From 35ed6cf0df743175688b49a4559793cb7f6e9d66 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sat, 1 Feb 2020 21:24:00 +0100
Subject: IMPORTANT: reproduce/software/bash renamed to
reproduce/software/shell
Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.
With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.
---
README-hacking.md | 4 +-
project | 4 +-
reproduce/analysis/make/initialize.mk | 4 +-
reproduce/software/bash/bashrc.sh | 45 -
reproduce/software/bash/configure.sh | 1407 ----------------------------
reproduce/software/bash/git-post-checkout | 66 --
reproduce/software/bash/git-pre-commit | 83 --
reproduce/software/make/README.md | 2 +-
reproduce/software/make/basic.mk | 6 +-
reproduce/software/make/high-level.mk | 4 +-
reproduce/software/shell/bashrc.sh | 45 +
reproduce/software/shell/configure.sh | 1407 ++++++++++++++++++++++++++++
reproduce/software/shell/git-post-checkout | 66 ++
reproduce/software/shell/git-pre-commit | 83 ++
14 files changed, 1613 insertions(+), 1613 deletions(-)
delete mode 100755 reproduce/software/bash/bashrc.sh
delete mode 100755 reproduce/software/bash/configure.sh
delete mode 100755 reproduce/software/bash/git-post-checkout
delete mode 100755 reproduce/software/bash/git-pre-commit
create mode 100755 reproduce/software/shell/bashrc.sh
create mode 100755 reproduce/software/shell/configure.sh
create mode 100755 reproduce/software/shell/git-post-checkout
create mode 100755 reproduce/software/shell/git-pre-commit
diff --git a/README-hacking.md b/README-hacking.md
index 324ada4..244cb23 100644
--- a/README-hacking.md
+++ b/README-hacking.md
@@ -959,8 +959,8 @@ for the benefit of others.
- *Environment of each recipe*: If you need to define a special
environment (or alises, or scripts to run) for all the recipes in
- your Makefiles, you can use the Bash startup file
- `reproduce/software/bash/bashrc.sh`. This file is loaded before every
+ your Makefiles, you can use a Bash startup file
+ `reproduce/software/shell/bashrc.sh`. This file is loaded before every
Make recipe is run, just like the `.bashrc` in your home directory is
loaded everytime you start a new interactive, non-login terminal. See
the comments in that file for more.
diff --git a/project b/project
index 89361ae..f9a7537 100755
--- a/project
+++ b/project
@@ -294,7 +294,7 @@ controlled_env() {
# Do requested operation
# ----------------------
perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x"
-configscript=./reproduce/software/bash/configure.sh
+configscript=./reproduce/software/shell/configure.sh
case $operation in
# Build the project's software.
@@ -314,7 +314,7 @@ case $operation in
# `reproduce/*/bash' should need executable flags, so we are giving
# them executable flags by default. If any other file in your project
# needs such flags, add them here.
- chmod +x reproduce/software/bash/* reproduce/analysis/bash/*
+ chmod +x reproduce/software/shell/* reproduce/analysis/bash/*
# If the user requested, clean the TeX directory from the extra
# (to-be-built) directories that may already be there (and will not
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 1137f28..79f9266 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -156,9 +156,9 @@ export DYLD_LIBRARY_PATH :=
# remote-shell accesss through this environment variable.
export OMPI_MCA_plm_rsh_agent=/bin/false
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
export PROJECT_STATUS := make
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
diff --git a/reproduce/software/bash/bashrc.sh b/reproduce/software/bash/bashrc.sh
deleted file mode 100755
index b2a151f..0000000
--- a/reproduce/software/bash/bashrc.sh
+++ /dev/null
@@ -1,45 +0,0 @@
-# Bash startup file for better control of project environment.
-#
-# To have better control over the environment of each analysis step (Make
-# recipe), besides having environment variables (directly included from
-# Make), it may also be useful to have a Bash startup file (this file). All
-# of the Makefiles set this file as the `BASH_ENV' environment variable, so
-# it is loaded into all the Make recipes within the project.
-#
-# The special `PROJECT_STATUS' environment variable is defined in every
-# top-level Makefile of the project. It defines the the state of the Make
-# that is calling this script. It can have three values:
-#
-# configure_basic
-# ---------------
-# When doing basic configuration, therefore the executed steps cannot
-# make any assumptions about the version of Bash (or any other
-# program). Therefore it is important for any step in this step to be
-# highly portable.
-#
-# configure_highlevel
-# -------------------
-# When building the higher-level programs, so the versions of the
-# most basic tools are set and you may safely assume certain
-# features.
-#
-# make
-# ----
-# When doing the project's analysis: all software have known
-# versions.
-#
-#
-# Copyright (C) 2019-2020 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/>.
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
deleted file mode 100755
index a6fbc4e..0000000
--- a/reproduce/software/bash/configure.sh
+++ /dev/null
@@ -1,1407 +0,0 @@
-#! /bin/sh
-#
-# Necessary preparations/configurations for the reproducible project.
-#
-# Copyright (C) 2018-2020 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
-
-
-
-
-
-# Internal directories
-# --------------------
-#
-# These are defined to help make this script more readable.
-topdir=$(pwd)
-optionaldir="/optional/path"
-adir=reproduce/analysis/config
-cdir=reproduce/software/config
-
-sbdir=$cdir/installation
-
-pconf=$sbdir/LOCAL.conf
-ptconf=$sbdir/LOCAL_tmp.conf
-poconf=$sbdir/LOCAL_old.conf
-depverfile=$cdir/installation/versions.conf
-depshafile=$cdir/installation/checksums.conf
-# --------- Delete for no Gnuastro ---------
-glconf=$cdir/gnuastro/gnuastro-local.conf
-# ------------------------------------------
-
-
-
-
-
-# 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.
-create_file_with_notice ()
-{
- if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
- then
- echo "#" >> "$1"
- echo "# This file was created during configuration" >> "$1"
- echo "# ('./project configure'). Therefore, it is not under" >> "$1"
- echo "# version control and any manual changes to it will be" >> "$1"
- echo "# over-written if the project 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.
-absolute_dir ()
-{
- if stat "$1" 1> /dev/null; then
- echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
- else
- exit 1;
- fi
-}
-
-
-
-
-
-# Check for C/C++ compilers
-# -------------------------
-#
-# To build the software, we'll need some basic tools (the compilers in
-# particular) to be present.
-hascc=0;
-if type cc > /dev/null 2>/dev/null; then
- if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
-else
- if type gcc > /dev/null 2>/dev/null; then
- if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
- else
- if type clang > /dev/null 2>/dev/null; then
- if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
- fi
- fi
-fi
-if [ $hascc = 0 ]; then
- cat <<EOF
-______________________________________________________
-!!!!!!! C/C++ Compiler NOT FOUND !!!!!!!
