From 6ef4cc854d1df46b719de5d66b45537b0aa11f92 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 28 Jul 2019 02:32:20 +0100
Subject: Single wrapper instead of old ./configure, Makefile and ./for-group

Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.

This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).

With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:

   $ ./project configure
   $ ./project make

To work on the project with other users in a group these commands can be
used:

  $ ./project configure --group=GROUPNAME
  $ ./project make      --group=GROUPNAME

The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:

  $ ./project configure -e --host-cc
  $ ./project make -j8

The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.

On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).

This fixes bug #56682.
---
 project | 291 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 291 insertions(+)
 create mode 100755 project

(limited to 'project')

diff --git a/project b/project
new file mode 100755
index 0000000..b366e00
--- /dev/null
+++ b/project
@@ -0,0 +1,291 @@
+#!/bin/bash
+#
+# High-level script to manage the project.
+# Run `./project --help' for a description of how to use it.
+#
+# Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This script 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 script 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. See <http://www.gnu.org/licenses/>.
+
+
+# Basic settings
+# --------------
+# Stop the script if there are any errors.
+set -e
+
+# Default option values
+jobs=0     # 0 is for the default for the `configure.sh' script.
+group=
+debug=
+host_cc=0
+operation=
+build_dir=
+input_dir=
+make_targets=
+software_dir=
+existing_conf=0
+scriptname="./project"
+minmapsize=10000000000
+
+
+
+
+
+# Parse the options
+# -----------------
+#
+# Separate command-line arguments from options. Then put the option value
+# into the respective variable.
+#
+# Each option has two lines because we want to process both these formats:
+# `--name=value' and `--name value'. The former (with `=') is a single
+# command-line argument, so we just need to shift the counter by one. The
+# latter (without `=') is two arguments, so we'll need two shifts.
+#
+# Note on the case strings: for every option, we need three lines: one when
+# the option name and value are separate. Another when there is an equal
+# between them, and finally one where the value is immediately after the
+# short-format. This exact order is important. Otherwise, there will be a
+# conflict between them.
+
+print_help() {
+    # Print the output.
+    cat <<EOF
+Usage: $scriptname configure [OPTIONS]
+       $scriptname make      [OPTIONS]
+
+Top-level script to manage the reproducible project. The high-level
+operation is defined by the (mandatory) second argument:
+
+  configure    - Configure project for this machine (e.g., build software).
+  make         - Run the project (do analysis and build outputs).
+
+RECOMMENDATION: If this is the first time you are configuring this
+template, please don't use the options and let the script explain each
+parameter in full detail by simply running './project configure'.
+
+With the options below you can modify the default behavior.
+
+Configure options:
+  -b, --build-dir=STR     Top directory to build the project in.
+  -e, --existing-conf     Use (possibly existing) local configuration.
+      --host-cc           Use host system's C compiler, don't build GCC.
+  -i, --input-dir=STR     Directory containing input datasets (optional).
+  -m, --minmapsize=INT    [Gnuastro] Minimum number of bytes to use RAM.
+  -s, --software-dir=STR  Directory containing necessary software tarballs.
+
+Configure and Make options:
+  -g, --group=STR         Build and run with write permissions for a group.
+  -j, --jobs=INT          Number of threads to build/run the software.
+  -?, --help              Print this help list.
+
+Make options:
+  -d, --debug=FLAGS       Print various types of debugging information.
+
+Mandatory or optional arguments to long options are also mandatory or optional
+for any corresponding short options.
+
+Reproducible paper template: https://gitlab.com/makhlaghi/reproducible-paper
+
+Report bugs to mohammad@akhlaghi.org
+EOF
+}
+
+on_off_option_error() {
+    if [ "x$2" = x ]; then
+        echo "$scriptname: '$1' doesn't take any values."
+    else
+        echo "$scriptname: '$1' (or '$2') doesn't take any values."
+    fi
+    exit 1
+}
+
+check_v() {
+    if [ x"$2" = x ]; then
+        echo "$scriptname: option '$1' requires an argument."
+        echo "Try '$scriptname --help' for more information."
+        exit 1;
+    fi
+}
+
+func_operation_set() {
+    if [ x$operation = x ]; then
+        operation=$1
+    else
+        echo "Only one operation ('configure' or 'make') may be given."
+        exit 1
+    fi
+}
+
+while [[ $# -gt 0 ]]
+do
+ case $1 in
+  # Main operation.
+  configure)    func_operation_set $1; shift;;
+  make)         func_operation_set $1; shift;;
+
+
+  # Configure options:
+  -b|--builddir)         build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
+  -b=*|--build-dir=*)    build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
+  -b*)                   build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
+  -e|--existing-conf)    existing_conf=1;                                                          shift;;
+  -e*|--existing-conf=*) on_off_option_error --existing-conf -e;;
+  --host-cc)             host_cc=1;                                                                shift;;
+  --host-cc=*)           on_off_option_error --host-cc;;
+  -i|--inputdir)         input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
+  -i=*|--inputdir=*)     input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
+  -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//'); check_v "$1" "$input_dir";    shift;;
