path: root/configure

#! /bin/bash
#
# Necessary preparations/configurations for the reproduction pipeline.
#
# Copyright (C) 2018-2019 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.
#
# A copy of the GNU General Public License is available at
# <http://www.gnu.org/licenses/>.


# Script settings
# ---------------
# Stop the script if there are any errors.
set -e





# Default option values
jobs=0
build_dir=
input_dir=
host_cc=0
software_dir=
existing_conf=0
minmapsize=10000000000
scriptname="./configure"





# Output of --help
# ----------------
print_help() {
    # Print the output.
    cat <<EOF
Usage: $scriptname [OPTION]...

Configure the reproducible paper template for this system (set local
settings for this system). The local settings can be given on the
command-line through the options below. If not, the configure script will
interactively ask for a value to each one (with basic necessary background
information printed before them). Alternatively, if you have already
configured this script for your system, you can use the '--existing-conf'
to use its values directly.

RECOMMENDATION: If this is the first time you are running this pipeline,
please don't use the options and let the script explain each parameter in
full detail by simply running './configure'.

The only mandatory value for this script is the local build directory. This
is where all the pipeline's outputs will be stored. Optionally, you can
also provide directories that host input data, or software source codes. If
the necessary files don't exist there, the template will automatically
download them.

With the options below you can modify the default behavior. Just note that
you should not put an '=' sign between an option name and its value.

Configure options:
 Top-level directory settings:
  -b, --build-dir=STR     Top directory to build the project in.
  -i, --input-dir=STR     Directory containing input datasets (optional).
  -s, --software-dir=STR  Directory containing necessary software tarballs.

 Operating mode options:
      --host-cc           Use host system's C compiler, don't build GCC.
  -m, --minmapsize=INT    (Gnuastro) Minimum number of bytes to use RAM.
  -j, --jobs=INT          Number of threads to build the software.
  -e, --existing-conf     Use (possibly existing) local configuration.
  -h, --help              Print this help list.

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
}





# Functions to check option values and complain if necessary.
function 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
}

function check_v() {
    if [ x"$2" = x ]; then
        echo "$scriptname: option '$1' requires an argument."
        echo "Try '$scriptname --help' for more information."
        exit 1;
    fi
}





# 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.
while [[ $# -gt 0 ]]
do
 case $1 in
  # Input parameters.
  -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;;
  -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;;
  -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;;
  -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;;

  # Operating mode options
  --host-cc)              host_cc=1;                                                shift;;
  --host-cc=*)            on_off_option_error --host-cc;;
  -j|--jobs)              jobs="$2";                          check_v "$1" "$jobs"; shift;shift;;
  -j=*|--jobs=*)          jobs="${1#*=}";                     check_v "$1" "$jobs"; shift;;
  -j*)                    jobs=$(echo "$1" | sed -e's/-j//'); check_v "$1" "$jobs"; shift;;
  -e|--existing-conf)     existing_conf=1;                                          shift;;
  -e*|--existing-conf=*)  on_off_option_error --existing-conf -e;;
  -?|--help)              print_help; exit 0;;
  -'?'*|--help=*)         on_off_option_error --help -?;;

  # Unrecognized option:
  -*) echo "$scriptname: unknown option '$1'"; exit 1;;

  # Not an option, an argument.
  *) echo "The configure script doesn't accept arguments.";
     echo "For a description of options, please run with '--help'."; exit 1;;
 esac
done





# Internal directories
# --------------------
#
# These are defined to help make this script more readable.
topdir=$(pwd)
lbdir=.build
installedlink=.local
cdir=reproduce/config
optionaldir="/optional/path"

pdir=$cdir/pipeline
pconf=$pdir/LOCAL.mk
ptconf=$pdir/LOCAL_tmp.mk
poconf=$pdir/LOCAL_old.mk
# --------- Delete for no Gnuastro ---------
glconf=$cdir/gnuastro/gnuastro-local.conf
# ------------------------------------------





# Delete final target of configuration
# ------------------------------------
#
# Without the top-level `Makefile' the user can't run `make' in this
# directory. But we only want to make it available when we know everything
# else is set up. So we'll delete it at the start of this configuration and
# reset the link in the absolute end.
rm -f Makefile





