{bio}[GCC/14.2.0,gfbf/2025a] python-parasail v1.3.4, parasail v2.6.2 by JarneRenders · Pull Request #25891 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-04-30T08:50:54Z

(created using eb --new-pr)

….2-GCC-14.2.0.eb and patches: parasail-2.6.2_gcc14-fix.patch

github-actions · 2026-04-30T08:51:24Z

Updated software `parasail-2.6.2-GCC-14.2.0.eb`

Diff against parasail-2.6.2-GCC-13.3.0.eb

easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
index a4749648f0..b9285c044b 100644
--- a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
@@ -8,14 +8,18 @@ description = """parasail is a SIMD C (C99) library containing implementations
  of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global
  pairwise sequence alignment algorithms. """
 
-toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchain = {'name': 'GCC', 'version': '14.2.0'}
 
 github_account = 'jeffdaily'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b']
+patches = ['parasail-2.6.2_gcc14-fix.patch']
+checksums = [
+    {'v2.6.2.tar.gz': '9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'},
+    {'parasail-2.6.2_gcc14-fix.patch': '7d47890f10fabca123bd06defe9cf97a8f679b40edb829d058fd630479f0ecad'},
+]
 
-builddependencies = [('CMake', '3.29.3')]
+builddependencies = [('CMake', '3.31.3')]
 
 sanity_check_paths = {
     'files': ['bin/parasail_aligner', 'bin/parasail_stats',

Diff against parasail-2.6.2-GCC-13.2.0.eb

easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
index ddb3e791f3..b9285c044b 100644
--- a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
@@ -8,14 +8,18 @@ description = """parasail is a SIMD C (C99) library containing implementations
  of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global
  pairwise sequence alignment algorithms. """
 
-toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchain = {'name': 'GCC', 'version': '14.2.0'}
 
 github_account = 'jeffdaily'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b']
+patches = ['parasail-2.6.2_gcc14-fix.patch']
+checksums = [
+    {'v2.6.2.tar.gz': '9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'},
+    {'parasail-2.6.2_gcc14-fix.patch': '7d47890f10fabca123bd06defe9cf97a8f679b40edb829d058fd630479f0ecad'},
+]
 
-builddependencies = [('CMake', '3.27.6')]
+builddependencies = [('CMake', '3.31.3')]
 
 sanity_check_paths = {
     'files': ['bin/parasail_aligner', 'bin/parasail_stats',

Diff against parasail-2.6.2-GCC-12.3.0.eb

easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
index 25f71f7e3a..b9285c044b 100644
--- a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-14.2.0.eb
@@ -8,14 +8,18 @@ description = """parasail is a SIMD C (C99) library containing implementations
  of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global
  pairwise sequence alignment algorithms. """
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '14.2.0'}
 
 github_account = 'jeffdaily'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b']
+patches = ['parasail-2.6.2_gcc14-fix.patch']
+checksums = [
+    {'v2.6.2.tar.gz': '9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'},
+    {'parasail-2.6.2_gcc14-fix.patch': '7d47890f10fabca123bd06defe9cf97a8f679b40edb829d058fd630479f0ecad'},
+]
 
-builddependencies = [('CMake', '3.26.3')]
+builddependencies = [('CMake', '3.31.3')]
 
 sanity_check_paths = {
     'files': ['bin/parasail_aligner', 'bin/parasail_stats',

Updated software `python-parasail-1.3.4-gfbf-2025a.eb`

Diff against python-parasail-1.3.4-foss-2024a.eb

easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2024a.eb

diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2024a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
index b7f126f7cd..503c88d652 100644
--- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2024a.eb
+++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
@@ -1,4 +1,4 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-parasail'
 version = '1.3.4'
@@ -6,24 +6,24 @@ version = '1.3.4'
 homepage = 'https://github.com/jeffdaily/parasail-python'
 description = "Python Bindings for the Parasail C Library"
 
-toolchain = {'name': 'foss', 'version': '2024a'}
-
-source_urls = [PYPI_SOURCE.replace('%(name)s', 'parasail')]
-sources = ['parasail-%(version)s.tar.gz']
-checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f']
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 builddependencies = [
     ('parasail', '2.6.2'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
 ]
 
-# make sure setup.py finds the parasail library
-preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT
-
-options = {'modulename': 'parasail'}
+exts_list = [
+    ('parasail', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'],
+        # make sure setup.py finds the parasail library
+        'preinstallopts': f"ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.{SHLIB_EXT} && ",
+    }),
+]
 
 moduleclass = 'bio'

Diff against python-parasail-1.3.4-foss-2023b.eb

easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
index e195aef9b2..503c88d652 100644
--- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
@@ -1,4 +1,4 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-parasail'
 version = '1.3.4'
@@ -6,24 +6,24 @@ version = '1.3.4'
 homepage = 'https://github.com/jeffdaily/parasail-python'
 description = "Python Bindings for the Parasail C Library"
 
-toolchain = {'name': 'foss', 'version': '2023b'}
-
-source_urls = [PYPI_SOURCE.replace('%(name)s', 'parasail')]
-sources = ['parasail-%(version)s.tar.gz']
-checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f']
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 builddependencies = [
     ('parasail', '2.6.2'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
 ]
 
-# make sure setup.py finds the parasail library
-preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT
-
-options = {'modulename': 'parasail'}
+exts_list = [
+    ('parasail', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'],
+        # make sure setup.py finds the parasail library
+        'preinstallopts': f"ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.{SHLIB_EXT} && ",
+    }),
+]
 
 moduleclass = 'bio'

