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.

7 files changed, 0 insertions, 585 deletions

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 <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.
-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 <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
-#
-# 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 <mohammad@akhlaghi.org>
-#
-# 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
-# <http://www.gnu.org/licenses/>.
-
-
-
-
-
-# Basic/low-level programs and libraires (installed in any case)
-# --------------------------------------------------------------
-bash-checksum = a93f221fe800908e335584837f63d02a350d9c8b2711f1923e946980b960fb2d4a21e4321f722c70e5faf5554991a6b9ef6722d214a1921f71030896cf134639
-binutils-checksum = a5e1f77e985d7d66e3ec6ed62a51a61c82ed0964a5108a1f318bf717f3f2af4dcd018ec3a66c10d6dc7525bad801b118f468eca07b2502c836895f4091bbeed4
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-
-
-
-
-
-# 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
-# `-checksum' suffix from the list below.
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diff --git a/reproduce/software/config/installation/numpy-scipy.cfg b/reproduce/software/config/installation/numpy-scipy.cfg
deleted file mode 100644
index 82cc1e1..0000000
--- a/reproduce/software/config/installation/numpy-scipy.cfg
+++ /dev/null
@@ -1,47 +0,0 @@
-# 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 <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
-#
-# 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 <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.
-
-
-# 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 \
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-                   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 <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.
-selected_scheme scheme-basic
-TEXDIR @installdir@/texlive/maneage
-TEXMFCONFIG @installdir@/texlive-maneage/texmf-config
-TEXMFLOCAL @installdir@/texlive/texmf-local
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-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 <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
-#
-# 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
-# <http://www.gnu.org/licenses/>.
-
-
-
-
-
-# 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)