-
-To build the project's software, the host system needs to have basic C and
-C++ compilers. The executables that were checked are 'cc', 'gcc' and
-'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
-compiler. If you have a relevant compiler that is not checked, please get
-in touch with us (with the form below) so we add it:
-
- https://savannah.nongnu.org/support/?func=additem&group=reproduce
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
-fi
-
-
-
-
-
-# Special directory for compiler testing
-# --------------------------------------
-#
-# This directory will be deleted when the compiler testing is finished.
-compilertestdir=.compiler_test_dir_please_delete
-if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
-
-
-
-
-
-# Check C compiler
-# ----------------
-gcc_works=0
-testprog=$compilertestdir/test
-testsource=$compilertestdir/test.c
-echo; echo; echo "Checking host C compiler...";
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void){printf("...C compiler works.\n");
- return EXIT_SUCCESS;}
-EOF
-if $CC $testsource -o$testprog && $testprog; then
- rm $testsource $testprog
-else
- rm $testsource
- cat <<EOF
-
-______________________________________________________
-!!!!!!! C compiler doesn't work !!!!!!!
-
-Host C compiler ('gcc') can't build a simple program.
-
-A working C compiler is necessary for building the project's software.
-Please use the error message above to find a good solution and re-run the
-project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
- $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
-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.
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void) {return EXIT_SUCCESS;}
-EOF
-if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
- export rpath_command="-Wl,-rpath-link=$instdir/lib"
-else
- export rpath_command=""
-fi
-rm -f $testprog $testsource
-
-
-
-
-
-# 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 linking. So we'll check here to see if
-# it is present (thus necessary) or not.
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <dlfcn.h>
-int
-main(void) {
- void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
- return 0;
-}
-EOF
-if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
- needs_ldl=no;
-else
- needs_ldl=yes;
-fi
-rm -f $testprog $testsource
-
-
-
-
-
-# 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
-
-
-
-
-
-# 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
- host_cc=0
- on_mac_os=no
-fi
-
-
-
-
-
-# Necessary C library element positions
-# -------------------------------------
-#
-# On some systems (in particular Debian-based OSs), the static C library
-# and necessary headers in a non-standard place, and we can't build GCC. So
-# we need to find them first. The `sys/cdefs.h' header is also in a
-# similarly different location.
-sys_cpath=""
-sys_library_path=""
-if [ x"$$on_mac_os" != xyes ]; then
-
- # Get the GCC target name of the compiler, when its given, special
- # C libraries and headers are in a sub-directory of the host.
- gcctarget=$(gcc -v 2>&1 \
- | tr ' ' '\n' \
- | awk '/\-\-target/' \
- | sed -e's/\-\-target=//')
- if [ x"$gcctarget" != x ]; then
- if [ -f /usr/lib/$gcctarget/libc.a ]; then
- export sys_library_path=/usr/lib/$gcctarget
- export sys_cpath=/usr/include/$gcctarget
- fi
- fi
-
- # For a check:
- #echo "sys_library_path: $sys_library_path"
- #echo "sys_cpath: $sys_cpath"
-fi
-
-
-
-
-
-# See if a link-able static C library exists
-# ------------------------------------------
-#
-# After building GCC, we must use PatchELF to correct its RPATHs. However,
-# PatchELF links internally with `libstdc++'. So a dynamicly linked
-# PatchELF cannot be used to correct the links to `libstdc++' in general
-# (on some systems this causes no problem, but on others it doesn't!).
-#
-# However, to build a Static PatchELF, we need to be able to link with the
-# static C library, which is not always available on some GNU/Linux
-# systems. Therefore we need to check this here. If we can't build a static
-# PatchELF, we won't build any GCC either.
-if [ x"$host_cc" = x0 ]; then
- echo; echo; echo "Checking if static C library is available...";
- cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/cdefs.h>
-int main(void){printf("...yes\n");
- return EXIT_SUCCESS;}
-EOF
- cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
- if $cc_call && $testprog; then
- gccwarning=0
- good_static_libc=1
- rm $testsource $testprog
- else
- echo; echo "Compilation command:"; echo "$cc_call"
- good_static_libc=0
- rm $testsource
- gccwarning=1
- host_cc=1
- cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-The 'sys/cdefs.h' header cannot be included, or a usable static C library
-('libc.a', in any directory) cannot be used with the current settings of
-this system. SEE THE ERROR MESSAGE ABOVE.
-
-Because of this, we can't build GCC. You either 1) don't have them, or 2)
-the default system environment aren't enough to find them.
-
-1) If you don't have them, your operating system provides them as separate
-packages that you must manually install. Please look into your operating
-system documentation or contact someone familiar with it. For example on
-some Redhat-based GNU/Linux distributions, the static C library package can
-be installed with this command:
-
- $ sudo yum install glibc-static
-
-2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
-example in '/PATH/TO/STATIC/LIBC/libc.a' and
-'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
-re-configure the project to fix this problem.
-
- $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
- $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- fi
-fi
-
-# Print a warning if GCC is not meant to be built.
-if [ x"$gccwarning" = x1 ]; then
- cat <<EOF
-
-PLEASE SEE THE WARNINGS ABOVE.
-
-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(s) to complete your C
-compiler, then re-run './project configure'.
-
-EOF
- sleep 5
-fi
-
-
-
-
-
-# Fortran compiler
-# ----------------
-#
-# If GCC is ultimately build within the project, the user won't need to
-# have a fortran compiler, we'll build it internally for high-level
-# programs. However, when the host C compiler is to be used, the user needs
-# to have a Fortran compiler available.
-if [ $host_cc = 1 ]; then
-
- # See if a Fortran compiler exists.
- hasfc=0;
- if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
- if [ $hasfc = 0 ]; then
- cat <<EOF
-______________________________________________________
-!!!!!!! Fortran Compiler NOT FOUND !!!!!!!
-
-Because the project won't be building its own GCC (which includes a Fortran
-compiler), you need to have a Fortran compiler available. Fortran is
-commonly necessary for many lower-level scientific programs. Currently we
-search for 'gfortran'. If you have a Fortran compiler that is not checked,
-please get in touch with us (with the form below) so we add it:
-
- https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-Note: GCC will not be built because you are either using the '--host-cc'
-option, or you are using an operating system that currently has bugs when
-building GCC.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
- fi
-
- # See if the Fortran compiler works
- testsource=$compilertestdir/test.f
- echo; echo; echo "Checking host Fortran compiler...";
- echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource
- echo " END" >> $testsource
- if gfortran $testsource -o$testprog && $testprog; then
- rm $testsource $testprog
- else
- rm $testsource
- cat <<EOF
-
-______________________________________________________
-!!!!!!! Fortran compiler doesn't work !!!!!!!
-
-Host Fortran compiler ('gfortran') can't build a simple program.
-
-A working Fortran compiler is necessary for building some of the project's
-software. Please use the error message above to find a good solution and
-re-run the project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
- $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
- fi
-fi
-
-
-
-
-
-# Delete the compiler testing directory
-# -------------------------------------
-#
-# This directory was made above to make sure the necessary compilers can be
-# run.
