From 3c9bf3aff30f02c7d31bd86f36c4db2520f8ffa4 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Fri, 3 May 2024 13:07:41 +0200 Subject: Configuration: no dependency on /bin/sh and useful run-time options SUMMARY: no change necessary in your project, this commit only involves changes in how already-existing software are built. Some handy options have also been added to the top-level project script and the copyright years have been updated. Until now, if the host's '/bin/sh' had conflicts with the Maneage environment, the configuration of Maneage would crash as soon as we entered the building of high-level software. The full scenario is described in the comments of the newly added 'reproduce/software/shell/prep-source.sh'. This is most relevant when building older Maneage'd project in newer environments. With this commit, the following changes were made to avoid the problem above: - Maneage edits the source code of all installed software to replace '/bin/sh' with Maneage's own shell before the programs are built. Through this, we were able to solve the problem described above. - The portable '#!/usr/bin/env sh' shebangs are now used at the start of the scripts that run during configure time so it uses the first available shell that it finds in its PATH (the system's before Dash is built), then Dash, and after Dash is built, Bash. - For TeXLive, since we don't install it from source, it was necessary to add the libraries necessary for the local '/bin/sh' in LD_LIBRARY_PATH. Some high-level options have been added to the './project' script to simplify certain operations: --keep-going: do not stop upon the first crash, but keep going on to build targets until all build-able targets have been built. This is very useful for debugging large pipelines and allows you to isolate the problematic part of your project. --highlight-all: equivalent to calling both '--highlight-new' & '--highlight-notes'. --- project | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) (limited to 'project') diff --git a/project b/project index 0c65211..9d4d6df 100755 --- a/project +++ b/project @@ -3,8 +3,8 @@ # High-level script to manage the project. # Run './project --help' for a description of how to use it. # -# Copyright (C) 2019-2023 Mohammad Akhlaghi -# Copyright (C) 2021-2023 Raul Infante-Sainz +# Copyright (C) 2019-2025 Mohammad Akhlaghi +# Copyright (C) 2021-2025 Raul Infante-Sainz # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -37,6 +37,7 @@ host_cc=0 operation= build_dir= input_dir= +keep_going= check_config= make_targets= software_dir= @@ -118,6 +119,7 @@ Configure options: Configure and Make options: -d, --debug[=FLAGS] In configure: use -j1, no -k, and no Zenodo check. In make: 'FLAGS' will be directly passed to 'make'. + -k, --keep-going Keep going when some targets can't be made. -g, --group=STR Build and run with write permissions for a group. -j, --jobs=INT Number of threads to build/run the software. -?, --help Print this help list. @@ -127,6 +129,7 @@ Make (analysis) options: Make (final PDF) options: --refresh-bib Force refresh the bibliography. + --highlight-all Activate '--highlight-new' & '--highlight-notes'. --highlight-new Highlight '\new' parts of text as green. --highlight-notes Show '\tonote' regions as red text in PDF. @@ -201,15 +204,20 @@ do -j|--jobs) jobs="$2"; check_v jobs "$jobs"; shift;shift;; -j=*|--jobs=*) jobs="${1#*=}"; check_v jobs "$jobs"; shift;; -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v jobs "$jobs"; shift;; + -k|--keep-going) keep_going="--keep-going"; shift;; + -k=*|--keep-going=*) on_off_option_error --keep-going -k;; + -k*) on_off_option_error --keep-going -k;; -'?'|--help) print_help; exit 0;; -'?'*|--help=*) on_off_option_error --help -?;; - # Make options - # ------------ - # - # Note that Make's 'debug' can take values, but when called without any - # value, it is like giving it a value of 'a'): + # Make options (analysis): + -p|--prepare-redo) prepare_redo=1; shift;; + -p=*|--prepare-redo=*) on_off_option_error --prepare-redo; shift;; + + # Make options (final PDF): --refresh-bib) [ -f tex/src/references.tex ] && touch tex/src/references.tex; shift;; + --highlight-all) highlightnew=1; highlightnotes=1; shift;; + --highlight-all=*) on_off_option_error --highlight-new;; --highlight-new) highlightnew=1; shift;; --highlight-new=*) on_off_option_error --highlight-new;; --highlight-notes) highlightnotes=1; shift;; @@ -218,15 +226,14 @@ do echo "Please set the operation before calling '--debug'"; exit 1 elif [ x$operation = xconfigure ]; then debug=a; shift; elif [ x$operation = xmake ]; then - if [ x"$2" = x ]; then echo "In make-mode, '--debug' needs a value"; exit 1 + if [ x"$2" = x ]; then + echo "In make-mode, '--debug' needs a value; see GNU