+  -m|--minmapsize)       minmapsize="$2";                            check_v "$1" "$minmapsize";   shift;shift;;
+  -m=*|--minmapsize=*)   minmapsize="${1#*=}";                       check_v "$1" "$minmapsize";   shift;;
+  -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//'); check_v "$1" "$minmapsize";   shift;;
+  -s|--software-dir)     software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
+  -s=*|--software-dir=*) software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
+  -s*)                   software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
+
+  # Configure and Make options:
+  -g|--group)             group="$2";                            check_v group "$group";   shift;shift;;
+  -g=*|--group=*)         group="${1#*=}";                       check_v group "$group";   shift;;
+  -g*)                    group=$(echo   "$1" | sed -e's/-g//'); check_v group "$group";   shift;;
+  -j|--jobs)              jobs="$2";                             check_v jobs  "$jobs";    shift;shift;;
+  -j=*|--jobs=*)          jobs="${1#*=}";                        check_v jobs  "$jobs";    shift;;
+  -j*)                    jobs=$(echo "$1" | sed -e's/-j//');    check_v jobs  "$jobs";    shift;;
+  -'?'|--help)            print_help; exit 0;;
+  -'?'*|--help=*)         on_off_option_error --help -?;;
+
+  # Make options (note that Make's `debug' can take values, but when called
+  # without any value, it is like giving it a value of `a'):
+  -d|--debug)             if [ x"$2" = x ]; then debug=a;          shift;
+                          else debug="$2"; check_v debug "$debug"; shift;shift; fi;;
+  -d=*|--debug=*)         debug="${1#*=}";                       check_v debug "$debug";   shift;;
+  -d*)                    debug=$(echo "$1" | sed -e's/-d//');   check_v debug "$debug";   shift;;
+
+  # Unrecognized option:
+  -*) echo "$scriptname: unknown option '$1'"; exit 1;;
+
+  # Not an option, an argument (so its a Make target).
+  *) make_targets="$make_targets $1"; shift;;
+ esac
+done
+
+
+
+
+
+# Basic group settings
+# --------------------
+if ! [ x$group = x ]; then
+
+    # Check if group is usable.
+    if ! sg "$group" "echo test &> /dev/null" &> /dev/null; then
+        echo "$scriptname: '$group' is not a usable group name on this system.";
+        echo "(TIP: you can use the 'groups' command to see your groups)"
+        exit 1
+    fi
+
+    # Set the group option for running Make.
+    gopt="reproducible_paper_group_name=$group"
+fi
+
+
+
+
+
+# Do requested operation
+# ----------------------
+perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x"
+configscript=./reproduce/software/bash/configure.sh
+case $operation in
+
+    # Build the project's software.
+    configure)
+
+        # Variables to pass to the configuration script.
+        export jobs=$jobs
+        export host_cc=$host_cc
+        export build_dir=$build_dir
+        export input_dir=$input_dir
+        export scriptname=$scriptname
+        export minmapsize=$minmapsize
+        export software_dir=$software_dir
+        export existing_conf=$existing_conf
+        export reproducible_paper_group_name=$group
+
+        # Run the configuration script
+        if [ x"$group" = x ]; then
+            $configscript
+        else
+            # Set the group and permission flags.
+            sg "$group" "umask $perms && $configscript"
+
+            # Set the group writing permission for everything in the
+            # installed software directory. The common build process sets
+            # the writing permissions of the installed programs/libraries
+            # to `755'. So group members can't write over a file. This
+            # creates problems when another group member wants to update
+            # the software for example. We thus need to manually add the
+            # group writing flag to all installed software files.
+            echo "Enabling group writing permission on all installed software..."
+            .local/bin/chmod -R g+w .local/;
+        fi
+        ;;
+
+    # Run the project
+    make)
+
+        # Make sure the configure script has been completed properly
+        # (`configuration-done.txt' exists).
+        if ! [ -f .build/software/configuration-done.txt ]; then
+            cat <<EOF
+
+The project isn't configured for this system, or the configuration wasn't
+successful. To configure the project, please use this command:
+
+      '$ ./project configure'
+
+(TIP: if you have already ran this command once, run it with '-e' to use
+the previous configuration, run with '--help' for more info)
+
+EOF
+            exit 1
+        fi
+
+        # Get the full address of the build directory:
+        bdir=`.local/bin/realpath .build`
+
+
+        # Remove all existing environment variables (with `env -i') and
+        # only use some pre-defined environment variables, then build the
+        # project.
+        envmake=".local/bin/env -i HOME= sys-rm=$(which rm) $gopt"
+        envmake="$envmake .local/bin/make -f reproduce/analysis/make/top.mk"
+        if ! [ x"$debug" = x  ]; then envmake="$envmake --debug=$debug"; fi
+
+        # Set the number of jobs. Note that for the `configure.sh' script
+        # the default value has to be 0, so the default is the maximum
+        # number of threads. But here, the default value is 1.
+        if ! [ x"$jobs"  = x0 ]; then envmake="$envmake -j$jobs";  fi
+
+        # Run the project
+        if [ x"$group" = x ]; then
+            $envmake $make_targets
+        else
+            # Set the group and permission flags.
+            sg "$group" "umask $perms && $envmake $make_targets"
+        fi
+        ;;
+
+    # Operation not specified.
+    *)
+        echo "No operation defined (you can give 'configure' or 'make')."
+        exit 1
+    ;;
+esac
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