-rm -rf $compilertestdir
-
-
-
-
-
-# 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
-
------------------------------
-Project's 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.conf' is the top-most local configuration for the project. 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 `./project 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="./project configure"
- else
- status="configured for '$oldgroupname' group"
- confcommand="./project configure --group=$oldgroupname"
- fi
- echo "Project was previously $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 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 project 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.
-
-'.build' (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.
-
---- CAUTION ---
-Do not choose any directory under the top source directory (this
-directory). The build directory cannot be a subdirectory of the source.
----------------
-
-EOF
- bdir=
- currentdir=$(pwd)
- 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
- instring="the already existing"
- bdir=$(absolute_dir $build_dir)
- rm -rf $build_dir/$junkname
- else
- echo " -- Can't write in '$build_dir'"; echo
- fi
- else
- if mkdir $build_dir 2> /dev/null; then
- instring="the newly created"
- bdir=$(absolute_dir $build_dir)
- else
- echo " -- Can't create '$build_dir'"; echo
- fi
- fi
-
- # If its given, make sure it isn't a subdirectory of the source
- # directory.
- if ! [ x"$bdir" = x ]; then
- echo "Given build directory: $bdir"
- if echo "$bdir/" \
- | grep '^'$currentdir 2> /dev/null > /dev/null; then
-
- # If it was newly created, it will be empty, so delete it.
- if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
-
- # Inform the user that this is not acceptable and reset `bdir'.
- bdir=
- echo " -- The build-directory cannot be under the source-directory."
- echo " Please specify another build-directory that is outside of the source."
- echo ""
- else
- echo " -- Build directory set to ($instring): '$bdir'"
- 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}' $adir/INPUTS.conf)
-wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $adir/INPUTS.conf)
-wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $adir/INPUTS.conf)
-wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $adir/INPUTS.conf)
-if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
- cat <<EOF
-
-----------------------------------
-(OPTIONAL) Input dataset directory
-----------------------------------
-
-This project 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 project will use its own
-build of the programs it needs. Therefore the tarball of the relevant
-programs are necessary. If a tarball isn't present in the specified
-directory, *IT WILL BE DOWNLOADED* automatically.
-
-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
-project 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
-
- # Add commented notice.
- create_file_with_notice $pconf
-
- # Write the values.
- sed -e's|@bdir[@]|'"$bdir"'|' \
- -e's|@indir[@]|'"$indir"'|' \
- -e's|@ddir[@]|'"$ddir"'|' \
- -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
- -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.
-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
- cat <<EOF
-______________________________________________________
-!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!
-
-Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball
-version that this project was designed to use in '$depverfile'
-($gversion). Please re-run after removing the former file:
-
- $ rm $glconf
- $ ./project configure
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
- fi
-fi
-# ------------------------------------------
-
-
-
-
-
-# Delete final configuration target
-# ---------------------------------
-#
-# We only want to start running the project later if this script has
-# completed successfully. To make sure it hasn't crashed in the middle
-# (without the user noticing), in the end of this script we make a file and
-# we'll delete it here (at the start). Therefore if the script crashed in
-# the middle that file won't exist.
-sdir=$bdir/software
-finaltarget=$sdir/configuration-done.txt
-if ! [ -d $sdir ]; then mkdir $sdir; fi
-rm -f $finaltarget
-
-
-
-
-
-# Project's top-level directories
-# -------------------------------
-#
-# These directories are possibly needed by many steps of process, so to
-# avoid too many directory dependencies throughout the software and
-# analysis Makefiles (thus making them hard to read), we are just building
-# them here
-# Software tarballs
-tardir=$sdir/tarballs
-if ! [ -d $tardir ]; then mkdir $tardir; fi
-
-# Installed software
-instdir=$sdir/installed
-if ! [ -d $instdir ]; then mkdir $instdir; fi
-
-# To record software versions and citation.
-verdir=$instdir/version-info
-if ! [ -d $verdir ]; then mkdir $verdir; fi
-
-# Program and library versions and citation.
-ibidir=$verdir/proglib
-if ! [ -d $ibidir ]; then mkdir $ibidir; fi
-
-# Python module versions and citation.
-ipydir=$verdir/python
-if ! [ -d $ipydir ]; then mkdir $ipydir; fi
-
-# Used software BibTeX entries.
-ictdir=$verdir/cite
-if ! [ -d $ictdir ]; then mkdir $ictdir; fi
-
-# TeXLive versions.
-itidir=$verdir/tex
-if ! [ -d $itidir ]; then mkdir $itidir; fi
-
-# Top-level LaTeX.
-texdir=$bdir/tex
-if ! [ -d $texdir ]; then mkdir $texdir; fi
-
-# LaTeX macros.
-mtexdir=$texdir/macros
-if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
-
-
-# TeX build directory. If built in a group scenario, the TeX build
-# directory must be separate for each member (so they can work on their
-# relevant parts of the paper without conflicting with each other).
-if [ "x$reproducible_paper_group_name" = x ]; then
- texbdir=$texdir/build
-else
- user=$(whoami)
- texbdir=$texdir/build-$user
-fi
-if ! [ -d $texbdir ]; then mkdir $texbdir; fi
-
-# TiKZ (for building figures within LaTeX).
-tikzdir=$texbdir/tikz
-if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
-
-
-# Set the symbolic links for easy access to the top project build
-# directories. Note that these are put in each user's source/cloned
-# directory, not in the build directory (which can be shared between many
-# users and thus may already exist).
-#
-# Note: if we don't delete them first, it can happen that an extra link
-# will be created in each directory that points to its parent. So to be
-# safe, we are deleting all the links on each re-configure of the project.
-rm -f .build .local tex/build tex/tikz .gnuastro
-ln -s $bdir .build
-ln -s $instdir .local
-ln -s $texdir tex/build
-ln -s $tikzdir tex/tikz
-# --------- Delete for no Gnuastro ---------
-ln -s $topdir/reproduce/software/config/gnuastro .gnuastro
-# ------------------------------------------
-
-
-# Temporary software un-packing/build directory: if the host has the
-# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
-# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
-# today (>8GB) is large enough for the parallel building of the software.
-#
-# For the name of the directory under `/dev/shm' (for this project), we'll
-# use the names of the two parent directories to the current/running
-# directory, separated by a `-' instead of `/'. We'll then appended that
-# with the user's name (in case multiple users may be working on similar
-# project names). Maybe later, we can use something like `mktemp' to add
-# random characters to this name and make it unique to every run (even for
-# a single user).
-tmpblddir=$sdir/build-tmp
-rm -rf $tmpblddir/* $tmpblddir # If its a link, we need to empty its
- # contents first, then itself.
-
-# Set the top-level shared memory location.
-if [ -d /dev/shm ]; then shmdir=/dev/shm
-else shmdir=""
-fi
-
-# If a shared memory mounted directory exists and there is enough space
-# there (in RAM), build a temporary directory for this project.
