{bio,tools}[foss/2025b,gompi/2025b] bakta v1.12.0, PyHMMER v0.12.0 by SethosII · Pull Request #25764 · easybuilders/easybuild-easyconfigs

SethosII · 2026-04-15T08:11:09Z

(created using eb --new-pr)

This version of bakta needs at least PyHMMER version 0.12.0, therefore the current version available in the toolchain was not sufficient.

…2025b.eb

github-actions · 2026-04-15T08:11:37Z

Updated software `bakta-1.12.0-foss-2025b.eb`

Diff against bakta-1.12.0-foss-2024a.eb

easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2024a.eb

diff --git a/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2024a.eb b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
index c0b7dff67c..5c0b01fe26 100644
--- a/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2024a.eb
+++ b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
@@ -8,49 +8,49 @@ description = """Bakta is a tool for the rapid & standardized annotation of bact
  from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations
  in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis."""
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 
 builddependencies = [
-    ('scikit-build-core', '0.11.1'),
-    ('Cython', '3.0.10'),
+    ('scikit-build-core', '0.11.5'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Biopython', '1.84'),
+    ('Python', '3.13.5'),
+    ('Biopython', '1.86'),
     ('PyYAML', '6.0.2'),
     ('PyHMMER', '0.12.0'),
-    ('matplotlib', '3.9.2'),
+    ('matplotlib', '3.10.5'),
     ('python-isal', '1.7.0'),
-    ('zlib-ng', '2.2.1'),
+    ('python-zlib-ng', '0.5.1'),
     ('archspec', '0.2.5'),
 ]
 
 exts_list = [
     ('about_time', '4.2.1', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['8bbf4c75fe13cbd3d72f49a03b02c5c7dca32169b6d49117c257e7eb3eaee341'],
     }),
     ('grapheme', '0.6.0', {
         'checksums': ['44c2b9f21bbe77cfb05835fec230bd435954275267fea1858013b102f8603cca'],
     }),
     ('alive_progress', '3.2.0', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['0677929f8d3202572e9d142f08170b34dbbe256cc6d2afbf75ef187c7da964a8'],
     }),
     ('pyCirclize', '1.7.1', {
-        'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl',
+        'source_tmpl': SOURCELOWER_PY3_WHL,
         'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'],
     }),
     ('pyrodigal', '3.7.0', {
         'checksums': ['415940f07a9e6e60ca023b99381f2d5f62f801914b9edd6da5a28dd7307b091d'],
     }),
     ('xopen', '2.0.2', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['74e7f7fb7e7f42bd843c798595fa5a52086d7d1bf3de0e8513c6615516431313'],
     }),
     (name, version, {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'source_tmpl': SOURCE_PY3_WHL,
         'checksums': ['6772bc9defe423648a2e69976d91cb6ee109bf528aee01f235f4228e1a590b34'],
     }),
 ]
@@ -64,4 +64,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ['%s --help' % bin for bin in local_bins]
 
-moduleclass = 'bio'
+moduleclass = 'tools'

Diff against bakta-1.10.1-foss-2023a.eb

easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023a.eb b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
index 0b6381d74d..5c0b01fe26 100644
--- a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
@@ -1,28 +1,29 @@
 easyblock = 'PythonBundle'
 
 name = 'bakta'
-version = '1.10.1'
+version = '1.12.0'
 
 homepage = "https://github.com/oschwengers/bakta"
 description = """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids
  from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations
  in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 
 builddependencies = [
-    ('scikit-build-core', '0.9.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Biopython', '1.83'),
-    ('PyYAML', '6.0'),
-    ('PyHMMER', '0.10.15'),
-    ('matplotlib', '3.7.2'),
-    ('python-isal', '1.6.1'),
-    ('zlib-ng', '2.1.6'),
-    ('archspec', '0.2.1'),
+    ('Python', '3.13.5'),
+    ('Biopython', '1.86'),
+    ('PyYAML', '6.0.2'),
+    ('PyHMMER', '0.12.0'),
+    ('matplotlib', '3.10.5'),
+    ('python-isal', '1.7.0'),
+    ('python-zlib-ng', '0.5.1'),
+    ('archspec', '0.2.5'),
 ]
 
 exts_list = [
@@ -41,9 +42,8 @@ exts_list = [
         'source_tmpl': SOURCELOWER_PY3_WHL,
         'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'],
     }),
-    ('pyrodigal', '3.6.3', {
-        'source_tmpl': '%(name)s-%(version)s-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl',
-        'checksums': ['e9f2f2aa99299971d52e8e097d2fe3059a6bfc1d42674cfcba2b7ec18e8df8ea'],
+    ('pyrodigal', '3.7.0', {
+        'checksums': ['415940f07a9e6e60ca023b99381f2d5f62f801914b9edd6da5a28dd7307b091d'],
     }),
     ('xopen', '2.0.2', {
         'source_tmpl': SOURCE_PY3_WHL,
@@ -51,7 +51,7 @@ exts_list = [
     }),
     (name, version, {
         'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['82967b4eefd2a1084743211fe955fa394972c2d2c878c6682e00b13dabc5a445'],
+        'checksums': ['6772bc9defe423648a2e69976d91cb6ee109bf528aee01f235f4228e1a590b34'],
     }),
 ]

