{bio}[foss/2023a] chewBBACA v3.3.10 #22038

pavelToman · 2024-12-16T17:42:18Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#473

github-actions · 2024-12-16T17:42:47Z

Updated software `chewBBACA-3.3.10-foss-2023a.eb`

Diff against chewBBACA-3.3.9-foss-2022b.eb

easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb

diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb
index b9964db690..64194b1357 100644
--- a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb
+++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb
@@ -1,43 +1,55 @@
 easyblock = 'PythonBundle'
 
 name = 'chewBBACA'
-version = '3.3.9'
+version = '3.3.10'
 
 homepage = 'https://github.com/B-UMMI/chewBBACA'
-description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome 
-MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm".
-BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and 
-could be thought of as "Comprehensive and Highly Efficient Workflow"."""
+description = """
+chewBBACA is a software suite for the creation and evaluation of core genome and
+whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+The "BBACA" stands for "BSR-Based Allele Calling Algorithm".
+BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.
+The "chew" part adds extra coolness to the name and could be thought of as
+"Comprehensive and Highly Efficient Workflow"."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('scikit-build-core', '0.9.3'),
+    ('poetry', '1.5.1'),
+]
 dependencies = [
-    ('Python', '3.10.8'),
-    ('SciPy-bundle', '2023.02'),
-    # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40
-    # Cython included with Python-bundle-PyPI (0.29.35) is too old
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Biopython', '1.83'),
+    ('plotly.py', '5.16.0'),
     ('Cython', '3.0.8'),
-    ('Biopython', '1.81'),
-    ('plotly.py', '5.13.1'),
-    ('BLAST+', '2.14.0'),
-    ('prodigal', '2.6.3'),
-    ('MAFFT', '7.505', '-with-extensions'),
+    ('BLAST+', '2.14.1'),
+    ('MAFFT', '7.520', '-with-extensions'),
     ('FastTree', '2.1.11'),
-    ('archspec', '0.2.0'),
+    ('archspec', '0.2.1'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
+local_preinstallopts = (
+    "sed -i "
+    "-e 's/numpy~=1.24.3/numpy>=1.24.3/g' "
+    "-e 's/scipy~=1.10.1/scipy>=1.10.1/g' "
+    'pyproject.toml && '
+)
+
 exts_list = [
-    ('pyrodigal', '3.5.1', {
-        'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'],
+    ('pyrodigal', '3.6.3', {
+        'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'],
     }),
     ('isodate', '0.6.1', {
         'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
     }),
-    ('rdflib', '7.0.0', {
-        'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'],
+    ('rdflib', '7.1.1', {
+        'checksums': ['164de86bd3564558802ca983d84f6616a4a1a420c7a17a8152f5016076b2913e'],
     }),
     ('SPARQLWrapper', '2.0.0', {
         'modulename': 'SPARQLWrapper',
@@ -45,11 +57,11 @@ exts_list = [
     }),
     (name, version, {
         'modulename': 'CHEWBBACA',
-        # relax numpy version requirement
-        'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ",
+        'sources': [SOURCELOWER_TAR_GZ],
+        'preinstallopts': local_preinstallopts,
+        'testinstall': True,
         'runtest': "python setup.py test",
-        'sources': ['%(namelower)s-%(version)s.tar.gz'],
-        'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'],
+        'checksums': ['f22cc90a3ac55c203669fc3d6647aabd4f939999c44ddd9d4d44881f7304cb0e'],
     }),
 ]

Diff against chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb

easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb

diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb
index f06cb56a0c..64194b1357 100644
--- a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb
+++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.10-foss-2023a.eb
@@ -1,58 +1,78 @@
 easyblock = 'PythonBundle'
 
 name = 'chewBBACA'
-version = '2.5.5'
-versionsuffix = '-Python-%(pyver)s'
+version = '3.3.10'
 
 homepage = 'https://github.com/B-UMMI/chewBBACA'
-description = """chewBBACA stands for "BSR-Based Allele Calling Algorithm".
-chewBBACA is a comprehensive pipeline including a set of functions for the
-creation and validation of whole genome and core genome MultiLocus Sequence
-Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast
-Score Ratio that can be run in multiprocessor settings and a set of functions to
-visualize and validate allele variation in the loci."""
+description = """
+chewBBACA is a software suite for the creation and evaluation of core genome and
+whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+The "BBACA" stands for "BSR-Based Allele Calling Algorithm".
+BSR stands for BLAST Score Ratio as proposed by Rasko DA et al.
+The "chew" part adds extra coolness to the name and could be thought of as
+"Comprehensive and Highly Efficient Workflow"."""
 