-needed_space=2000000
-if [ x"$shmdir" != x ]; then
- available_space=$(df $shmdir | awk 'NR==2{print $4}')
- if [ $available_space -gt $needed_space ]; then
- dirname=$(pwd | sed -e's/\// /g' \
- | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
- tbshmdir=$shmdir/"$dirname"-$(whoami)
- if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
- fi
-else
- tbshmdir=""
-fi
-
-# If a shared memory directory was created set `build-tmp' to be a
-# symbolic link to it. Otherwise, just build the temporary build
-# directory under the project build directory.
-if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
-else ln -s $tbshmdir $tmpblddir;
-fi
-
-
-
-
-
-# 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 project. They
-will be installed in:
-
- $sdir/installed
-
-**TIP**: you can see which software is being installed at every moment with
-the following command. See "Inspecting status" section of
-'README-hacking.md' for more. In short, run it while the project is being
-configured (in another terminal, but on this same directory: 'pwd'):
-
- $ ./project --check-config
-
--------------------------
-
-EOF
- sleep $tsec
-fi
-
-
-
-
-
-# Number of threads for basic builds
-# ----------------------------------
-#
-# 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; then
- if [ $jobs = 0 ]; then
- numthreads=$(nproc --all);
- else
- numthreads=$jobs
- fi
-else
- numthreads=1;
-fi
-
-
-
-
-
-# Build `flock' before other program
-# ----------------------------------
-#
-# Flock (or file-lock) is a unique program 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 in non-GNU/Linux systems, we will be using our own build.
-#
-# The reason that `flock' is sepecial is that we need it to serialize the
-# download process of the software tarballs.
-flockversion=$(awk '/flock-version/{print $3}' $depverfile)
-flockchecksum=$(awk '/flock-checksum/{print $3}' $depshafile)
-flocktar=flock-$flockversion.tar.gz
-flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/
-
-# Prepare/download the tarball.
-if ! [ -f $tardir/$flocktar ]; then
- flocktarname=$tardir/$flocktar
- ucname=$flocktarname.unchecked
- if [ -f $ddir/$flocktar ]; then
- cp $ddir/$flocktar $ucname
- else
- if ! $downloader $ucname $flockurl/$flocktar; then
- rm -f $ucname;
- 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
-
- # Make sure this is the correct tarball.
- if type sha512sum > /dev/null 2>/dev/null; then
- checksum=$(sha512sum "$ucname" | awk '{print $1}')
- if [ x$checksum = x$flockchecksum ]; then mv "$ucname" "$flocktarname"
- else echo "ERROR: Non-matching checksum for '$flocktar'."; exit 1
- fi;
- else mv "$ucname" "$flocktarname"
- 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 $tmpblddir
- tar xf $tardir/$flocktar
- cd flock-$flockversion
- ./configure --prefix=$instdir
- make
- make install
- cd $topdir
- rm -rf $tmpblddir/flock-$flockversion
- echo "Discoteq flock $flockversion" > $ibidir/flock
-fi
-
-
-
-
-
-# Paths needed by the host compiler (only for `basic.mk')
-# -------------------------------------------------------
-#
-# At the end of the basic build, we need to build GCC. But GCC will build
-# in multiple phases, making its own simple compiler in order to build
-# itself completely. The intermediate/simple compiler doesn't recognize
-# some system specific locations like `/usr/lib/ARCHITECTURE' that some
-# operating systems use. We thus need to tell the intermediate compiler
-# where its necessary libraries and headers are.
-if [ x"$sys_library_path" != x ]; then
- if [ x"$LIBRARY_PATH" = x ]; then
- export LIBRARY_PATH="$sys_library_path"
- else
- export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
- fi
- if [ x"$CPATH" = x ]; then
- export CPATH="$sys_cpath"
- else
- export CPATH="$CPATH:$sys_cpath"
- fi
-fi
-
-
-
-
-
-# Build basic software
-# --------------------
-#
-# When building these software we don't have our own un-packing software,
-# Bash, Make, or AWK. In this step, we'll install such low-level basic
-# tools, but we have to be very portable (and use minimal features in all).
-echo; echo "Building necessary software (if necessary)..."
-make -f reproduce/software/make/basic.mk \
- good_static_libc=$good_static_libc \
- rpath_command=$rpath_command \
- static_build=$static_build \
- numthreads=$numthreads \
- needs_ldl=$needs_ldl \
- on_mac_os=$on_mac_os \
- host_cc=$host_cc \
- -j$numthreads
-
-
-
-
-
-# All other software
-# ------------------
-#
-# 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.
-if [ $jobs = 0 ]; then
- numthreads=$($instdir/bin/nproc --all)
-else
- numthreads=$jobs
-fi
-.local/bin/env -i HOME=$bdir \
- .local/bin/make -f reproduce/software/make/high-level.mk \
- sys_library_path=$sys_library_path \
- rpath_command=$rpath_command \
- static_build=$static_build \
- numthreads=$numthreads \
- on_mac_os=$on_mac_os \
- sys_cpath=$sys_cpath \
- host_cc=$host_cc \
- -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 project 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 project's
-# configuration and building if its not present.
-if [ -f $itidir/texlive-ready-tlmgr ]; then
- texlive_result=$(cat $itidir/texlive-ready-tlmgr)
-else
- texlive_result="NOT!"
-fi
-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
-project, 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
- ./project 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.
-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/proglib/*)
-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 output 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
-
-
-
-
-
-# Clean the temporary build directory
-# ---------------------------------
-#
-# By the time the script reaches here the temporary software build
-# directory should be empty, so just delete it. Note `tmpblddir' may be a
-# symbolic link to shared memory. So, to work in any scenario, first delete
-# the contents of the directory (if it has any), then delete `tmpblddir'.
-.local/bin/rm -rf $tmpblddir/* $tmpblddir
-
-
-
-
-
-# Register successful completion
-# ------------------------------
-echo `.local/bin/date` > $finaltarget
-
-
-
-
-
-
-# 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="./project make -j8"
-else
- buildcommand="./project make --group=$reproducible_paper_group_name -j8"
-fi
-cat <<EOF
-
-----------------
-The project and its environment are configured with no errors.
-
-Please run the following command to start.
-(Replace '8' with the number of CPU threads on your system)
-
- $buildcommand
-
-To change the configuration later, please re-run './project configure', DO
-NOT manually edit the relevant files.
