Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

{bio}[foss/2023b] pmx v20241209 #22158

Open
wants to merge 1 commit into
base: develop
Choose a base branch
from

Conversation

PetrKralCZ
Copy link
Collaborator

@PetrKralCZ PetrKralCZ commented Jan 15, 2025

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#491

Copy link

Updated software pmx-20241209-foss-2023b.eb

Diff against pmx-2.0-foss-2020b-Python-2.7.18.eb

easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb
index 00f2bd3ae2..2d7d95cf93 100644
--- a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/p/pmx/pmx-20241209-foss-2023b.eb
@@ -1,32 +1,35 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'pmx'
-version = '2.0'
-versionsuffix = '-Python-%(pyver)s'
+version = '20241209'
+local_commit = '09b57c6'  # develop branch
 
-homepage = 'https://github.com/deGrootLab/pmx'
-description = """pmx (formerly pymacs) is a small bunch of classes to
-read structure files such as pdb or gro and trajectory data in gromacs
-xtc format. Over the years it has been extended towards a versatile
-(bio-) molecular structure manipulation package with some additional
-functionalities, e.g. gromacs file parsers and scripts for setup and
-analysis of free energy calculations."""
+homepage = 'https://degrootlab.github.io/pmx/'
+description = "Toolkit for free-energy calculation setup/analysis and biomolecular structure handling."
 
-toolchain = {'name': 'foss', 'version': '2020b'}
-
-sources = [SOURCE_TAR_GZ]
-checksums = ['323dd5091c62255f1f6cbfc6b4869ef9672a188ce7e3439ed1bb6e9cf2c3804c']
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '2.7.18'),
-    ('SciPy-bundle', '2020.11', versionsuffix),
-    ('matplotlib', '2.2.5', versionsuffix),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
 ]
 
-download_dep_fail = True
 use_pip = True
 sanity_pip_check = True
 
-sanity_check_commands = ['pmx --help']
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/deGrootLab/pmx/archive/'],
+        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['b76d64a54fd05cb859d5bb4799f0929c9af3f789a2277d699a08962fbe6c4075'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from pmx.gmx import set_gmxlib; set_gmxlib()'",
+    'pmx --help',
+    'echo "no" | pmx gmxlib',
+]
 
-moduleclass = 'tools'
+moduleclass = 'bio'

@PetrKralCZ
Copy link
Collaborator Author

@boegelbot please test @ generoso

@boegelbot
Copy link
Collaborator

@PetrKralCZ: Request for testing this PR well received on login1

PR test command 'EB_PR=22158 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22158 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14946

Test results coming soon (I hope)...

- notification for comment with ID 2592902338 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/10aea11c48a4d2ba961e36a7186ded7c for a full test report.

@PetrKralCZ
Copy link
Collaborator Author

@boegelbot please test @ jsc-zen3

@boegelbot
Copy link
Collaborator

@PetrKralCZ: 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=22158 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22158 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5530

Test results coming soon (I hope)...

- notification for comment with ID 2592972268 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

@boegelbot
Copy link
Collaborator

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/d8c9f8d1cb3db6aced2ae29269a119f1 for a full test report.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

pmx
2 participants