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-rw-r--r--reproduce/software/shell/apptainer-README.md6
-rwxr-xr-xreproduce/software/shell/apptainer.sh53
-rwxr-xr-xreproduce/software/shell/bashrc.sh2
-rwxr-xr-xreproduce/software/shell/configure.sh13
-rw-r--r--reproduce/software/shell/docker-README.md2
-rwxr-xr-xreproduce/software/shell/docker.sh2
-rwxr-xr-xreproduce/software/shell/git-post-checkout2
-rwxr-xr-xreproduce/software/shell/git-pre-commit2
-rwxr-xr-xreproduce/software/shell/pre-make-build.sh2
-rwxr-xr-xreproduce/software/shell/prep-source.sh22
-rwxr-xr-xreproduce/software/shell/run-parts.in4
-rwxr-xr-xreproduce/software/shell/tarball-prepare.sh9
12 files changed, 71 insertions, 48 deletions
diff --git a/reproduce/software/shell/apptainer-README.md b/reproduce/software/shell/apptainer-README.md
index a7826ec..d2a14c8 100644
--- a/reproduce/software/shell/apptainer-README.md
+++ b/reproduce/software/shell/apptainer-README.md
@@ -1,7 +1,7 @@
# Maneage'd projects in Apptainer
-Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
-Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>\
+Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es>\
See the end of the file for license conditions.
For an introduction on containers, see the "Building in containers" section
@@ -47,7 +47,7 @@ software environment) to easily move it from one computer to another.
project. This file is necessary for future runs of your project
within the container.
- 3. To execute your project remote the `--build-only` and use `./run.sh` to
+ 3. To execute your project remove the `--build-only` and use `./run.sh` to
execute it. If you want to enter your Maneage'd project shell, add the
`--project-shell` option to the call inside `./run.sh`.
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index c581ade..1785977 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -41,8 +41,8 @@
#
# Known problems:
#
-# Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>
+# Copyright (C) 2025-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es>
#
# 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
@@ -71,14 +71,14 @@ set -e
# Default option values
+sif=""
jobs=0
quiet=0
source_dir=
build_only=
-base_name=""
+base_sif=""
shm_size=20gb
scriptname="$0"
-project_name=""
project_shell=0
container_shell=0
base_os=debian:stable-slim
@@ -97,9 +97,9 @@ Top-level script to build and run a Maneage'd project within Apptainer.
--source-dir=STR Directory of source code (default: 'pwd -P').
Apptainer images
+ --sif=STR Project's apptainer image (a '.sif' file).
--base-os=STR Base OS name (default: '$base_os').
- --base-name=STR Base OS apptainer image (a '.sif' file).
- --project-name=STR Project's apptainer image (a '.sif' file).
+ --base-sif=STR Base OS apptainer image (a '.sif' file).
Interactive shell
--project-shell Open the project's shell within the container.
@@ -155,10 +155,12 @@ do
--source-dir=*) source_dir="${1#*=}"; check_v "$1" "$source_dir"; shift;;
# Container options.
- --base-name) base_name="$2"; check_v "$1" "$base_name"; shift;shift;;
- --base-name=*) base_name="${1#*=}"; check_v "$1" "$base_name"; shift;;
- --project-name) project_name="$2"; check_v "$1" "$project_name"; shift;shift;;
- --project-name=*) project_name="${1#*=}"; check_v "$1" "$project_name"; shift;;
+ --sif) sif="$2"; check_v "$1" "$sif"; shift;shift;;
+ --sif=*) sif="${1#*=}"; check_v "$1" "$sif"; shift;;
+ --base-os) base_os="$2"; check_v "$1" "$base_os"; shift;shift;;
+ --base-os=*) base_os="${1#*=}"; check_v "$1" "$base_os"; shift;;
+ --base-sif) base_sif="$2"; check_v "$1" "$base_sif"; shift;shift;;
+ --base-sif=*) base_sif="${1#*=}"; check_v "$1" "$base_sif"; shift;;