-
-EOF
diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/bash/git-post-checkout
deleted file mode 100755
index f6366dc..0000000
--- a/reproduce/software/bash/git-post-checkout
+++ /dev/null
@@ -1,66 +0,0 @@
-#!@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) 2018-2020 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
deleted file mode 100755
index 9d550db..0000000
--- a/reproduce/software/bash/git-pre-commit
+++ /dev/null
@@ -1,83 +0,0 @@
-#!@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) 2018-2020 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
diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index fc04dfb..d71a3d5 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -2,7 +2,7 @@ Software building instructions
==============================
This directory contains Makefiles that are called by the high-level
-`reproduce/software/bash/configure.sh` script. The main target for the
+`reproduce/software/shell/configure.sh` script. The main target for the
installation of each software is a simple plain text file that contains the
name of the software and its version (which is put in the paper in the
end). Once built, these plain-text files are all put in the proper
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 7e900b8..d08ba62 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -74,9 +74,9 @@ export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
export PROJECT_STATUS := configure_basic
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Define the top-level basic programs (that don't depend on any other).
top-level-programs = low-level-links gcc
@@ -1067,7 +1067,7 @@ $(ibidir)/metastore: $(needlibbsd) \
-e's|@GROUP[@]|'$$group'|g' \
-e's|@BINDIR[@]|$(ibdir)|g' \
-e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
- reproduce/software/bash/git-$$f > .git/hooks/$$f \
+ reproduce/software/shell/git-$$f > .git/hooks/$$f \
&& chmod +x .git/hooks/$$f; \
done; \
fi \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 02ae1a5..53bef55 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -96,9 +96,9 @@ export DYLD_LIBRARY_PATH :=
# for `ld'.
export LIBRARY_PATH := $(sys_library_path)
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script, see `reproduce/software/shell/bashrc.sh'.
export PROJECT_STATUS := configure_highlevel
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Building flags:
#
diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
new file mode 100755
index 0000000..b2a151f
--- /dev/null
+++ b/reproduce/software/shell/bashrc.sh
@@ -0,0 +1,45 @@
+# Bash startup file for better control of project environment.
+#
+# To have better control over the environment of each analysis step (Make
+# recipe), besides having environment variables (directly included from
+# Make), it may also be useful to have a Bash startup file (this file). All
+# of the Makefiles set this file as the `BASH_ENV' environment variable, so
+# it is loaded into all the Make recipes within the project.
+#
+# The special `PROJECT_STATUS' environment variable is defined in every
+# top-level Makefile of the project. It defines the the state of the Make
+# that is calling this script. It can have three values:
+#
+# configure_basic
+# ---------------
+# When doing basic configuration, therefore the executed steps cannot
+# make any assumptions about the version of Bash (or any other
+# program). Therefore it is important for any step in this step to be
+# highly portable.
+#
+# configure_highlevel
+# -------------------
+# When building the higher-level programs, so the versions of the
+# most basic tools are set and you may safely assume certain
+# features.
+#
+# make
+# ----
+# When doing the project's analysis: all software have known
+# versions.
+#
+#
+# Copyright (C) 2019-2020 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/>.
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
new file mode 100755
index 0000000..a6fbc4e
--- /dev/null
+++ b/reproduce/software/shell/configure.sh
@@ -0,0 +1,1407 @@
+#! /bin/sh
+#
+# Necessary preparations/configurations for the reproducible project.
+#
+# Copyright (C) 2018-2020 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
+
+
+
+
+
+# Internal directories
+# --------------------
+#
+# These are defined to help make this script more readable.
+topdir=$(pwd)
+optionaldir="/optional/path"
+adir=reproduce/analysis/config
+cdir=reproduce/software/config
+
+sbdir=$cdir/installation
+
+pconf=$sbdir/LOCAL.conf
+ptconf=$sbdir/LOCAL_tmp.conf
+poconf=$sbdir/LOCAL_old.conf
+depverfile=$cdir/installation/versions.conf
+depshafile=$cdir/installation/checksums.conf
+# --------- Delete for no Gnuastro ---------
+glconf=$cdir/gnuastro/gnuastro-local.conf
+# ------------------------------------------
+
+
+
+
+
+# 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.
+create_file_with_notice ()
+{
+ if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
+ then
+ echo "#" >> "$1"
+ echo "# This file was created during configuration" >> "$1"
+ echo "# ('./project configure'). Therefore, it is not under" >> "$1"
+ echo "# version control and any manual changes to it will be" >> "$1"
+ echo "# over-written if the project 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.
+absolute_dir ()
+{
+ if stat "$1" 1> /dev/null; then
+ echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
+ else
+ exit 1;
+ fi
+}
+
+
+
+
+
+# Check for C/C++ compilers
+# -------------------------
+#
+# To build the software, we'll need some basic tools (the compilers in
+# particular) to be present.
+hascc=0;
+if type cc > /dev/null 2>/dev/null; then
+ if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
+else
+ if type gcc > /dev/null 2>/dev/null; then
+ if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
+ else
+ if type clang > /dev/null 2>/dev/null; then
+ if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
+ fi
+ fi
+fi
+if [ $hascc = 0 ]; then
+ cat <<EOF
+______________________________________________________
+!!!!!!! C/C++ Compiler NOT FOUND !!!!!!!
+
+To build the project's software, the host system needs to have basic C and
+C++ compilers. The executables that were checked are 'cc', 'gcc' and
+'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
+compiler. If you have a relevant compiler that is not checked, please get
+in touch with us (with the form below) so we add it:
+
+ https://savannah.nongnu.org/support/?func=additem&group=reproduce
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+fi
+
+
+
+
+
+# Special directory for compiler testing
+# --------------------------------------
+#
+# This directory will be deleted when the compiler testing is finished.
+compilertestdir=.compiler_test_dir_please_delete
+if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
+
+
+
+
+
+# Check C compiler
+# ----------------
+gcc_works=0
+testprog=$compilertestdir/test
+testsource=$compilertestdir/test.c
+echo; echo; echo "Checking host C compiler...";
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void){printf("...C compiler works.\n");
+ return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog && $testprog; then
+ rm $testsource $testprog
+else
+ rm $testsource
+ cat <<EOF
+
+______________________________________________________
+!!!!!!! C compiler doesn't work !!!!!!!
+
+Host C compiler ('gcc') can't build a simple program.
+
+A working C compiler is necessary for building the project's software.
+Please use the error message above to find a good solution and re-run the
+project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+ $ ./project configure -e
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+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.
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void) {return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
+ export rpath_command="-Wl,-rpath-link=$instdir/lib"
+else
+ export rpath_command=""
+fi
+rm -f $testprog $testsource
+
+
+
+
+
+# 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 linking. So we'll check here to see if
+# it is present (thus necessary) or not.
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <dlfcn.h>
+int
+main(void) {
+ void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
+ return 0;
+}
+EOF
+if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
+ needs_ldl=no;
+else
+ needs_ldl=yes;
+fi
+rm -f $testprog $testsource
+
+
+
+
+
+# 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
+
+
+
+
+
+# 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
+ host_cc=0
+ on_mac_os=no
+fi
+
+
+
+
+
+# Necessary C library element positions
+# -------------------------------------
+#
+# On some systems (in particular Debian-based OSs), the static C library
+# and necessary headers in a non-standard place, and we can't build GCC. So
+# we need to find them first. The `sys/cdefs.h' header is also in a
+# similarly different location.
