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-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)6
-rw-r--r--reproduce/software/config/gnuastro/astbuildprog.conf16
-rw-r--r--reproduce/software/config/gnuastro/astconvertt.conf33
-rw-r--r--reproduce/software/config/gnuastro/aststatistics.conf36
-rw-r--r--reproduce/software/config/gnuastro/gnuastro.conf43
-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)2
-rw-r--r--reproduce/software/make/basic.mk10
-rw-r--r--reproduce/software/make/high-level.mk16
-rw-r--r--reproduce/software/make/python.mk4
-rwxr-xr-xreproduce/software/shell/configure.sh14
15 files changed, 27 insertions, 155 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 d2d5e2c..84962f7 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 7531749..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
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 c53e170..c53e170 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 39642d4..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
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
# ------------------------------------------