# Notice for top of generated files
# ---------------------------------
#
# In case someone opens the files output from the configuration scripts in
# a text editor and wants to edit them, it is important to let them know
# that their changes are not going to be permenant.
function create_file_with_notice() {
    if echo "# IMPORTANT: file can be RE-WRITTEN after './configure'"  > "$1"
    then
        echo "#"                                                      >> "$1"
        echo "# This file was created during the reproduction"        >> "$1"
        echo "# pipeline's configuration ('./configure'). Therefore," >> "$1"
        echo "# it is not under version control and any manual "      >> "$1"
        echo "# changes to it will be over-written if the pipeline "  >> "$1"
        echo "# is re-configured."                                    >> "$1"
        echo "#"                                                      >> "$1"
    else
        echo; echo "Can't write to "$1""; echo;
        exit 1
    fi
}





# Get absolute address
# --------------------
#
# Since the build directory will go into a symbolic link, we want it to be
# an absolute address. With this function we can make sure of that.
function absolute_dir() {
    if stat "$1" 1> /dev/null; then
        echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
    else
        exit 1;
    fi
}





# Inform the user
# ---------------
#
# Print some basic information so the user gets a feeling of what is going
# on and is prepared on what will happen next.
cat <<EOF

-----------------------------------------
Reproduction pipeline local configuration
-----------------------------------------

Local configuration includes things like top-level directories, or
processing steps.

It is STRONGLY recommended to read the comments, and set the best values
for your system (where necessary).

EOF





# What to do with possibly existing configuration file
# ----------------------------------------------------
#
# `LOCAL.mk' is the top-most local configuration for the pipeline. If it
# already exists when this script is run, we'll make a copy of it as backup
# (for example the user might have ran `./configure' by mistake).
printnotice=yes
rewritepconfig=yes
rewritegconfig=yes
if [ -f $pconf ] || [ -f $glconf ]; then
    if [ $existing_conf = 1 ]; then
        printnotice=no
        if [ -f $pconf  ]; then rewritepconfig=no; fi
        if [ -f $glconf ]; then rewritegconfig=no; fi
    fi
fi




# Make sure the group permissions satisfy the previous configuration (if it
# exists and we don't want to re-write it).
if [ $rewritepconfig = no ]; then
    oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf)
    if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then
        just_a_place_holder_to_avoid_not_equal_test=1;
    else
        echo "-----------------------------"
        echo "!!!!!!!!    ERROR    !!!!!!!!"
        echo "-----------------------------"
        if [ "x$oldgroupname" = x ]; then
            status="NOT configured for groups"
            confcommand="./configure"
        else
            status="configured for '$oldgroupname' group"
            confcommand="./for-group $oldgroupname configure"
        fi
        echo "Previous pipeline was $status!"
        echo "Either enable re-write of this configuration file,"
        echo "or re-run this configuration like this:"
        echo
        echo "   $confcommand"; echo
        exit 1
    fi
fi





# Identify the downloader tool
# ----------------------------
#
# After this `./configure' script finishes, we will have both Wget and cURL
# for downloading any necessary dataset during the processing. However, to
# complete the configuration, we may also need to download the source code
# of some necessary software packages (including the downloaders). So we
# need to check the host's available tool for downloading at this step.
if [ $rewritepconfig = yes ]; then
    if type wget > /dev/null 2>/dev/null; then
        name=$(which wget)

        # By default Wget keeps the remote file's timestamp, so we'll have
        # to disable it manually.
        downloader="$name --no-use-server-timestamps -O";
    elif type curl > /dev/null 2>/dev/null; then
        name=$(which curl)

        # - cURL doesn't keep the remote file's timestamp by default.
        # - With the `-L' option, we tell cURL to follow redirects.
        downloader="$name -L -o"
    else
        cat <<EOF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Couldn't find GNU Wget, or cURL on this system. These programs are used for
downloading necessary programs and data if they aren't already present (in
directories that you can specify with this configure script). Therefore if
the necessary files are not present, the pipeline will crash.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
        downloader="no-downloader-found"
    fi;
fi





# Build directory
# ---------------
if [ $rewritepconfig = yes ]; then
    cat <<EOF

===============
Build directory
===============

The project's "source" (this directory) and "build" directories are treated
separately. This greatly helps in managing the many intermediate files that
are created during the build. The intermediate build files don't need to be
archived or backed up: you can always re-build them with the contents of
the source directory. The build directory also needs a relatively large
amount of free space (atleast serveral Giga-bytes), while the source
directory (all plain text) will usually be a mega-byte or less.