+sys_cpath=""
+sys_library_path=""
+if [ x"$$on_mac_os" != xyes ]; then
+
+ # Get the GCC target name of the compiler, when its given, special
+ # C libraries and headers are in a sub-directory of the host.
+ gcctarget=$(gcc -v 2>&1 \
+ | tr ' ' '\n' \
+ | awk '/\-\-target/' \
+ | sed -e's/\-\-target=//')
+ if [ x"$gcctarget" != x ]; then
+ if [ -f /usr/lib/$gcctarget/libc.a ]; then
+ export sys_library_path=/usr/lib/$gcctarget
+ export sys_cpath=/usr/include/$gcctarget
+ fi
+ fi
+
+ # For a check:
+ #echo "sys_library_path: $sys_library_path"
+ #echo "sys_cpath: $sys_cpath"
+fi
+
+
+
+
+
+# See if a link-able static C library exists
+# ------------------------------------------
+#
+# After building GCC, we must use PatchELF to correct its RPATHs. However,
+# PatchELF links internally with `libstdc++'. So a dynamicly linked
+# PatchELF cannot be used to correct the links to `libstdc++' in general
+# (on some systems this causes no problem, but on others it doesn't!).
+#
+# However, to build a Static PatchELF, we need to be able to link with the
+# static C library, which is not always available on some GNU/Linux
+# systems. Therefore we need to check this here. If we can't build a static
+# PatchELF, we won't build any GCC either.
+if [ x"$host_cc" = x0 ]; then
+ echo; echo; echo "Checking if static C library is available...";
+ cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/cdefs.h>
+int main(void){printf("...yes\n");
+ return EXIT_SUCCESS;}
+EOF
+ cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
+ if $cc_call && $testprog; then
+ gccwarning=0
+ good_static_libc=1
+ rm $testsource $testprog
+ else
+ echo; echo "Compilation command:"; echo "$cc_call"
+ good_static_libc=0
+ rm $testsource
+ gccwarning=1
+ host_cc=1
+ cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+The 'sys/cdefs.h' header cannot be included, or a usable static C library
+('libc.a', in any directory) cannot be used with the current settings of
+this system. SEE THE ERROR MESSAGE ABOVE.
+
+Because of this, we can't build GCC. You either 1) don't have them, or 2)
+the default system environment aren't enough to find them.
+
+1) If you don't have them, your operating system provides them as separate
+packages that you must manually install. Please look into your operating
+system documentation or contact someone familiar with it. For example on
+some Redhat-based GNU/Linux distributions, the static C library package can
+be installed with this command:
+
+ $ sudo yum install glibc-static
+
+2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
+example in '/PATH/TO/STATIC/LIBC/libc.a' and
+'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
+re-configure the project to fix this problem.
+
+ $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
+ $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ fi
+fi
+
+# Print a warning if GCC is not meant to be built.
+if [ x"$gccwarning" = x1 ]; then
+ cat <<EOF
+
+PLEASE SEE THE WARNINGS ABOVE.
+
+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(s) to complete your C
+compiler, then re-run './project configure'.
+
+EOF
+ sleep 5
+fi
+
+
+
+
+
+# Fortran compiler
+# ----------------
+#
+# If GCC is ultimately build within the project, the user won't need to
+# have a fortran compiler, we'll build it internally for high-level
+# programs. However, when the host C compiler is to be used, the user needs
+# to have a Fortran compiler available.
+if [ $host_cc = 1 ]; then
+
+ # See if a Fortran compiler exists.
+ hasfc=0;
+ if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
+ if [ $hasfc = 0 ]; then
+ cat <<EOF
+______________________________________________________
+!!!!!!! Fortran Compiler NOT FOUND !!!!!!!
+
+Because the project won't be building its own GCC (which includes a Fortran
+compiler), you need to have a Fortran compiler available. Fortran is
+commonly necessary for many lower-level scientific programs. Currently we
+search for 'gfortran'. If you have a Fortran compiler that is not checked,
+please get in touch with us (with the form below) so we add it:
+
+ https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+Note: GCC will not be built because you are either using the '--host-cc'
+option, or you are using an operating system that currently has bugs when
+building GCC.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+ fi
+
+ # See if the Fortran compiler works
+ testsource=$compilertestdir/test.f
+ echo; echo; echo "Checking host Fortran compiler...";
+ echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource
+ echo " END" >> $testsource
+ if gfortran $testsource -o$testprog && $testprog; then
+ rm $testsource $testprog
+ else
+ rm $testsource
+ cat <<EOF
+
+______________________________________________________
+!!!!!!! Fortran compiler doesn't work !!!!!!!
+
+Host Fortran compiler ('gfortran') can't build a simple program.
+
+A working Fortran compiler is necessary for building some of the project's
+software. Please use the error message above to find a good solution and
+re-run the project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+ $ ./project configure -e
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+ fi
+fi
+
+
+
+
+
+# Delete the compiler testing directory
+# -------------------------------------
+#
+# This directory was made above to make sure the necessary compilers can be
+# run.
+rm -rf $compilertestdir
+
+
+
+
+
+# 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
+
+-----------------------------
+Project's 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.conf' is the top-most local configuration for the project. 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 `./project 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="./project configure"
+ else
+ status="configured for '$oldgroupname' group"
+ confcommand="./project configure --group=$oldgroupname"
+ fi
+ echo "Project was previously $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 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 project will crash.
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ downloader="no-downloader-found"
+ fi;
+fi
+
+
+
+
+
+# Build directory
+# ---------------
+if [ $rewritepconfig = yes ]; then
+ cat <<EOF
+
+===============
+Build directory
+===============
+
+The project's "source" (this directory) and "build" directories are treated
+separately. This greatly helps in managing the many intermediate files that
+are created during the build. The intermediate build files don't need to be
+archived or backed up: you can always re-build them with the contents of
+the source directory. The build directory also needs a relatively large
+amount of free space (atleast serveral Giga-bytes), while the source
+directory (all plain text) will usually be a mega-byte or less.
+
+'.build' (a symbolic link to the build directory) will also be created
+during this configuration. It can help encourage you to set the actual
+build directory in a very different address from this one (one that can be
+deleted and has large volume), while having easy access to it from here.
+
+--- CAUTION ---
+Do not choose any directory under the top source directory (this
+directory). The build directory cannot be a subdirectory of the source.
+---------------
+
+EOF
+ bdir=
+ currentdir=$(pwd)
+ 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
+ instring="the already existing"
+ bdir=$(absolute_dir $build_dir)
+ rm -rf $build_dir/$junkname
+ else
+ echo " -- Can't write in '$build_dir'"; echo
+ fi
+ else
+ if mkdir $build_dir 2> /dev/null; then
+ instring="the newly created"
+ bdir=$(absolute_dir $build_dir)
+ else
+ echo " -- Can't create '$build_dir'"; echo
+ fi
+ fi
+
+ # If its given, make sure it isn't a subdirectory of the source
+ # directory.
