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Summary: this commit has no effect on your project's analysis steps, just
check the list of changed Python software versions (if you used them).
Until now, the Python packages of Maneage had not been maintained for some
time, there were several portability issues: updates to the GNU C Library
needed an update to some of the basic software, and the latest macOS
features caused some crashes.
With this commit, along with the software version updates of [1], the
removed software of [2] and newly added software of [3], the following
issues in Maneage have been addressed:
- README-hacking:
- Published paper list: Added links to two published papers.
- Publication checklist: added tips on how to squash the full LaTeX
source of a Maneage'd projet (which includes many LaTeX files) into a
single LaTeX file for some journals.
- A new "Maneage Development Workflow" section has been added; see it
for details.
- paper.mk: empty macro files are not included in the built 'project.tex'
since they have no effect and because they can cause problems with
uploading to arXiv (which removes empty files).
- verify.mk: when verification is activated:
- When a macro file does not exist (can happen by mistake), an error is
printed to remind the author.
- Better dealing with empty macro files (no need to add their hash).
- versions.conf: 26 Python packages that cannot currently be built with
the new Python build system of Maneage have been separated and commented
to cause an early crash if they are required; and encourage volunteers
to help update them.
This commit is a git "squash" of contributions from the following people
- Boud Roukema: updated/added Python packages and fixed many portability
issues.
- Faezeh Bidjarchian: fixed some portability issues on macOS.
- Giacomo Lorenzetti: tested and fixed issues in newly added software.
- Khalid Masum: fixed issue with order of LD_LIBRARY_PATH in 'basic.mk'.
- Mohammad Akhlaghi: fixed basic software issues and reviewed edits for
the merge.
- Raul Infante-Sainz: fixed portability issues on macOS.
- Sepideh Eskandarlou: helped in finding the verification fixes.
[1] Updated software
Name Group Version (old -> new)
---- ----- --------------------
GNU Coreutils basic 9.9 -> 9.11
GNU Gettext basic 0.26 -> 1.0
GNU libunistring basic 1.4.1 -> 1.4.2
GNU M4 basic 1.4.20 -> 1.4.21
GNU Nano basic 8.7 -> 9.0
Ninja high-level 1.12.1 -> 1.13.2
OpenMPI high-level 4.1.1 -> 5.0.10
SWIG high-level 4.0.2 -> 4.3.1
Zip high-level 3.0 -> 3.0-15
Astropy python 7.0.1 -> 7.1.0
mpi4py python 3.1.3 -> 4.0.3
setuptools python 75.8.0 -> 80.8.0
[2] Removed software: 'podlators' has been removed from basic software
because the necessary scripts that it provided are included in Perl's
default installation.
[3] New software:
Name Group Version
---- ----- -------
framel high-level 8.47.3
GNU Parallel high-level 20260322
Healpix high-level 3.83-2024Nov13
Metaio high-level 8.5.0-a5da19d
PCRE2 high-level 10.45
SQLite high-level 3.53.0
TCL high-level 9.1a1
TK high-level 9.1a1
tzdb high-level 2026a
lalsuite high-level v7.26-15-g1e4c5e5080
astropy-healpix python 1.1.2
colorama python 0.4.6
cosmodesi-mpytools python 1.0.0-04369fc9
exceptiongroup python 1.3.0
filt-scm python 1.7.0
hatchling python 1.27.0
hatch-vcs python 0.5.0
healpy python 1.18.1
joblib python 1.5.0
igwn-ligolw python 2.1.0
igwn-segments python 2.1.0
iniconfig python 2.1.0
ligo-skymap python 2.4.0
lscsoft-glue python 4.1.0
networkx python 3.5
pandas python 2.2.3
pathspec python 0.12.1
pluggy python 1.6.0
pyfftw python 0.15.1
pygments python 2.19.2
pytest python 8.4.1
python3-fitsio python 1.3.0
pytz python 2025.2
scikit-base python 0.12.2
scikit-learn python 1.6.1
threadpoolctl python 3.6.0
tqdm python 4.67.1
trove-classifiers python 2025.5.9.12
versioneer python 0.29
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Summary: after merging this commit into your project, it should be
re-configured since the location of software installation files like
'LOCAL.conf' or the LaTeX macros of the software environment have
changed. But it should not affect the analysis phase of your project.