Make manual"; exit 1 else debug="$2"; check_v debug "$debug"; shift;shift; fi else echo "Operation '$operation' not recognized, please use 'configure' or 'make'" fi;; -d=*|--debug=*) debug="${1#*=}"; check_v debug "$debug"; shift;; -d*) debug=$(echo "$1" | sed -e's/-d//'); check_v debug "$debug"; shift;; - -p|--prepare-redo) prepare_redo=1; shift;; - -p=*|--prepare-redo=*) on_off_option_error --prepare-redo; shift;; # Unrecognized option: -*) echo "$scriptname: unknown option '$1'"; exit 1;; @@ -390,6 +397,7 @@ controlled_env() { envmake="$envmake highlightnew=$highlightnew" envmake="$envmake highlightnotes=$highlightnotes .local/bin/make" envmake="$envmake --no-builtin-rules --no-builtin-variables -f $1" + envmake="$envmake $keep_going" if ! [ x"$debug" = x ]; then envmake="$envmake --debug=$debug"; fi # Set the number of jobs. Note that for the 'configure.sh' script the -- cgit v1.2.1 From 890858795fd6e0c8c1f3050adec7f4bc78e9e47c Mon Sep 17 00:00:00 2001 From: Giacomo Lorenzetti Date: Tue, 21 Jan 2025 18:57:10 +0100 Subject: IMPORTANT: 73 software upgrades and added offline mode Summary: This is a software update to make Maneage more portable and up to date. It does not involve any Maneage infrastructure changes. You should just re-build your project to make sure the updated software haven't removed/changed any of their features that you were using. Until now, the software in Maneage had not been updated for almost 2.5 years (since August 2022) and were starting to get dated! Also, when no internet is available (for example in a HPC), the Zenodo check would always cause a crash and needed to be commented manually. With this commit, all the basic software that had been updated as well as the dependencies of Gnuastro (which we commit to maintaining) have been updated after a check of their webpage (see the full list below). To fix the offline issue, a new '--offline' option has been added to the project script. The other following changes were made: - tarball-prepare: has become more resilient (for dealing with file name with spaces or Lzip, which should not be compressed). - Readme: improve documentation when used in Docker. Below you can see the list of basic software that have been updated. The only basic software that have not been updated upstream since the previous Maneage software update are 'bison', 'flock', 'm4', 'pkgconfig', 'unzip' and 'zip'. bash 5.2-rc2 5.2.37 binutils 2.39 2.43.1 coreutils 9.1 9.6 curl 7.84.0 8.11.1 dash 0.5.11-057cd65 0.5.12 diffutils 3.8 3.10 file 5.42 5.46 findutils 4.9.0 4.10.0 gawk 5.1.1 5.3.1 gcc 12.1.0 14.2.0 gettext 0.21 0.23.1 git 2.37.1 2.48.1 gmp 6.2.1 6.3.0 grep 3.7 3.11 gzip 1.12 1.13 help2man 1.49.2 1.49.3 isl 0.24 0.27 less 590 668 libiconv 1.17 1.18 libtool 2.4.7 2.5.4 libunistring 1.0 1.3 libxml2 2.9.12 2.13.5 lzip 1.23 1.25 make 4.3 4.4.1 mpc 1.2.1 1.3.1 mpfr 4.1.0 4.2.1 nano 6.4 8.3 ncurses 6.3 6.5 openssl 3.0.5 3.4.0 perl 5.36.0 5.40.1 podlators 4.14 6.0.2 readline 8.2-rc2 8.2.13 sed 4.8 4.9 tar 1.34 1.35 texinfo 6.8 7.2 wget 1.21.2 1.25.0 which 2.21 2.23 xz 5.2.5 5.6.3 zlib 1.2.11 1.3.1 The high-level software that have been updated. autoconf 2.71 2.72 automake 1.16.5 1.17 cfitsio 4.1.0 4.5.0 cmake 3.24.0 3.31.5 expat 2.4.1 2.6.4 fontconfig 2.14.0 2.16.0 freetype 2.11.0 2.13.3 ghostscript 9.56.1 10.04.0 gnuastro 0.18 0.23 gsl 2.7 2.8 libffi 3.4.2 3.4.7 libgit2 1.3.0 1.9.0 libice 1.0.10 1.1.2 libidn 1.38 1.42 libjpeg 9e 9f libpaper 1.1.28 1.1.29 libpng 1.6.37 1.6.46 libpthread-stubs 0.4 0.5 libsm 1.2.3 1.2.5 libtiff 4.4.0 4.7.0 libxau 1.0.9 1.0.12 libxcb 1.15 1.17 libxdmcp 1.1.3 1.1.5 libxext 1.3.4 1.3.6 libxt 1.2.1 1.3.1 python 3.10.6 3.13.12 util-macros 1.19.3 1.20.2 wcslib 7.11 8.4 xcb-proto 1.15 1.17 xorgproto 2022.1 2024.1 xtrans 1.4.0 1.5.2 --- project | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'project') diff --git a/project b/project index 9d4d6df..ac801b8 100755 --- a/project +++ b/project @@ -34,6 +34,7 @@ jobs=0 # 0 is for the default for the 'configure.sh' script. group= debug= host_cc=0 +offline= operation= build_dir= input_dir= @@ -184,6 +185,8 @@ do -e*|--existing-conf=*) on_off_option_error --existing-conf -e;; --host-cc) host_cc=1; shift;; --host-cc=*) on_off_option_error --host-cc;; + --offline) offline=1; shift;; + --offline=*) on_off_option_error --offline;; -i|--input-dir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;; -i=*|--input-dir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;; -i*) input_dir=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$input_dir"; shift;; @@ -455,6 +458,7 @@ case $operation in export jobs=$jobs export debug=$debug export host_cc=$host_cc + export offline=$offline export build_dir=$build_dir export input_dir=$input_dir export scriptname=$scriptname -- cgit v1.2.1