysis/config/gnuastro/astbuildprog.conf
index 7adb4d1..7adb4d1 100644
--- a/reproduce/software/config/gnuastro/astbuildprog.conf
+++ b/reproduce/analysis/config/gnuastro/astbuildprog.conf
diff --git a/reproduce/software/config/gnuastro/astconvertt.conf b/reproduce/analysis/config/gnuastro/astconvertt.conf
index 770ac39..770ac39 100644
--- a/reproduce/software/config/gnuastro/astconvertt.conf
+++ b/reproduce/analysis/config/gnuastro/astconvertt.conf
diff --git a/reproduce/software/config/gnuastro/aststatistics.conf b/reproduce/analysis/config/gnuastro/aststatistics.conf
index 90f985d..90f985d 100644
--- a/reproduce/software/config/gnuastro/aststatistics.conf
+++ b/reproduce/analysis/config/gnuastro/aststatistics.conf
diff --git a/reproduce/software/config/gnuastro/gnuastro.conf b/reproduce/analysis/config/gnuastro/gnuastro.conf
index 82cb100..82cb100 100644
--- a/reproduce/software/config/gnuastro/gnuastro.conf
+++ b/reproduce/analysis/config/gnuastro/gnuastro.conf
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 2736f2a..c804aaf 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -313,8 +313,8 @@ $(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 30d537a..5461f71 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/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/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
# ------------------------------------------