Until this commit, it was not possible to run a pre-built Maneage'd project
(in a container) on a newly cloned Maneage'd project source. This was
because the containers should be read-only, but during the various checks
of the configuration (to verify that we are using the same software
environment in the container and the source), we were writing/testing many
things in the build directory, and 'LOCAL.conf' which was actually in the
source directory!
Furthermore, the '.local' and '.build' were built at configure time, making
it hard to run the same container from a newly cloned Maneage'd project. To
make things harder for the scenario above, the 'configure.sh' script would
pause on every message and didn't have a quiet mode (making it practically
impossible to run './project configure' before './project make' on every
container run).
With this commit, all these issues have been addressed and it is now
possible to simply get a built container, clone a Maneage'd project and run
the analysis (using the built environment of the container that is verified
on every run). The respective changes/additions are described below:
- The high-level container scripts ('apptainer.sh' and 'docker.sh', along
with their READMEs) have been moved to the 'reproduce/software/shell'
directory and the old 'reproduce/software/containers' directory has been
deleted. This is because we have classified the software files by their
language/format and the container scripts are scripts in the end.
- The './project' script:
- Now has two extra options: '--quiet' and '--no-pause'. Both are
directly passed to the 'configure.sh' script. They will respectively
disable any informative printed message or any pause after that
message (if it is printed).
- The '--build-dir' option is now also relevant for './project make':
when it is given, it will re-create the two '.build' and '.local'
symbolic links at the top source directory in all scenarios
('configure', 'make' or 'shell'). This will allow both the
configuration, analysis and shell phases to safely assume they exist
and match the user's desire at run-time.
- The build/analysis directory's sub-directories that need to be built
before 'top-make.mk' are now built in a separate function to help in
readability.
- The 'configure.sh' script:
- For developers: a new 'check_elapsed' variable has been defined that
will enable the newly added 'elapsed_time_from_prev_step'
function. This function should be used from now on at the end of
every major step to help find bottlenecks.
- The targets of the software in 'pre-make-build.sh' now also have the
version of the software in their file name. Until now, they didn't have
the version, so there was no way to detect if the software has been
updated or not in the source. For Lzip and Make (that also get built
after GCC), the ones in this script have a '-pre-make' suffix also.
- 'Local.conf.in' now has descriptions for every variable.
- The '-std=gnu17' option is now used instead of '-std=c17' for basic
software that cannot be built without specifying the C standard in GCC
15.1 (described in previous commit: 2881fc0a6205). See [1] for more
details; in summary: '-std=gnu17' is also supported on macOS's Clang and
has some features that 'pkg-config' needs
- Generally: some longer code lines have been broken or indentation
decreased to fit the 75 character line length. This has not reduced
readability however. For example the long 'echo' commands are now
replaced by multiple 'printf's, or the indentation is still clearly
visible.
The seeds of the work on this commit started by a branch containing three
commits by Giacomo Lorenzetti (133 insertions, 100 deletions). Upon merging
with the main 'maneage' branch, they were generalized and re-organized to
become this commit.
The following issues have also been addressed with this commit:
- The LaTeX calls (during the building of 'paper.pdf') do not contain
Maneage'd dynamic libraries. This is because we don't build the LaTeX
binaries from source, an TeXLive manager uses the host environment.
- The 'docker.sh' script:
- Adds the '--project-name' option: its internal variable existed, but
the option for the user to define it at run-time was not.
- Ported to macOS: it does not check being a member of the 'docker'
group, and finds the number of threads using macOS-specific tools.
- The 'apptainer.sh' script:
- Now installs 'wget' in the base container also (necessary when the
user doesn't have the tarballs).
[1] https://savannah.nongnu.org/bugs/?67068#comment2
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