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).

1 files changed, 120 insertions, 0 deletions

diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
new file mode 100644
index 0000000..a8c8731
--- /dev/null
+++ b/reproduce/software/make/build-rules.mk
@@ -0,0 +1,120 @@
+# Generic configurable recipes to build packages with GNU Build system or
+# CMake. This is Makefile is not intended to be run directly, it will be
+# imported into `dependencies-basic.mk' and `dependencies.mk'. They should
+# be activated with Make's `Call' function.
+#
+# Copyright (C) 2018-2019 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/>.
+
+
+
+
+
+# IMPORTANT note
+# --------------
+#
+# Without using `&&', if a step fails, the process will continue. However,
+# in the `if' statements, we need `;' (particularly between `]' and
+# `then'). So we need to put any necessary checks at the start, then when
+# we start the process, every command will be separated by an `&&'.
+
+
+
+
+
+# GNU Build system
+# ----------------
+#
+# Arguments:
+#  1: Tarball full address.
+#  2: Directory name after unpacking.
+#  3: Set to `static' for a static build.
+#  4: Extra configuration options.
+#  5: Extra options/arguments to pass to Make.
+#  6: Step to run between `make' and `make install': usually `make check'.
+#  7: The configuration script (`configure' by default).
+#  8: Arguments for `make install'.
+#
+# NOTE: Unfortunately the configure script of `zlib' doesn't recognize
+# `SHELL'. So we'll have to remove it from the call to the configure
+# script.
+#
+# NOTE: A program might not contain any configure script. In this case,
+# we'll just pass a non-relevant function like `pwd'. So SED should be used
+# to modify `confscript' or to set `configop'.
+gbuild = if [ x$(static_build) = xyes ] && [ "x$(3)" = xstatic ]; then        \
+	   export LDFLAGS="$$LDFLAGS -static";                                \
+	 fi;                                                                  \
+	 check="$(6)";                                                        \
+	 if [ x"$$check" = x ]; then check="echo Skipping-check"; fi;         \
+	 cd $(ddir); rm -rf $(2);                                             \
+	 if ! tar xf $(1); then echo; echo "Tar error"; exit 1; fi;           \
+	 cd $(2);                                                             \
+                                                                              \
+	 if   [ x"$(strip $(7))" = x ]; then confscript=./configure;          \
+	 else confscript="$(strip $(7))";                                     \
+	 fi;                                                                  \
+                                                                              \
+	 if   [ -f $(ibdir)/bash ]; then                                      \
+	   if [ -f $$confscript ]; then                                       \
+	     sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|'                       \
+	         -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|'                        \
+	         $$confscript > $$confscript-tmp;                             \
+	     mv $$confscript-tmp $$confscript;                                \
+	     chmod +x $$confscript;                                           \
+	   fi;                                                                \
+	   shellop="SHELL=$(ibdir)/bash";                                     \
+	 elif [ -f /bin/bash ]; then shellop="SHELL=/bin/bash";               \
+	 else shellop="SHELL=/bin/sh";                                        \
+	 fi;                                                                  \
+                                                                              \
+	 if [ -f $$confscript ]; then                                         \
+	   if [ x"$(strip $(2))" = x"zlib-$(zlib-version)" ]; then            \
+	     configop="--prefix=$(idir)";                                     \
+	   else configop="$$shellop --prefix=$(idir)";                        \
+	   fi;                                                                \
+	 fi;                                                                  \
+                                                                              \
+	 echo; echo "Using '$$confscript' to configure:"; echo;               \
+	 echo "$$confscript $(4) $$configop"; echo;                           \
+	 $$confscript $(4) $$configop  &&                                     \
+	 make "$$shellop" $(5) &&                                             \
+	 $$check &&                                                           \
+	 make "$$shellop" install $(8) &&                                     \
+	 cd .. && rm -rf $(2)
+
+
+
+
+# CMake
+# -----
+#
+# According to the link below, in CMake `/bin/sh' is hardcoded, so there is
+# no way to change it.
+#
+# https://stackoverflow.com/questions/21167014/how-to-set-shell-variable-in-makefiles-generated-by-cmake
+cbuild = if [ x$(static_build) = xyes ] && [ $(3)x = staticx ]; then          \
+	   export LDFLAGS="$$LDFLAGS -static";                                \
+	   opts="-DBUILD_SHARED_LIBS=OFF";                                    \
+	 fi;                                                                  \
+	 cd $(ddir) && rm -rf $(2) && tar xf $(1) && cd $(2) &&               \
+	 rm -rf project-build && mkdir project-build &&                       \
+	 cd project-build &&                                                  \
+	 cmake .. -DCMAKE_LIBRARY_PATH=$(ildir)                               \
+	          -DCMAKE_INSTALL_PREFIX=$(idir)                              \
+	          -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON $$opts $(4) &&             \
+	 make && make install &&                                              \
+	 cd ../.. &&                                                          \
+	 rm -rf $(2)