'$lbdir' (a symbolic link to the build directory) will also be created
during this configuration. It can help encourage you to set the actual
build directory in a very different address from this one (one that can be
deleted and has large volume), while having easy access to it from here.

EOF
    bdir=
    junkname=pure-junk-974adfkj38
    while [ x$bdir == x ]
    do
        # Ask the user (if not already set on the command-line).
        if [ x"$build_dir" = x ]; then
            read -p"Please enter the top build directory: " build_dir
        fi

        # If it exists, see if we can write in it. If not, try making it.
        if [ -d $build_dir ]; then
            if mkdir $build_dir/$junkname 2> /dev/null; then
                bdir=$(absolute_dir $build_dir)
                echo " -- Build directory: '$bdir'"
                rm -rf $build_dir/$junkname
            else
                echo " -- Can't write in '$build_dir'"
            fi
        else
            if mkdir $build_dir 2> /dev/null; then
                bdir=$(absolute_dir $build_dir)
                echo " -- Build directory set to (the newly created): '$bdir'"
            else
                echo " -- Can't create '$build_dir'"
            fi
        fi

        # Reset `build_dir' to blank, so it continues asking when the
        # previous value wasn't usable.
        build_dir=
    done
fi





# Input directory
# ---------------
if [ x"$input_dir" = x ]; then
    indir=$optionaldir
else
    indir=$input_dir
fi
wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $pdir/INPUTS.mk)
wfpc2md5=$(awk  '!/^#/ && $1=="WFPC2MD5"   {print $3}' $pdir/INPUTS.mk)
wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE"  {print $3}' $pdir/INPUTS.mk)
wfpc2url=$(awk  '!/^#/ && $1=="WFPC2URL"   {print $3}' $pdir/INPUTS.mk)
if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
    cat <<EOF

----------------------------------
(OPTIONAL) Input dataset directory
----------------------------------

This pipeline needs the dataset(s) listed below. If you already have them,
please specify the directory hosting them on this system. If you don't,
they will be downloaded automatically. Each file is shown with its total
volume and its 128-bit MD5 checksum in parenthesis.

  $wfpc2name ($wfpc2size, $wfpc2md5):
    A 100x100 Hubble Space Telescope WFPC II image used in the FITS
    standard webpage as a demonstration of this file format.
    URL: $wfpc2url/$wfpc2name

NOTE I: This directory, or the datasets above, are optional. If it doesn't
exist, the files will be downloaded in the build directory and used.

NOTE II: This directory (if given) will only be read, nothing will be
written into it, so no writing permissions are necessary.

TIP: If you have these files in multiple directories on your system and
don't want to download them or make duplicates, you can create symbolic
links to them and put those symbolic links in the given top-level
directory.

EOF
    read -p"(OPTIONAL) Input datasets directory ($indir): " inindir
    if [ x$inindir != x ]; then
        indir=$inindir
        echo " -- Using '$indir'"
    fi
fi





# Dependency tarball directory
# ----------------------------
if [ x"$software_dir" = x ]; then
    ddir=$optionaldir
else
    ddir=$software_dir
fi
if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then
    cat <<EOF

---------------------------------------
(OPTIONAL) Software tarball directory
---------------------------------------

To ensure an identical build environment, the pipeline will use its own
build of the programs it needs. Therefore the tarball of the relevant
programs are necessary for this pipeline. If a tarball isn't present in the
specified directory, *IT WILL BE DOWNLOADED* by the pipeline.

Therefore, if you don't specify any directory here, or it doesn't contain
the tarball of a dependency, it is necessary to have an internet
connection. The pipeline will download the tarballs it needs automatically.

EOF
    read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir
    if [ x"$tmpddir" != x ]; then
        ddir=$tmpddir
        echo " -- Using '$ddir'"
    fi
fi





# Write the parameters into the local configuration file.
if [ $rewritepconfig = yes ]; then

    # Make the pipeline configuration's initial comments.
    create_file_with_notice $pconf

    # Write the values.
    sed -e's|@bdir[@]|'"$bdir"'|'              \
        -e's|@indir[@]|'"$indir"'|'            \
        -e's|@ddir[@]|'"$ddir"'|'              \
        -e's|@downloader[@]|'"$downloader"'|'  \
        -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
        $pconf.in >> $pconf
else
    # Read the values from existing configuration file.
    inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)