# Interactive shell.
--project-shell) project_shell=1; shift;;
@@ -206,8 +208,8 @@ fi
# Set the default project and base-OS image names (inside the build
# directory).
-if [ x"$base_name" = x ]; then base_name=$build_dir/maneage-base.sif; fi
-if [ x"$project_name" = x ]; then project_name=$build_dir/maneaged.sif; fi
+if [ x"$base_sif" = x ]; then base_sif=$build_dir/maneage-base.sif; fi
+if [ x"$sif" = x ]; then sif=$build_dir/maneaged.sif; fi
@@ -278,9 +280,9 @@ fi
#
# Build the base operating system using Maneage's './project configure'
# step.
-if [ -f $project_name ]; then
+if [ -f $sif ]; then
if [ $quiet = 0 ]; then
- printf "$scriptname: info: project's image ('$project_name') "
+ printf "$scriptname: info: project's image ('$sif') "
printf "already exists and will be used. If you want to build a "
printf "new project image, give a new name to '--project-name'. "
printf "To remove this message run with '--quiet'\n"
@@ -289,12 +291,13 @@ else
# Build the basic definition, with just Debian-slim with minimal
# necessary tools.
- if [ -f $base_name ]; then
+ if [ -f $base_sif ]; then
if [ $quiet = 0 ]; then
- printf "$scriptname: info: base OS docker image ('$base_name') "
- printf "already exists and will be used. If you want to build a "
- printf "new base OS image, give a new name to '--base-name'. "
- printf "To remove this message run with '--quiet'\n"
+ printf "$scriptname: info: base OS apptainer image "
+ printf "('$base_sif') already exists and will be used. "
+ printf "If you want to build a new base OS image, give "
+ printf "a new name to '--base-sif'. To remove this "
+ printf "message run with '--quiet'\n"
fi
else
@@ -308,7 +311,7 @@ From: $base_os
EOF
# Build the base operating system container and delete the
# temporary definition file.
- apptainer build $base_name $base_def
+ apptainer build $base_sif $base_def
rm $base_def
fi
@@ -329,7 +332,7 @@ EOF
maneage_def=$build_dir/maneage.def
cat <<EOF > $maneage_def
Bootstrap: localimage
-From: $base_name
+From: $base_sif
%setup
mkdir -p \${APPTAINER_ROOTFS}/home/maneager/input
@@ -384,7 +387,7 @@ EOF
$software_dir_mnt \
--ignore-fakeroot-command \
\
- $project_name \
+ $sif \
$maneage_def
# Clean up.
@@ -396,7 +399,7 @@ fi
if ! [ x"$build_only" = x ]; then
if [ $quiet = 0 ]; then
printf "$scriptname: info: Maneaged project has been configured "
- printf "successfully in the '$project_name' image"
+ printf "successfully in the '$sif' image"
fi
exit 0
fi
@@ -418,7 +421,7 @@ else
fi
# Build the hostname from the name of the SIF file of the project name.
-hstname=$(echo "$project_name" \
+hstname=$(echo "$sif" \
| awk 'BEGIN{FS="/"}{print $NF}' \
| sed -e's|.sif$||')
@@ -453,4 +456,4 @@ apptainer $aopt \
--hostname $hstname \
--cwd /home/maneager/source \
\
- $project_name
+ $sif
diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
index 6bbd774..d88b84a 100755
--- a/reproduce/software/shell/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
@@ -34,7 +34,7 @@
# shell').
#
#
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 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
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index a409920..ca3bf6e 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -2,9 +2,9 @@
#
# Necessary preparations/configurations for the reproducible project.
#
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
#
# 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
@@ -1891,9 +1891,10 @@ ______________________________________________________
!!!!!!!!!!!!!!! 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.
+there were downloading problems, or you used the '--offline' option). 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.
diff --git a/reproduce/software/shell/docker-README.md b/reproduce/software/shell/docker-README.md
index d651e22..9e09282 100644
--- a/reproduce/software/shell/docker-README.md
+++ b/reproduce/software/shell/docker-README.md
@@ -1,6 +1,6 @@
# Maneage'd projects in Docker
-Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2021-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
See the end of the file for license conditions.