+ if ! [ x"$bdir" = x ]; then
+ echo "Given build directory: $bdir"
+ if echo "$bdir/" \
+ | grep '^'$currentdir 2> /dev/null > /dev/null; then
+
+ # If it was newly created, it will be empty, so delete it.
+ if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
+
+ # Inform the user that this is not acceptable and reset `bdir'.
+ bdir=
+ echo " -- The build-directory cannot be under the source-directory."
+ echo " Please specify another build-directory that is outside of the source."
+ echo ""
+ else
+ echo " -- Build directory set to ($instring): '$bdir'"
+ fi
+ fi
+
+ # Reset `build_dir' to blank, so it continues asking when the
+ # previous value wasn't usable.
+ build_dir=
+ done
+fi
+
+
+
+
+
+# Input directory
+# ---------------
+if [ x"$input_dir" = x ]; then
+ indir=$optionaldir
+else
+ indir=$input_dir
+fi
+wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.conf)
+wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $adir/INPUTS.conf)
+wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $adir/INPUTS.conf)
+wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $adir/INPUTS.conf)
+if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
+ cat <<EOF
+
+----------------------------------
+(OPTIONAL) Input dataset directory
+----------------------------------
+
+This project 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 project will use its own
+build of the programs it needs. Therefore the tarball of the relevant
+programs are necessary. If a tarball isn't present in the specified
+directory, *IT WILL BE DOWNLOADED* automatically.
+
+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
+project 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
+
+ # Add commented notice.
+ create_file_with_notice $pconf
+
+ # Write the values.
+ sed -e's|@bdir[@]|'"$bdir"'|' \
+ -e's|@indir[@]|'"$indir"'|' \
+ -e's|@ddir[@]|'"$ddir"'|' \
+ -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
+ -e's|@downloader[@]|'"$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
+'$pconf'.
+EOF
+ fi
+
+ cat <<EOF
+
+Please run the configure script again (accepting to re-write existing
+configuration file) so all the values can be filled and checked.
+#################################################################
+EOF
+ fi
+fi
+
+
+
+
+
+# --------- Delete for no Gnuastro ---------
+# Get the version of Gnuastro that must be used.
+gversion=$(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$gversion ]; then
+ cat <<EOF
+______________________________________________________
+!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!
+
+Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball
+version that this project was designed to use in '$depverfile'
+($gversion). Please re-run after removing the former file:
+
+ $ rm $glconf
+ $ ./project configure
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+ fi
+fi
+# ------------------------------------------
+
+
+
+
+
+# Delete final configuration target
+# ---------------------------------
+#
+# We only want to start running the project later if this script has
+# completed successfully. To make sure it hasn't crashed in the middle
+# (without the user noticing), in the end of this script we make a file and
+# we'll delete it here (at the start). Therefore if the script crashed in
+# the middle that file won't exist.
+sdir=$bdir/software
+finaltarget=$sdir/configuration-done.txt
+if ! [ -d $sdir ]; then mkdir $sdir; fi
+rm -f $finaltarget
+
+
+
+
+
+# Project's top-level directories
+# -------------------------------
+#
+# These directories are possibly needed by many steps of process, so to
+# avoid too many directory dependencies throughout the software and
+# analysis Makefiles (thus making them hard to read), we are just building
+# them here
+# Software tarballs
+tardir=$sdir/tarballs
+if ! [ -d $tardir ]; then mkdir $tardir; fi
+
+# Installed software
+instdir=$sdir/installed
+if ! [ -d $instdir ]; then mkdir $instdir; fi
+
+# To record software versions and citation.
+verdir=$instdir/version-info
+if ! [ -d $verdir ]; then mkdir $verdir; fi
+
+# Program and library versions and citation.
+ibidir=$verdir/proglib
+if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+
+# Python module versions and citation.
+ipydir=$verdir/python
+if ! [ -d $ipydir ]; then mkdir $ipydir; fi
+
+# Used software BibTeX entries.
+ictdir=$verdir/cite
+if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+
+# TeXLive versions.
+itidir=$verdir/tex
+if ! [ -d $itidir ]; then mkdir $itidir; fi
+
+# Top-level LaTeX.
+texdir=$bdir/tex
+if ! [ -d $texdir ]; then mkdir $texdir; fi
+
+# LaTeX macros.
+mtexdir=$texdir/macros
+if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
+
+
+# TeX build directory. If built in a group scenario, the TeX build
+# directory must be separate for each member (so they can work on their
+# relevant parts of the paper without conflicting with each other).
+if [ "x$reproducible_paper_group_name" = x ]; then
+ texbdir=$texdir/build
+else
+ user=$(whoami)
+ texbdir=$texdir/build-$user
+fi
+if ! [ -d $texbdir ]; then mkdir $texbdir; fi
+
+# TiKZ (for building figures within LaTeX).
+tikzdir=$texbdir/tikz
+if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
+
+
+# Set the symbolic links for easy access to the top project build
+# directories. Note that these are put in each user's source/cloned
+# directory, not in the build directory (which can be shared between many
+# users and thus may already exist).
+#
+# Note: if we don't delete them first, it can happen that an extra link
+# will be created in each directory that points to its parent. So to be
+# safe, we are deleting all the links on each re-configure of the project.
+rm -f .build .local tex/build tex/tikz .gnuastro
+ln -s $bdir .build
+ln -s $instdir .local
+ln -s $texdir tex/build
+ln -s $tikzdir tex/tikz
+# --------- Delete for no Gnuastro ---------
+ln -s $topdir/reproduce/software/config/gnuastro .gnuastro
+# ------------------------------------------
+
+
+# Temporary software un-packing/build directory: if the host has the
+# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
+# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
+# today (>8GB) is large enough for the parallel building of the software.
+#
+# For the name of the directory under `/dev/shm' (for this project), we'll
+# use the names of the two parent directories to the current/running
+# directory, separated by a `-' instead of `/'. We'll then appended that
+# with the user's name (in case multiple users may be working on similar
+# project names). Maybe later, we can use something like `mktemp' to add
+# random characters to this name and make it unique to every run (even for
+# a single user).
+tmpblddir=$sdir/build-tmp
+rm -rf $tmpblddir/* $tmpblddir # If its a link, we need to empty its
+ # contents first, then itself.
+
+# Set the top-level shared memory location.
+if [ -d /dev/shm ]; then shmdir=/dev/shm
+else shmdir=""
+fi
+
+# If a shared memory mounted directory exists and there is enough space
+# there (in RAM), build a temporary directory for this project.
+needed_space=2000000
+if [ x"$shmdir" != x ]; then
+ available_space=$(df $shmdir | awk 'NR==2{print $4}')
+ if [ $available_space -gt $needed_space ]; then
+ dirname=$(pwd | sed -e's/\// /g' \
+ | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
+ tbshmdir=$shmdir/"$dirname"-$(whoami)
+ if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
+ fi
+else
+ tbshmdir=""
+fi
+
+# If a shared memory directory was created set `build-tmp' to be a
+# symbolic link to it. Otherwise, just build the temporary build
+# directory under the project build directory.