    # Read the software directory.
    ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)

    # The downloader command may contain multiple elements, so we'll just
    # change the (in memory) first and second tokens to empty space and
    # write the full line (the original file is unchanged).
    downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf)

    # Make sure all necessary variables have a value
    err=0
    verr=0
    novalue=""
    if [ x"$inbdir"     = x ]; then novalue="BDIR, ";              fi
    if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER;  fi
    if [ x"$novalue"   != x ]; then verr=1; err=1;                 fi

    # Make sure `bdir' is an absolute path and it exists.
    berr=0
    ierr=0
    bdir=$(absolute_dir $inbdir)

    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
    if [ $err = 1 ]; then
        cat <<EOF

#################################################################
########  ERORR reading existing configuration file  ############
#################################################################
EOF
        if [ $verr = 1 ]; then
            cat <<EOF

These variables have no value: $novalue.
EOF
        fi
        if [ $berr = 1 ]; then
           cat <<EOF

Couldn't create the build directory '$bdir' (value to 'BDIR') in
'$pconf'.
EOF
        fi

        cat <<EOF

Please run the configure script again (accepting to re-write existing
configuration file) so all the values can be filled and checked.
#################################################################
EOF
    fi
fi





# --------- Delete for no Gnuastro ---------
# Get the version of Gnuastro that must be used.
depverfile=reproduce/config/pipeline/dependency-versions.mk
gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile)

# Gnuastro's local configuration settings
if [ $rewritegconfig = yes ]; then
    create_file_with_notice $glconf
    echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf
    echo " minmapsize $minmapsize"                                  >> $glconf
    echo                                                            >> $glconf
    echo "# Version of Gnuastro that must be used."                 >> $glconf
    echo " onlyversion $gversion"                                   >> $glconf
else
    ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf)
    if [ x$ingversion != x$gversion ]; then
        echo "______________________________________________________"
        echo "!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!"
        echo
        echo "Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball version that this pipeline was designed to use in '$depverfile' ($gversion). Please re-run after removing the former file:"
        echo
        echo "   $ rm $glconf"
        echo "   $ ./configure"
        echo
        echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
        echo
        exit 1
    fi
fi
# ------------------------------------------





# Setup the top-level directories
# -------------------------------
rm -f $lbdir
ln -s $bdir $lbdir

depdir=$bdir/dependencies
if ! [ -d $depdir ];  then mkdir $depdir; fi

tardir=$depdir/tarballs
if ! [ -d $tardir ];  then mkdir $tardir; fi

instdir=$depdir/installed
if ! [ -d $instdir ]; then mkdir $instdir; fi

verdir=$instdir/version-info
if ! [ -d $verdir ]; then mkdir $verdir; fi

ibidir=$verdir/bin
if ! [ -d $ibidir ]; then mkdir $ibidir; fi

ilidir=$verdir/lib
if ! [ -d $ilidir ]; then mkdir $ilidir; fi

ipydir=$verdir/python
if ! [ -d $ipydir ]; then mkdir $ipydir; fi

ictdir=$verdir/cite
if ! [ -d $ictdir ]; then mkdir $ictdir; fi

itidir=$verdir/tex
if ! [ -d $itidir ]; then mkdir $itidir; fi

texdir=$bdir/tex
if ! [ -d $texdir ]; then mkdir $texdir; ln -s $texdir tex/pipeline; fi

mtexdir=$texdir/macros
if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi

rm -f $installedlink
ln -s $instdir $installedlink
# --------- Delete for no Gnuastro ---------
rm -f .gnuastro
ln -s $(pwd)/reproduce/config/gnuastro .gnuastro
# ------------------------------------------





# See if the C compiler can build static libraries
# ------------------------------------------------

# We are manually only working with shared libraries: because some
# high-level programs like Wget and cURL need dynamic linking and if we
# build the libraries statically, our own builds will be ignored and these
# programs will go and find their necessary libraries on the host system.
#
# Another good advantage of shared libraries is that we can actually use
# the shared library tool of the system (`ldd' with GNU C Library) and see
# exactly where each linked library comes from. But in static building,
# unless you follow the build closely, its not easy to see if the source of
# the library came from the system or our build.
static_build=no

