New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

8 files changed, 0 insertions, 280 deletions

diff --git a/reproduce/config/pipeline/INPUTS.mk b/reproduce/config/pipeline/INPUTS.mk
deleted file mode 100644
index eb38295..0000000
--- a/reproduce/config/pipeline/INPUTS.mk
+++ /dev/null
@@ -1,15 +0,0 @@
-# Input files necessary for this project.
-#
-# This file is read by the configure script and running Makefiles.
-#
-# Copyright (C) 2018-2019 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.
-
-WFPC2IMAGE = WFPC2ASSNu5780205bx.fits
-WFPC2MD5   = a4791e42cd1045892f9c41f11b50bad8
-WFPC2SIZE  = 62kb
-WFPC2URL   = https://fits.gsfc.nasa.gov/samples
diff --git a/reproduce/config/pipeline/LOCAL.mk.in b/reproduce/config/pipeline/LOCAL.mk.in
deleted file mode 100644
index 785bb6a..0000000
--- a/reproduce/config/pipeline/LOCAL.mk.in
+++ /dev/null
@@ -1,16 +0,0 @@
-# Local project configuration.
-#
-# This is just a template for the `./configure' script to fill in. Please
-# don't make any change to this file.
-#
-# Copyright (C) 2018-2019 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@
-DOWNLOADER       = @downloader@
-GROUP-NAME       = @groupname@
diff --git a/reproduce/config/pipeline/delete-me-num.mk b/reproduce/config/pipeline/delete-me-num.mk
deleted file mode 100644
index 17f608c..0000000
--- a/reproduce/config/pipeline/delete-me-num.mk
+++ /dev/null
@@ -1,2 +0,0 @@
-# Number of samples to create
-delete-me-num = 50
diff --git a/reproduce/config/pipeline/dependency-numpy-scipy.cfg b/reproduce/config/pipeline/dependency-numpy-scipy.cfg
deleted file mode 100644
index 4b7a7b0..0000000
--- a/reproduce/config/pipeline/dependency-numpy-scipy.cfg
+++ /dev/null
@@ -1,46 +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) 2018-2019 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.
-
-# 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/config/pipeline/dependency-texlive.mk b/reproduce/config/pipeline/dependency-texlive.mk
deleted file mode 100644
index 0acf5ab..0000000
--- a/reproduce/config/pipeline/dependency-texlive.mk
+++ /dev/null
@@ -1,22 +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) 2018-2019 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   \
-                   preprint ulem biblatex biber logreq pgf pgfplots fp    \
-                   courier tex-gyre txfonts times
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
deleted file mode 100644
index c6c8043..0000000
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ /dev/null
@@ -1,123 +0,0 @@
-# Versions of the various dependencies
-#
-# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019 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/>.
-
-# C/C++ programs and libraries.
-atlas-version              = 3.10.3
-bash-version               = 5.0
-binutils-version           = 2.31.1
-cfitsio-version            = 3.45
-cmake-version              = 3.12.4
-coreutils-version          = 8.30
-curl-version               = 7.63.0
-diffutils-version          = 3.7
-fftw-version               = 3.3.8
-file-version               = 5.36
-findutils-version          = 4.6.0.199-e3fc
-flock-version              = 0.2.3
-freetype-version           = 2.9
-gawk-version               = 4.2.1
-gcc-version                = 8.3.0
-ghostscript-version        = 9.26
-git-version                = 2.20.1
-gmp-version                = 6.1.2
-gnuastro-version           = 0.8
-grep-version               = 3.3
-gsl-version                = 2.5
-gzip-version               = 1.10
-hdf5-version               = 1.10.5
-isl-version                = 0.18
-libbsd-version             = 0.9.1
-libffi-version             = 3.2.1
-libjpeg-version            = v9b
-libpng-version             = 1.6.36
-libtiff-version            = 4.0.10
-libtool-version            = 2.4.6
-lzip-version               = 1.20
-m4-version                 = 1.4.18
-make-version               = 4.2.90
-metastore-version          = 1.1.2-23-fa9170b
-mpfr-version               = 4.0.2
-mpc-version                = 1.1.0
-ncurses-version            = 6.1
-openblas-version           = 0.3.5
-openmpi-version            = 4.0.1
-openssl-version            = 1.1.1a
-patchelf-version           = 0.9
-pkgconfig-version          = 0.29.2
-python-version             = 3.6.8
-readline-version           = 8.0
-sed-version                = 4.7
-tar-version                = 1.31
-unzip-version              = 6.0
-wget-version               = 1.20.1
-which-version              = 2.21
-xz-version                 = 5.2.4
-zip-version                = 3.0
-zlib-version               = 1.2.11
-
-# Special 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.
