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).

3 files changed, 38 insertions, 0 deletions

diff --git a/reproduce/analysis/config/INPUTS.mk b/reproduce/analysis/config/INPUTS.mk
new file mode 100644
index 0000000..eb38295
--- /dev/null
+++ b/reproduce/analysis/config/INPUTS.mk
@@ -0,0 +1,15 @@
+# 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/analysis/config/delete-me-num.mk b/reproduce/analysis/config/delete-me-num.mk
new file mode 100644
index 0000000..17f608c
--- /dev/null
+++ b/reproduce/analysis/config/delete-me-num.mk
@@ -0,0 +1,2 @@
+# Number of samples to create
+delete-me-num = 50
diff --git a/reproduce/analysis/config/pdf-build.mk b/reproduce/analysis/config/pdf-build.mk
new file mode 100644
index 0000000..3a86ff3
--- /dev/null
+++ b/reproduce/analysis/config/pdf-build.mk
@@ -0,0 +1,21 @@
+# 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