#oprog=$depdir/static-test
#cprog=$depdir/static-test.c
#echo "#include <stdio.h>"          > $cprog
#echo "int main(void) {return 0;}" >> $cprog
#if [ x$CC = x ]; then CC=gcc; fi;
#if $CC $cprog -o$oprog -static &> /dev/null; then
#    export static_build="yes"
#else
#    export static_build="no"
#fi
#rm -f $oprog $cprog
#if [ $printnotice = yes ] && [ $static_build = "no" ]; then
#    cat <<EOF
#_________________________________________________________________________
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!      WARNING      !!!!!!!!!!!!!!!!!!!!!!!!!!
#
#Your system's C compiler ('$CC') doesn't support building static
#libraries. Therefore the dependencies will be built dynamically. This means
#that they will depend more strongly on changes/updates in the host
#system. For high-level applications (like most research projects in natural
#sciences), this shouldn't be a significant problem.
#
#But generally, for reproducibility, its better to build static libraries
#and programs. For more on their difference (and generally an introduction
#on linking), please see the link below:
#
#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html
#
#If you have other compilers on your system, you can select a different
#compiler by setting the 'CC' environment variable before running
#'./configure'.
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#
#EOF
#    sleep 5
#fi





# See if the linker accepts -Wl,-rpath-link
# -----------------------------------------
#
# `-rpath-link' is used to write the information of the linked shared
# library into the shared object (library or program). But some versions of
# LLVM's linker don't accept it an can cause problems.
oprog=$depdir/rpath-test
cprog=$depdir/rpath-test.c
echo "#include <stdio.h>"          > $cprog
echo "int main(void) {return 0;}" >> $cprog
if [ x$CC = x ]; then CC=gcc; fi;
if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then
    export rpath_command="-Wl,-rpath-link=$instdir/lib"
else
    export rpath_command=""
fi
rm -f $oprog $cprog





# See if we need the dynamic-linker (-ldl)
# ----------------------------------------
#
# Some programs (like Wget) need dynamic loading (using `libdl'). On
# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
# Mac OS doesn't need any explicit calling. So we'll check here to use in
# the building of programs.
oprog=$depdir/ldl-test
cprog=$depdir/ldl-test.c
cat > $cprog <<EOF
#include <stdio.h>
#include <dlfcn.h>
int
main(void) {
    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
    return 0;
}
EOF
if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi
rm -f $oprog $cprog





# inform the user that the build process is starting
# -------------------------------------------------
if [ $printnotice = yes ]; then
    tsec=10
    cat <<EOF

-------------------------
Building dependencies ...
-------------------------

Necessary dependency programs and libraries will be built in $tsec sec.

NOTE: the built software will NOT BE INSTALLED on your system (no root
access is required). They are only for local usage by this reproduction
pipeline. They will be installed in:

  $depdir/installed

EOF
    sleep $tsec
fi





# If we are on a Mac OS system
# ----------------------------
#
# For the time being, we'll use the existance of `otool' to see if we are
# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
# this.
#
# On Mac OS, the building of GCC crashes sometimes while building libiberty
# with CLang's `g++'. Until we find a solution, we'll just use the host's C
# compiler.
if type otool > /dev/null 2>/dev/null; then
    host_cc=1
    on_mac_os=yes
else
    on_mac_os=no
fi





# Build `flock' as first program
# ------------------------------
#
# Flock (or file-lock) is a unique program in the pipeline that is
# necessary to serialize the (generally parallel) processing of make when
# necessary. GNU/Linux machines have it as part of their `util-linux'
# programs. But to be consistent, we will be using our own build.
#
# The reason its sepecial is that we need it to serialize the download
# process of the dependency tarballs.
flockversion=$(awk '/flock-version/{print $3}' $pdir/dependency-versions.mk)
flocktar=flock-$flockversion.tar.gz
flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/

# Prepare/download the tarball.
if ! [ -f $tardir/$flocktar ]; then
    if [ -f $ddir/$flocktar ]; then
        cp $ddir/$flocktar $tardir/$flocktar
    else
        if ! $downloader $tardir/$flocktar $flockurl/$flocktar; then
            rm -f $tardir/$flocktar;
            echo
            echo "DOWNLOAD ERROR: Couldn't download the 'flock' tarball:"
            echo "  $flockurl"
            echo
            echo "You can manually place it in '$ddir' to avoid downloading."
            exit 1
        fi
    fi
fi

