Imported recent work in Maneage, minor conflicts fixed

A few minor conflicts came up that were easily fixed.

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
 # ------------------------------------------