+if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
+else ln -s $tbshmdir $tmpblddir;
+fi
+
+
+
+
+
+# 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 project. They
+will be installed in:
+
+ $sdir/installed
+
+**TIP**: you can see which software is being installed at every moment with
+the following command. See "Inspecting status" section of
+'README-hacking.md' for more. In short, run it while the project is being
+configured (in another terminal, but on this same directory: 'pwd'):
+
+ $ ./project --check-config
+
+-------------------------
+
+EOF
+ sleep $tsec
+fi
+
+
+
+
+
+# Number of threads for basic builds
+# ----------------------------------
+#
+# 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; then
+ if [ $jobs = 0 ]; then
+ numthreads=$(nproc --all);
+ else
+ numthreads=$jobs
+ fi
+else
+ numthreads=1;
+fi
+
+
+
+
+
+# Build `flock' before other program
+# ----------------------------------
+#
+# Flock (or file-lock) is a unique program that is necessary to serialize
+# the (generally parallel) processing of make when necessary. GNU/Linux
+# machines have it as part of their `util-linux' programs. But to be
+# consistent in non-GNU/Linux systems, we will be using our own build.
+#
+# The reason that `flock' is sepecial is that we need it to serialize the
+# download process of the software tarballs.
+flockversion=$(awk '/flock-version/{print $3}' $depverfile)
+flockchecksum=$(awk '/flock-checksum/{print $3}' $depshafile)
+flocktar=flock-$flockversion.tar.gz
+flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/
+
+# Prepare/download the tarball.
+if ! [ -f $tardir/$flocktar ]; then
+ flocktarname=$tardir/$flocktar
+ ucname=$flocktarname.unchecked
+ if [ -f $ddir/$flocktar ]; then
+ cp $ddir/$flocktar $ucname
+ else
+ if ! $downloader $ucname $flockurl/$flocktar; then
+ rm -f $ucname;
+ 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
+
+ # Make sure this is the correct tarball.
+ if type sha512sum > /dev/null 2>/dev/null; then
+ checksum=$(sha512sum "$ucname" | awk '{print $1}')
+ if [ x$checksum = x$flockchecksum ]; then mv "$ucname" "$flocktarname"
+ else echo "ERROR: Non-matching checksum for '$flocktar'."; exit 1
+ fi;
+ else mv "$ucname" "$flocktarname"
+ 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 $tmpblddir
+ tar xf $tardir/$flocktar
+ cd flock-$flockversion
+ ./configure --prefix=$instdir
+ make
+ make install
+ cd $topdir
+ rm -rf $tmpblddir/flock-$flockversion
+ echo "Discoteq flock $flockversion" > $ibidir/flock
+fi
+
+
+
+
+
+# Paths needed by the host compiler (only for `basic.mk')
+# -------------------------------------------------------
+#
+# At the end of the basic build, we need to build GCC. But GCC will build
+# in multiple phases, making its own simple compiler in order to build
+# itself completely. The intermediate/simple compiler doesn't recognize
+# some system specific locations like `/usr/lib/ARCHITECTURE' that some
+# operating systems use. We thus need to tell the intermediate compiler
+# where its necessary libraries and headers are.
+if [ x"$sys_library_path" != x ]; then
+ if [ x"$LIBRARY_PATH" = x ]; then
+ export LIBRARY_PATH="$sys_library_path"
+ else
+ export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
+ fi
+ if [ x"$CPATH" = x ]; then
+ export CPATH="$sys_cpath"
+ else
+ export CPATH="$CPATH:$sys_cpath"
+ fi
+fi
+
+
+
+
+
+# Build basic software
+# --------------------
+#
+# When building these software we don't have our own un-packing software,
+# Bash, Make, or AWK. In this step, we'll install such low-level basic
+# tools, but we have to be very portable (and use minimal features in all).
+echo; echo "Building necessary software (if necessary)..."
+make -f reproduce/software/make/basic.mk \
+ good_static_libc=$good_static_libc \
+ rpath_command=$rpath_command \
+ static_build=$static_build \
+ numthreads=$numthreads \
+ needs_ldl=$needs_ldl \
+ on_mac_os=$on_mac_os \
+ host_cc=$host_cc \
+ -j$numthreads
+
+
+
+
+
+# All other software
+# ------------------
+#
+# 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.
+if [ $jobs = 0 ]; then
+ numthreads=$($instdir/bin/nproc --all)
+else
+ numthreads=$jobs
+fi
+.local/bin/env -i HOME=$bdir \
+ .local/bin/make -f reproduce/software/make/high-level.mk \
+ sys_library_path=$sys_library_path \
+ rpath_command=$rpath_command \
+ static_build=$static_build \
+ numthreads=$numthreads \
+ on_mac_os=$on_mac_os \
+ sys_cpath=$sys_cpath \
+ host_cc=$host_cc \
+ -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 project 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 project's
+# configuration and building if its not present.
+if [ -f $itidir/texlive-ready-tlmgr ]; then
+ texlive_result=$(cat $itidir/texlive-ready-tlmgr)
+else
+ texlive_result="NOT!"
+fi
+if [ x"$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
+project, 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
+ ./project 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.
+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 $verdir/proglib/*)
+pymodules=$(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 $f ]; then hasentry=1; break; fi; done;
+
+# Make sure we start with an empty output file.
+pkgbib=$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
+
+
+
+
+
+# Clean the temporary build directory
+# ---------------------------------
+#
+# By the time the script reaches here the temporary software build
+# directory should be empty, so just delete it. Note `tmpblddir' may be a
+# symbolic link to shared memory. So, to work in any scenario, first delete
+# the contents of the directory (if it has any), then delete `tmpblddir'.
+.local/bin/rm -rf $tmpblddir/* $tmpblddir
+
+
+
+
+
+# Register successful completion
+# ------------------------------
+echo `.local/bin/date` > $finaltarget
+
+
+
+
+
+
+# Final notice
+# ------------
+#
+# The configuration is now complete, we can inform the user on the next
+# step(s) to take.
+if [ x$reproducible_paper_group_name = x ]; then
+ buildcommand="./project make -j8"
+else
+ buildcommand="./project make --group=$reproducible_paper_group_name -j8"
+fi
+cat <<EOF
+
+----------------
+The project and its environment are configured with no errors.
+
+Please run the following command to start.
+(Replace '8' with the number of CPU threads on your system)
+
+ $buildcommand
+
+To change the configuration later, please re-run './project configure', DO
+NOT manually edit the relevant files.
+
+EOF
diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout
new file mode 100755
index 0000000..f6366dc
--- /dev/null
+++ b/reproduce/software/shell/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) 2018-2020 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/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit
new file mode 100755
index 0000000..9d550db
--- /dev/null
+++ b/reproduce/software/shell/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) 2018-2020 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
--
cgit v1.2.1