# If the tarball is newer than the (possibly existing) program (the version
# has changed), then delete the program.
if [ -f .local/bin/flock ]; then
    if [ $tardir/$flocktar -nt $ibidir/flock ]; then
        rm $ibidir/flock
    fi
fi

# Build `flock' if necessary.
if ! [ -f $ibidir/flock ]; then
    cd $depdir
    tar xf $tardir/$flocktar
    cd flock-$flockversion
    ./configure --prefix=$instdir
    make; make install
    cd $topdir
    rm -rf $depdir/flock-$flockversion
    echo "Discoteq flock $flockversion" > $ibidir/flock
fi





# See if GCC can be built
# -----------------------
#
# On some GNU/Linux distros, the C compiler is broken into `multilib' (for
# 32-bit and 64-bit support, with their own headers). On these systems,
# `sys/cdefs.h' is not available by default. So if the user hasn't manually
# installed it before this configure script, GCC won't build. We are thus
# explicitly testing a small C program here to see if the host's C compiler
# won't have any problems in building GCC.
if [ $host_cc = 0 ]; then
    tfile=$depdir/gcc-cdefs-test.c;
    echo "#include <sys/cdefs.h>"     > $tfile;
    echo "int main(void){return 0;}" >> $tfile;
    if gcc $tfile -o $depdir/gcc-cdefs-test &> /dev/null; then
        rm $depdir/gcc-cdefs-test*;
    else
        host_cc=1
    fi;
    rm -f $tfile;

    if [ $host_cc = 1 ]; then
        cat <<EOF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

This system's C compiler (called with 'gcc') can't include
'sys/cdefs.h. Because of this, this pipeline can't build its custom GCC to
ensure better reproducibility. We strongly recommend installing the proper
package (for your operating system) that installs this necessary file. For
example on some Debian-based GNU/Linux distros, you need these two
packages: 'gcc-multilib' and 'g++-multilib'.

However, since GCC is pretty low-level, this configuration script will
continue in 5 seconds and use your system's C compiler (it won't build a
custom GCC). But please consider installing the necessary package to
complete your C compiler, then re-run the pipeline.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
        sleep 5
    fi
fi





# Build Basic dependencies
# ------------------------
#
# Since the system might not have GNU Make at this stage, and other Make
# implementations can't deal with parallel build properly, we'll just
# default to 1 thread. This is because some versions of Make complain about
# not having enough 'pipe' (memory) on some systems. After some searching,
# I found out its because of too many threads. GNU Make will be present on
# GNU systems (that have `nproc', part of GNU Coreutils). So to simplify
# the test for GNU Make, we'll just try running `nproc'.
if which nproc > /dev/null 2>/dev/null; then
    if [ $jobs = 0 ]; then
        numthreads=$(nproc --all);
    else
        numthreads=$jobs
    fi
else
    numthreads=1;
fi
make -f reproduce/src/make/dependencies-basic.mk \
     rpath_command=$rpath_command                \
     static_build=$static_build                  \
     needs_ldl=$needs_ldl                        \
     on_mac_os=$on_mac_os                        \
     numthreads=$numthreads                      \
     host_cc=$host_cc                            \
     -j$numthreads





# Rest of dependencies
# --------------------
#
# We will be making all the dependencies before running the top-level
# Makefile. To make the job easier, we'll do it in a Makefile, not a
# script. Bash and Make were the tools we need to run Makefiles, so we had
# to build them in this script. But after this, we can rely on Makefiles.
numthreads=$($instdir/bin/nproc)
./.local/bin/make -f reproduce/src/make/dependencies.mk    \
                  rpath_command=$rpath_command             \
                  static_build=$static_build               \
                  on_mac_os=$on_mac_os                     \
                  numthreads=$numthreads                   \
                  -j$numthreads





# Make sure TeX Live installed successfully
# -----------------------------------------
#
# TeX Live is managed over the internet, so if there isn't any, or it
# suddenly gets cut, it can't be built. However, when TeX Live isn't
# installed, the pipeline and can do all its processing independent of
# it. It will just stop at the stage when all the processing is complete
# and it is only necessary to build the PDF.  So we don't want to stop the
# pipeline if its not present.
texlive_result=$(cat $itidir/texlive-ready-tlmgr)
if [ x"$texlive_result" = x"NOT!" ]; then
    cat <<EOF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

TeX Live couldn't be installed during the configuration (probably because
there were downloading problems). TeX Live is only necessary in making the
final PDF (which is only done after all the analysis has been complete). It
is not used at all during the analysis.