For an introduction on containers, see the "Building in containers" section
diff --git a/reproduce/software/shell/docker.sh b/reproduce/software/shell/docker.sh
index 714c75f..ab454aa 100755
--- a/reproduce/software/shell/docker.sh
+++ b/reproduce/software/shell/docker.sh
@@ -47,7 +47,7 @@
# clipped, log limit 2MiB reached]" message. We need to find a way to
# fix this (so nothing gets clipped: useful for debugging).
#
-# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2026 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
diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout
index 7b521a3..7bf747a 100755
--- a/reproduce/software/shell/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
@@ -4,7 +4,7 @@
# controlled files (with each commit) using the 'metastore' program.
#
# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 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
diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 7b98ad0..e570346 100755
--- a/reproduce/software/shell/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit
@@ -4,7 +4,7 @@
# controlled files (with each commit) using the 'metastore' program.
#
# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# WARNING:
#
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 172bdb6..8236247 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -2,7 +2,7 @@
#
# Very basic tools necessary to start Maneage's default building.
#
-# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2026 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
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
index dcdc472..861f3bf 100755
--- a/reproduce/software/shell/prep-source.sh
+++ b/reproduce/software/shell/prep-source.sh
@@ -7,7 +7,7 @@
# directory that it is run in ):
# ./prep-source.sh /FULL/ADDRESS/TO/DESIRED/BIN
#
-# Copyright (C) 2024-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2024-2026 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
@@ -77,6 +77,20 @@ fi
if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash
else shpath="$bindir"/dash
fi
+
+# On MacOS the syntax for 'stat' is a bit different, so if we are using the
+# system one on mac we need a specific syntax. The one installed by maneage
+# instead uses the ordinary Linux syntax.
+if [ -f "$bindir/stat" ] || [ x"$on_mac_os" = xno ]; then
+ format="--format %a"
+else
+ format="-f %OLp"
+fi
+
+# On MacOS 'touch' wants the time expressed according to ISO8601 with a
+# precision up to the seconds. We then use 'sed' to remove the information
+# regarding the timezone, as the format is not accepted by 'touch'.
+# LCTYPE and LANG are also required on macos systems by sed.
grep -I -r -e'/bin/sh' $(pwd)/* \
| sed -e's|:|\t|' \
| awk 'BEGIN{FS="\t"}{print $1}' \
@@ -84,8 +98,10 @@ grep -I -r -e'/bin/sh' $(pwd)/* \
| uniq \
| while read filename; do \
tmp="$filename".tmp; \
- origtime="$(date -R -r "$filename")"; \
- origperm=$(stat -c '%a' "$filename"); \
+ origtimex="$(date -Iseconds -r "$filename")"; \
+ origtime=$(echo $origtimex | sed 's/.\{6\}$//'); \
+ origperm=$(stat $format "$filename"); \
+ LC_CTYPE=C; LANG=C; \
sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \
mv "$tmp" "$filename"; \
chmod $origperm "$filename"; \
diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in
index 053f5f3..21c347f 100755
--- a/reproduce/software/shell/run-parts.in
+++ b/reproduce/software/shell/run-parts.in
@@ -10,8 +10,8 @@
# However, it didn't have a copyright statement. So one is being added
# here.
#
-# Copyright (C) 2025 Authors mentioned above.
-# Copyright (C) 2025-2024 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2026 Authors mentioned above.
+# Copyright (C) 2026-2026 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
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index 8e30931..ed1cfd0 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -15,9 +15,9 @@
#
# Discussion: https://savannah.nongnu.org/task/?15699
#
-# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
-# Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>
+# Copyright (C) 2022-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2025-2026 Giacomo Lorenzetti <glorenzetti@cefca.es>
#
# 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
@@ -51,6 +51,9 @@ basedir=$PWD
scriptname=$0
+
+
+
# The --help output
print_help() {
cat <<EOF
generated by cgit v1.2.1 (git 2.18.0) at 2026-03-17 10:28:47 +0000