Diff against bakta-1.10.1-foss-2023b.eb

easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
index dc0cd1cd1b..5c0b01fe26 100644
--- a/easybuild/easyconfigs/b/bakta/bakta-1.10.1-foss-2023b.eb
+++ b/easybuild/easyconfigs/b/bakta/bakta-1.12.0-foss-2025b.eb
@@ -1,28 +1,29 @@
 easyblock = 'PythonBundle'
 
 name = 'bakta'
-version = '1.10.1'
+version = '1.12.0'
 
 homepage = "https://github.com/oschwengers/bakta"
 description = """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids
  from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations
  in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis."""
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025b'}
 
 builddependencies = [
-    ('scikit-build-core', '0.9.3'),
+    ('scikit-build-core', '0.11.5'),
+    ('Cython', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Biopython', '1.84'),
-    ('PyYAML', '6.0.1'),
-    ('PyHMMER', '0.10.15'),
-    ('matplotlib', '3.8.2'),
-    ('python-isal', '1.6.1'),
-    ('zlib-ng', '2.2.2'),
-    ('archspec', '0.2.2'),
+    ('Python', '3.13.5'),
+    ('Biopython', '1.86'),
+    ('PyYAML', '6.0.2'),
+    ('PyHMMER', '0.12.0'),
+    ('matplotlib', '3.10.5'),
+    ('python-isal', '1.7.0'),
+    ('python-zlib-ng', '0.5.1'),
+    ('archspec', '0.2.5'),
 ]
 
 exts_list = [
@@ -41,8 +42,8 @@ exts_list = [
         'source_tmpl': SOURCELOWER_PY3_WHL,
         'checksums': ['e0c049877b1ee47245866cc9968f2aded5fe3ead8a3333841536dc29fd14bc90'],
     }),
-    ('pyrodigal', '3.6.3', {
-        'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'],
+    ('pyrodigal', '3.7.0', {
+        'checksums': ['415940f07a9e6e60ca023b99381f2d5f62f801914b9edd6da5a28dd7307b091d'],
     }),
     ('xopen', '2.0.2', {
         'source_tmpl': SOURCE_PY3_WHL,
@@ -50,7 +51,7 @@ exts_list = [
     }),
     (name, version, {
         'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['82967b4eefd2a1084743211fe955fa394972c2d2c878c6682e00b13dabc5a445'],
+        'checksums': ['6772bc9defe423648a2e69976d91cb6ee109bf528aee01f235f4228e1a590b34'],
     }),
 ]

Updated software `PyHMMER-0.12.0-gompi-2025b.eb`

Diff against PyHMMER-0.12.0-gompi-2024a.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
index b856a2081f..86a52cfdae 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2024a.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
@@ -16,16 +16,16 @@ pyhmmer is a Python package, implemented using the Cython language, that
 provides bindings to HMMER3. It directly interacts with the HMMER internals,
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 
 builddependencies = [
-    ('Cython', '3.0.10'),
-    ('scikit-build-core', '0.11.1'),
+    ('Cython', '3.1.2'),
+    ('scikit-build-core', '0.11.5'),
 ]
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.13.5'),
     ('HMMER', '3.4'),
-    ('psutil', '6.0.0'),
+    ('psutil', '7.0.0'),
 ]

Diff against PyHMMER-0.11.3-gompi-2025b.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.11.3-gompi-2025b.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.11.3-gompi-2025b.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
index 3867afe5dc..86a52cfdae 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.11.3-gompi-2025b.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
@@ -4,7 +4,7 @@
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.11.3'
+version = '0.12.0'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
@@ -22,16 +22,21 @@ builddependencies = [
     ('Cython', '3.1.2'),
     ('scikit-build-core', '0.11.5'),
 ]
-
 dependencies = [
     ('Python', '3.13.5'),
     ('HMMER', '3.4'),
-    ('psutil', '7.0.0')
+    ('psutil', '7.0.0'),
 ]
 
+
 exts_list = [
-    ('%(namelower)s', version, {
-        'checksums': ['1d80300653f42db74e58be6727065bef78974a538821db55f9e38d3bb48a3304'],
+    ('pyhmmer', version, {
+        'patches': ['pyhmmer-disable-sabi-compat.patch'],
+        'preinstallopts': "export PYHMMER_FORCE_CYTHON=1 && ",
+        'checksums': [
+            {'pyhmmer-0.12.0.tar.gz': '27cdfd3cdf72abcc7a6670825fc0195e8ff01d4820efd0f99aec03d3972a922e'},
+            {'pyhmmer-disable-sabi-compat.patch': '972e4c2c31ab6ba564ea025b76afc8e5073194bbafa940c582aecd1f3ae81675'},
+        ],
     }),
 ]

