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).

2 files changed, 149 insertions, 0 deletions

diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/bash/git-post-checkout
new file mode 100644
index 0000000..9552f01
--- /dev/null
+++ b/reproduce/software/bash/git-post-checkout
@@ -0,0 +1,66 @@
+#!@BINDIR@/bash
+#
+# The example hook script to store the metadata information of version
+# controlled files (with each commit) using the `metastore' program.
+#
+# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
+# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This script is taken from the `examples/hooks/pre-commit' file of the
+# `metastore' package (installed within the project, with an MIT license
+# for copyright). We have just changed the name of the `MSFILE' and also
+# set special characters for the installation location of meta-store so our
+# own installation is found by Git.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to the
+# following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+# NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+# USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+# File containig the metadata and metastore executable.
+MSFILE=".file-metadata"
+MSBIN=@BINDIR@/metastore
+
+# If metastore is not installed, then ignore this script (exit with a
+# status of 0).
+if [ ! -f $MSBIN ]; then exit 0; fi
+
+# Delete all temporary files
+find @TOP_PROJECT_DIR@/ -name "*~" -type f -delete
+
+# Function to help in reporting a crash.
+exit_on_fail() {
+	"$@"
+	if [ $? -ne 0 ]; then
+		echo "Failed to execute: $@" >&2
+		exit 1
+	fi
+}
+
+# Check if the metadata file exists.
+if [ ! -e "$MSFILE" ]; then
+	echo "\"$MSFILE\" missing" >&2
+	exit 1
+fi
+
+# Run metastore.
+exit_on_fail \
+       $MSBIN -a -m -e -E -q -O @USER@ -G @GROUP@ -f "$MSFILE"
+
+# Return with a success code (0).
+exit 0
diff --git a/reproduce/software/bash/git-pre-commit b/reproduce/software/bash/git-pre-commit
new file mode 100644
index 0000000..dbe0ecc
--- /dev/null
+++ b/reproduce/software/bash/git-pre-commit
@@ -0,0 +1,83 @@
+#!@BINDIR@/bash
+#
+# The example hook script to store the metadata information of version
+# controlled files (with each commit) using the `metastore' program.
+#
+# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
+# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# WARNING:
+#
+# If the commit is aborted (e.g. by not entering any synopsis),
+# then updated metastore file (.metadata by default) is not reverted,
+# so its new version remains in the index.
+# To undo any changes in metastore file written since HEAD commit,
+# you may want to reset and checkout HEAD version of the file:
+#
+#     git reset HEAD -- .metadata
+#     git checkout HEAD -- .metadata
+#
+# This script is taken from the `examples/hooks/pre-commit' file of the
+# `metastore' package (installed within the project, with an MIT license
+# for copyright). Here, the name of the `MSFILE' and also set special
+# characters for the installation location of meta-store so our own
+# installation is found by Git.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to the
+# following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
+# NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+# USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+# File containig the metadata and metastore executable.
+MSFILE=".file-metadata"
+MSBIN=@BINDIR@/metastore
+
+# If metastore is not installed, then ignore this script (exit with a
+# status of 0).
+if [ ! -f $MSBIN ]; then exit 0; fi
+
+# Function to help in reporting a crash.
+exit_on_fail() {
+	"$@"
+	if [ $? -ne 0 ]; then
+		echo "Failed to execute: $@" >&2
+		exit 1
+	fi
+}
+
+# Run metastore.
+exit_on_fail \
+	$MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
+
+# If it's first metastore commit, store again to include $MSFILE in $MSFILE.
+if ! git-ls-tree --name-only HEAD 2>/dev/null | grep -Fqx "$MSFILE"; then
+	exit_on_fail \
+	        $MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
+fi
+
+# Check if the metadata file exists.
+if [ ! -e "$MSFILE" ]; then
+	echo "\"$MSFILE\" missing" >&2
+	exit 1
+fi
+
+# Add the metadata file to the Git repository.
+exit_on_fail \
+	git-add "$MSFILE"
+
+# Return with a success code (0).
+exit 0