[BUGFIX:GROMACS] Build with gmxapi distributed with the GROMACS source code

[gkaf89]

The gmxapi from PyPI is replaced with the version distributed with GROMACS. The version in GROMACS source code is slightly newer.

The version number mentioned in the TOML file is out of date. The correct number is located in

python_packaging/gmxapi/src/gmxapi/version.py

and agrees with the documentation. This commit also patches the TOML file to ensure that the package number in the Python environment is the same as the package number in version.py.

Related pull requests

• {bio}[foss/2025b] GROMACS v2025.4 #24956
• {bio}[foss/2023b] GROMACS v2024.2 w/ CUDA 12.5.0 #20809
• {bio}[foss/2024a] GROMACS v2024.4 w/ PLUMED 2.9.2 #25203
• {bio}[foss/2024a] GROMACS v2024.4 #25328

Related issues

Issue reported upstream: https://gitlab.com/gromacs/gromacs/-/issues/5554

[gkaf89]

Waiting for a response in the upstream issue to set to ready.

[gkaf89]

There was no reply in the issue in GROMACS, so I am marking as ready.

[boegel]

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16
EB_ARGS="--installpath /tmp/$USER/pr25188"

[boegelbot]

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=25188 EB_ARGS="--installpath /tmp/$USER/pr25188" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25188 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 10185

Test results coming soon (I hope)...

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