Therefore, if you don't need the final PDF, and just want to do the
analysis, you can safely ignore this warning and continue.

If you later have internet access and would like to add TeX live to your
pipeline, please delete the respective files, then re-run configure as
shown below. Within configure, answer 'n' (for "no") when asked to re-write
the configuration files.

    rm .local/version-info/tex/texlive-ready-tlmgr
    ./configure

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
fi





# Citation of installed software
#
# After everything is installed, we'll put all the names and versions in a
# human-readable paragraph and also prepare the BibTeX citation for the
# software.
function prepare_name_version() {

    # First see if the (possible) `*' in the input arguments corresponds to
    # anything. Note that some of the given directories may be empty (no
    # software installed).
    hasfiles=0
    for f in $@; do
        if [ -f $f ]; then hasfiles=1; break; fi;
    done

    # If there are any files, merge all the names in a paragraph.
    if [ $hasfiles = 1 ]; then

        # Count how many names there are. This is necessary to identify the
        # last element.
        num=$(.local/bin/cat $@               \
                  | .local/bin/sed '/^\s*$/d' \
                  | .local/bin/wc -l)

        # Put them all in one paragraph.
        .local/bin/cat $@                                     \
            | .local/bin/sort                                 \
            | .local/bin/awk 'NF>0 {                          \
                  c++;                                        \
                  if(c==1)                                    \
                    {                                         \
                      if('$num'==1) printf("%s", $0);         \
                      else          printf("%s", $0);         \
                    }                                         \
                  else if(c=='$num') printf(" and %s\n", $0); \
                  else printf(", %s", $0)                     \
                }'
    fi
}

# Report the different software in separate contexts (separating Python and
# TeX packages from the C/C++ programs and libraries).
proglibs=$(prepare_name_version $verdir/bin/* $verdir/lib/*)
pymodules=$(prepare_name_version $verdir/python/*)
texpkg=$(prepare_name_version $verdir/tex/texlive)

# Write them as one paragraph for LaTeX.
pkgver=$mtexdir/dependencies.tex
.local/bin/echo "This research was done with the following free" > $pkgver
.local/bin/echo "software programs and libraries: $proglibs."   >> $pkgver
if [ x"$pymodules" != x ]; then
    .local/bin/echo "Within Python, the following modules"      >> $pkgver
    echo "were used: $pymodules."                               >> $pkgver
fi
.local/bin/echo "The \LaTeX{} source of the paper was compiled" >> $pkgver
.local/bin/echo "to make the PDF using the following packages:" >> $pkgver
.local/bin/echo "$texpkg. We are very grateful to all their"    >> $pkgver
.local/bin/echo "creators for freely providing this necessary"  >> $pkgver
.local/bin/echo "infrastructure. This research (and many "      >> $pkgver
.local/bin/echo "others) would not be possible without them."   >> $pkgver

# Prepare the BibTeX entries for the used software (if there are any).
hasentry=0
bibfiles="$ictdir/*"
for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done;

# Make sure we start with an empty file.
pkgbib=$mtexdir/dependencies-bib.tex
echo "" > $pkgbib

# Fill it in with all the BibTeX entries in this directory. We'll just
# avoid writing any comments (usually copyright notices) and also put an
# empty line after each file's contents to make the output more readable.
if [ $hasentry = 1 ]; then
    for f in $bibfiles; do
        awk '!/^%/{print} END{print ""}' $f >> $pkgbib
    done
fi




# Final step: available Makefile
# ------------------------------
#
# We only want `make' to work after the configuration is complete. So we
# will only put in the top-level Makefile after all the steps above are
# done.
.local/bin/ln -s $(pwd)/reproduce/src/make/top.mk Makefile





# Final notice
# ------------
#
# The configuration is now complete, we can inform the user on the next
# step(s) to take.
if [ x$reproducible_paper_group_name = x ]; then
    buildcommand=".local/bin/make -j8"
else
    buildcommand="./for-group $reproducible_paper_group_name make -j8"
fi
cat <<EOF

----------------
The reproduction pipeline and its environment are configured with no errors.

Please run the following command to start.
(Replace '8' with the number of CPU threads)

    $buildcommand

To change the configuration later, please re-run './configure',
DO NOT manually edit the relevant files.

EOF