-bzip2-version              = 1.0.6
-lapack-version             = 3.8.0
-libgit2-version            = 0.26.0
-wcslib-version             = 6.2
-
-# Python packages
-# ---------------
-#
-# IMPORTANT: Fix url in `reproduce/src/make/dependencies.mk'
-# if changing the version
-asn1crypto-version         = 0.24.0
-astroquery-version         = 0.3.9
-astropy-version            = 3.1.1
-beautifulsoup4-version     = 4.7.1
-certifi-version            = 2018.11.29
-cffi-version               = 1.12.2
-chardet-version            = 3.0.4
-cryptography-version       = 2.6.1
-cycler-version             = 0.10.0
-cython-version             = 0.29.6
-entrypoints-version        = 0.3
-h5py-version               = 2.9.0
-html5lib-version           = 1.0.1
-idna-version               = 2.8
-jeepney-version            = 0.4
-kiwisolver-version         = 1.0.1
-keyring-version            = 18.0.0
-matplotlib-version         = 3.0.2
-mpi4py-version             = 3.0.1
-numpy-version              = 1.16.2
-pip-version                = 19.0.2
-pycparser-version          = 2.19
-pyparsing-version          = 2.3.1
-pypkgconfig-version        = 1.5.1
-python-dateutil-version    = 2.8.0
-requests-version           = 2.21.0
-scipy-version              = 1.2.1
-secretstorage-version      = 3.1.1
-setuptools-version         = 40.8.0
-setuptools_scm-version     = 3.2.0
-six-version                = 1.12.0
-soupsieve-version          = 1.8
-urllib3-version            = 1.24.1
-virtualenv-version         = 16.4.0
-webencodings-version       = 0.5.1
diff --git a/reproduce/config/pipeline/pdf-build.mk b/reproduce/config/pipeline/pdf-build.mk
deleted file mode 100644
index 3a86ff3..0000000
--- a/reproduce/config/pipeline/pdf-build.mk
+++ /dev/null
@@ -1,21 +0,0 @@
-# Make the final PDF?
-# -------------------
-#
-# During the project's early phases, it is usually not necessary to build
-# the PDF file (which makes a lot of output lines on the command-line and
-# can make it hard to find the commands and possible errors (and their
-# outputs). Also, in some cases, only the produced results may be of
-# interest and not the final PDF, so LaTeX (and its necessary packages) may
-# not be installed.
-#
-# If this variable is given any string, a PDF will be made with
-# LaTeX. Otherwise, a notice will just printed that for now, no PDF will be
-# created.
-#
-# Copyright (C) 2018-2019 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.
-pdf-build-final = yes
diff --git a/reproduce/config/pipeline/texlive.conf b/reproduce/config/pipeline/texlive.conf
deleted file mode 100644
index 53054e1..0000000
--- a/reproduce/config/pipeline/texlive.conf
+++ /dev/null
@@ -1,35 +0,0 @@
-# Basic profile for build. Values to set:
-#
-# installdir: Install directory
-#
-# Copyright (C) 2018-2019 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/2018
-TEXMFCONFIG @installdir@/texlive2018/texmf-config
-TEXMFLOCAL @installdir@/texlive/texmf-local
-TEXMFSYSCONFIG @installdir@/texlive/2018/texmf-config
-TEXMFSYSVAR @installdir@/texlive/2018/texmf-var
-TEXMFVAR @installdir@/texlive2018/texmf-var
-instopt_adjustpath 0
-instopt_adjustrepo 1
-instopt_letter 0
-instopt_portable 0
-instopt_write18_restricted 1
-tlpdbopt_autobackup 1
-tlpdbopt_backupdir @installdir@/texlive/2018/backups
-tlpdbopt_create_formats 1
-tlpdbopt_desktop_integration 1
-tlpdbopt_file_assocs 1
-tlpdbopt_generate_updmap 0
-tlpdbopt_install_docfiles 1
-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