-toolchain = {'name': 'intel', 'version': '2020a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('scikit-build-core', '0.9.3'),
+    ('poetry', '1.5.1'),
+]
 dependencies = [
-    ('Python', '3.8.2'),
-    ('SciPy-bundle', '2020.03', versionsuffix),
-    ('Biopython', '1.78', versionsuffix),
-    ('plotly.py', '4.8.1'),
-    ('BLAST+', '2.10.1'),
-    ('prodigal', '2.6.3'),
-    ('ClustalW2', '2.1'),
-    ('MAFFT', '7.453', '-with-extensions'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('Biopython', '1.83'),
+    ('plotly.py', '5.16.0'),
+    ('Cython', '3.0.8'),
+    ('BLAST+', '2.14.1'),
+    ('MAFFT', '7.520', '-with-extensions'),
+    ('FastTree', '2.1.11'),
+    ('archspec', '0.2.1'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
+local_preinstallopts = (
+    "sed -i "
+    "-e 's/numpy~=1.24.3/numpy>=1.24.3/g' "
+    "-e 's/scipy~=1.10.1/scipy>=1.10.1/g' "
+    'pyproject.toml && '
+)
+
 exts_list = [
-    ('isodate', '0.6.0', {
-        'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'],
+    ('pyrodigal', '3.6.3', {
+        'checksums': ['3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78'],
+    }),
+    ('isodate', '0.6.1', {
+        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
     }),
-    ('rdflib', '5.0.0', {
-        'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'],
+    ('rdflib', '7.1.1', {
+        'checksums': ['164de86bd3564558802ca983d84f6616a4a1a420c7a17a8152f5016076b2913e'],
     }),
-    ('SPARQLWrapper', '1.8.5', {
+    ('SPARQLWrapper', '2.0.0', {
         'modulename': 'SPARQLWrapper',
-        'checksums': ['d6a66b5b8cda141660e07aeb00472db077a98d22cb588c973209c7336850fb3c'],
+        'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'],
     }),
     (name, version, {
         'modulename': 'CHEWBBACA',
+        'sources': [SOURCELOWER_TAR_GZ],
+        'preinstallopts': local_preinstallopts,
+        'testinstall': True,
         'runtest': "python setup.py test",
-        'checksums': ['f8960b8485672f6d39d59e53b3521db406120abc2d7db42ce4c9eac06b024a5f'],
+        'checksums': ['f22cc90a3ac55c203669fc3d6647aabd4f939999c44ddd9d4d44881f7304cb0e'],
     }),
 ]
 
 sanity_check_paths = {
-    'files': ['bin/chewBBACA.py'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages/CHEWBBACA'],
+    'files': ['bin/chewBBACA.py', 'bin/chewie'],
+    'dirs': [],
 }
 
 sanity_check_commands = [
     'chewBBACA.py --help',
+    'chewie --help',
 ]
 
-moduleclass = 'chem'
+moduleclass = 'bio'

pavelToman · 2024-12-16T17:43:48Z

@boegelbot please test @ generoso

boegelbot · 2024-12-16T17:45:09Z

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

PR test command 'EB_PR=22038 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22038 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14873

Test results coming soon (I hope)...

- notification for comment with ID 2546259435 processed

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-16T17:49:47Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - 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/51d8658baaa11fc4f292cc0809e00694 for a full test report.

pavelToman · 2024-12-16T17:51:23Z

@boegelbot please test @ jsc-zen3

pavelToman · 2024-12-16T17:52:36Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4004.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/67c897ff6a7161be17bec8b0538d1b8a for a full test report.

boegelbot · 2024-12-16T18:00:09Z

@pavelToman: 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=22038 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22038 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5448

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-16T18:03:38Z

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 3.9.19
See https://gist.github.com/boegelbot/4c996c11570c6a8f3195c34c7d968bdf for a full test report.

pavelToman · 2024-12-17T10:03:20Z

@boegelbot please test @ jsc-zen3

pavelToman · 2024-12-17T10:10:09Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4004.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/f99de8a66d586f5446c2e0184f9ae9bc for a full test report.

boegelbot · 2024-12-17T10:10:11Z

@pavelToman: 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=22038 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22038 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
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Submitted batch job 5453

Test results coming soon (I hope)...

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boegelbot · 2024-12-17T10:13:21Z

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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 3.9.19
See https://gist.github.com/boegelbot/1d618370b441759886b5a1506896f5e4 for a full test report.

pavelToman · 2024-12-17T10:17:23Z

@boegelbot please test @ generoso

boegelbot · 2024-12-17T10:20:06Z

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

PR test command 'EB_PR=22038 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22038 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14878

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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boegelbot · 2024-12-17T10:24:41Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - 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/23b4470500d9987f7a7ca925448037e2 for a full test report.

adding easyconfigs: chewBBACA-3.3.10-foss-2023a.eb

6524c75

pavelToman added the update label Dec 16, 2024

pavelToman mentioned this pull request Dec 16, 2024

ChewBBACA vscentrum/vsc-software-stack#473

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Update chewBBACA-3.3.10-foss-2023a.eb - update Cython version

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{bio}[foss/2023a] chewBBACA v3.3.10 #22038

{bio}[foss/2023a] chewBBACA v3.3.10 #22038

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{bio}[foss/2023a] chewBBACA v3.3.10 #22038

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{bio}[foss/2023a] chewBBACA v3.3.10 #22038

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Updated software chewBBACA-3.3.10-foss-2023a.eb

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Updated software `chewBBACA-3.3.10-foss-2023a.eb`