{bio}[GCCcore/13.3.0,foss/2024a] Cython v3.2.4, learnMSA v3.0.0, logomaker v0.8.7, ...

[sassy-crick]

(created using eb --new-pr)

Based on PR #24919 , updated to latest 1.x branch and latest 2.y branch. The stopper for a newer toolchain is the dependency on TensorFlow, which dictates the toolchain-version. Cython-3.2.4 is needed for some builds.

[github-actions]

Updated software Cython-3.2.4-GCCcore-13.3.0.eb

Diff against Cython-3.2.4-GCCcore-14.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
index a6ab92ad23..5903ab7417 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
@@ -13,17 +13,17 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
 
 builddependencies = [
-    ('binutils', '2.44'),
+    ('binutils', '2.42'),
 ]
 
 dependencies = [
-    ('Python', '3.13.5'),
+    ('Python', '3.12.3'),
 ]
 
 sanity_check_paths = {

Diff against Cython-3.2.4-GCCcore-15.2.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
index 82b127ac3a..5903ab7417 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-15.2.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
@@ -13,13 +13,18 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
 
-builddependencies = [('binutils', '2.45')]
-dependencies = [('Python', '3.14.2')]
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+]
 
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],

Diff against Cython-0.29.37-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
index 786725bb50..5903ab7417 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.2.4-GCCcore-13.3.0.eb
@@ -1,7 +1,7 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '0.29.37'
+version = '3.2.4'
 
 homepage = 'https://cython.org/'
 description = """
@@ -15,33 +15,22 @@ docurls = [
 
 toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
 
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['84226ecd313b233da27dc2eb3601b4f222b8209c3a7216d8733b031da1dc64e6']
+
 builddependencies = [
     ('binutils', '2.42'),
-    ('PDM', '2.18.2'),
 ]
 
 dependencies = [
     ('Python', '3.12.3'),
 ]
 
-exts_list = [
-    ('imp2importlib', '0.1.1', {
-        'modulename': 'imp',
-        'checksums': ['42646ca533aae876cf5317033dc4e3f19142bd2ba8d0d7c34edd548629e6f240'],
-    }),
-    (name, version, {
-        'checksums': ['f813d4a6dd94adee5d4ff266191d1d95bf6d4164a4facc535422c021b2504cfb'],
-    }),
-]
-
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
-sanity_check_commands = [
-    "cython --version",
-    "python -c 'import pyximport'",
-]
+sanity_check_commands = ["cython --version"]
 
 moduleclass = 'lang'

[sassy-crick]

@boegelbot please test @ jsc-zen3

[boegelbot]

@sassy-crick: 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=26557 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26557 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 11065

Test results coming soon (I hope)...

Details

- notification for comment with ID 5106444476 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]

Test report by @boegelbot
SUCCESS
Build succeeded for 7 out of 7 (total: 13 mins 34 secs) (7 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.8, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/eb6821c734ae086f0ee53de8b2181fe1 for a full test report.