Diff against PyHMMER-0.10.15-gompi-2023a.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
index 212f4e8f79..86a52cfdae 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.12.0-gompi-2025b.eb
@@ -4,7 +4,7 @@
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.10.15'
+version = '0.12.0'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
@@ -16,25 +16,28 @@ pyhmmer is a Python package, implemented using the Cython language, that
 provides bindings to HMMER3. It directly interacts with the HMMER internals,
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 
 builddependencies = [
-    ('Cython', '3.0.8'),
+    ('Cython', '3.1.2'),
+    ('scikit-build-core', '0.11.5'),
 ]
-
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '3.13.5'),
     ('HMMER', '3.4'),
-    ('psutil', '5.9.8')
+    ('psutil', '7.0.0'),
 ]
 
+
 exts_list = [
-    ('%(namelower)s', version, {
-        # Requirement for `psutil` is too strict.
-        'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ",
-        'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'],
+    ('pyhmmer', version, {
+        'patches': ['pyhmmer-disable-sabi-compat.patch'],
+        'preinstallopts': "export PYHMMER_FORCE_CYTHON=1 && ",
+        'checksums': [
+            {'pyhmmer-0.12.0.tar.gz': '27cdfd3cdf72abcc7a6670825fc0195e8ff01d4820efd0f99aec03d3972a922e'},
+            {'pyhmmer-disable-sabi-compat.patch': '972e4c2c31ab6ba564ea025b76afc8e5073194bbafa940c582aecd1f3ae81675'},
+        ],
     }),
 ]
 
-
 moduleclass = 'bio'

Thyre · 2026-06-15T09:24:54Z

@boegelbot please test @ jsc-zen3

Thyre · 2026-06-15T09:33:04Z

Unrelated failure due to the Python checks introduced in EB v5.3.0.

Test report by @Thyre
FAILED
Build succeeded for 3 out of 6 (total: 7 mins 3 secs) (2 easyconfigs in total)
jrc0901.jureca - Linux Rocky Linux 9.7, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 595.71.05, Python 3.9.25
See https://gist.github.com/Thyre/0f80faf8c5f551cab8fc51d53c8312b4 for a full test report.

boegelbot · 2026-06-15T09:40:18Z

@Thyre: 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=25764 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25764 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10766

Test results coming soon (I hope)...

Details

- notification for comment with ID 4706433620 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 · 2026-06-15T09:47:11Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (total: 6 mins 36 secs) (2 easyconfigs in total)
jsczen3c3.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/f36c48195baa375c1a3bd9bfb098e085 for a full test report.

Thyre · 2026-06-15T09:49:38Z

    File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
    File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
    File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
    File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
    File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
    File "/project/def-maintainers/boegelbot/rocky9/zen3/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/lib/python3.13/site-packages/pbr/pbr_json.py", line 19, in <module>
      from pbr import git
    File "/project/def-maintainers/boegelbot/rocky9/zen3/software/Python-bundle-PyPI/2025.07-GCCcore-14.3.0/lib/python3.13/site-packages/pbr/git.py", line 28, in <module>
      import pkg_resources
  ModuleNotFoundError: No module named 'pkg_resources'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> No available output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.13.5-GCCcore-14.3.0/bin/python /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.13.5-GCCcore-14.3.0/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/eb-axdx7sjy/tmp4jvd79n7
  cwd: /tmp/boegelbot-25764/bakta/1.12.0/foss-2025b/grapheme/grapheme-0.6.0
  Preparing metadata (pyproject.toml): finished with status 'error'
error: metadata-generation-failed

adding easyconfigs: bakta-1.12.0-foss-2025b.eb, PyHMMER-0.12.0-gompi-…

650d1d5

…2025b.eb

github-actions Bot added 2025b issues & PRs related to 2025b common toolchains update labels Apr 15, 2026

Thyre added this to the release after 5.3.1 milestone Jun 15, 2026

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{bio,tools}[foss/2025b,gompi/2025b] bakta v1.12.0, PyHMMER v0.12.0 - #25764

{bio,tools}[foss/2025b,gompi/2025b] bakta v1.12.0, PyHMMER v0.12.0#25764
SethosII wants to merge 1 commit into
easybuilders:developfrom
SethosII:20260415101106_new_pr_bakta1120

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github-actions Bot commented Apr 15, 2026

Updated software bakta-1.12.0-foss-2025b.eb

Updated software PyHMMER-0.12.0-gompi-2025b.eb

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SethosII commented Apr 15, 2026 •

edited

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Updated software `bakta-1.12.0-foss-2025b.eb`

Updated software `PyHMMER-0.12.0-gompi-2025b.eb`

Thyre commented Jun 15, 2026 •

edited

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