Diff against python-parasail-1.3.4-foss-2023a.eb

easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
index 5c493355ea..503c88d652 100644
--- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-gfbf-2025a.eb
@@ -1,4 +1,4 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'python-parasail'
 version = '1.3.4'
@@ -6,25 +6,24 @@ version = '1.3.4'
 homepage = 'https://github.com/jeffdaily/parasail-python'
 description = "Python Bindings for the Parasail C Library"
 
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-source_urls = ['https://pypi.python.org/packages/source/p/parasail']
-sources = ['parasail-%(version)s.tar.gz']
-checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f']
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 builddependencies = [
     ('parasail', '2.6.2'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
 ]
 
-
-# make sure setup.py finds the parasail library
-preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT
-
-options = {'modulename': 'parasail'}
+exts_list = [
+    ('parasail', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'],
+        # make sure setup.py finds the parasail library
+        'preinstallopts': f"ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.{SHLIB_EXT} && ",
+    }),
+]
 
 moduleclass = 'bio'

verdurin · 2026-04-30T10:56:34Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-04-30T11:00:11Z

@verdurin: 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=25891 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25891 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10334

Test results coming soon (I hope)...

Details

- notification for comment with ID 4351852059 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 · 2026-04-30T11:04:07Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (total: 3 mins 38 secs) (2 easyconfigs in total)
jsczen3c1.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/d041b77d4036408acb83545cf6427d52 for a full test report.

verdurin · 2026-04-30T11:06:09Z

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (total: 9 mins 13 secs) (2 easyconfigs in total)
centos-stream-9 - Linux CentOS Stream 9, x86_64, Intel Core Processor (Skylake, IBRS), Python 3.12.12
See https://gist.github.com/verdurin/d75ceab4f4bdab1ea1eab83cf783c2e9 for a full test report.

verdurin · 2026-04-30T11:16:39Z

== 2026-04-30 12:06:05,553 build_log.py:233 ERROR EasyBuild encountered an error:
The following Python packages were likely specified with a wrong name because they are missing in the 'pip list' output:
python-parasail (close matches in 'pip list' output: parasail, python-dateutil (at easybuild/easyblocks/p/python.py:360 in run_pip_list)

JarneRenders · 2026-04-30T12:07:37Z

== 2026-04-30 12:06:05,553 build_log.py:233 ERROR EasyBuild encountered an error:
The following Python packages were likely specified with a wrong name because they are missing in the 'pip list' output:
python-parasail (close matches in 'pip list' output: parasail, python-dateutil (at easybuild/easyblocks/p/python.py:360 in run_pip_list)

Aah yes, it's the new pip list check failing since the actual package name for python-parasail is just parasail. Making it a PythonBundle instead with an extension of the correct name.

JarneRenders · 2026-04-30T12:17:20Z

Test report by @JarneRenders
SUCCESS
Build succeeded for 2 out of 2 (total: 2 mins 6 secs) (2 easyconfigs in total)
node511.anansi.os - Linux Rocky Linux 9.7 (Blue Onyx), x86_64, AMD EPYC 9335 32-Core Processor, Python 3.9.25
See https://gist.github.com/JarneRenders/d9521c515b570a2f864aa16881f2da07 for a full test report.

verdurin · 2026-05-01T08:27:20Z

@boegelbot please test @ jsc-zen3

verdurin · 2026-05-01T08:27:24Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (total: 4 mins 25 secs) (2 easyconfigs in total)
centos-stream-9 - Linux CentOS Stream 9, x86_64, Intel Core Processor (Skylake, IBRS), Python 3.12.12
See https://gist.github.com/verdurin/510dedaa45f29c513e24b3a46a02878c for a full test report.

boegelbot · 2026-05-01T08:30:10Z

@verdurin: 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=25891 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25891 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10336

Test results coming soon (I hope)...

Details

- notification for comment with ID 4358499574 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 · 2026-05-01T08:34:15Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 3 mins 36 secs) (2 easyconfigs in total)
jsczen3c1.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/cbeb06174f3382290e0d448b9ad1d7b8 for a full test report.

verdurin

Looks fine.

verdurin · 2026-05-01T08:38:04Z

Going in, thanks @JarneRenders!

adding easyconfigs: python-parasail-1.3.4-gfbf-2025a.eb, parasail-2.6…

4c20bef

….2-GCC-14.2.0.eb and patches: parasail-2.6.2_gcc14-fix.patch

github-actions Bot added 2025a issues & PRs related to 2025a common toolchains update labels Apr 30, 2026

JarneRenders mentioned this pull request Apr 30, 2026

{bio}[foss/2025a] medaka v2.2.1 w/ CUDA 12.8.0 #25895

Open

5 tasks

Change to PythonBundle to pass pip list check

c013070

verdurin approved these changes May 1, 2026

View reviewed changes

verdurin added this to the next release (5.3.1?) milestone May 1, 2026

verdurin merged commit 68b6cdc into easybuilders:develop May 1, 2026
6 checks passed

JarneRenders deleted the 20260430105049_new_pr_python-parasail134 branch May 4, 2026 09:41

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JarneRenders commented Apr 30, 2026

Uh oh!

github-actions Bot commented Apr 30, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Updated software parasail-2.6.2-GCC-14.2.0.eb

Updated software python-parasail-1.3.4-gfbf-2025a.eb

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verdurin commented Apr 30, 2026

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verdurin commented Apr 30, 2026

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JarneRenders commented Apr 30, 2026

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JarneRenders commented Apr 30, 2026

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verdurin commented May 1, 2026

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github-actions Bot commented Apr 30, 2026 •

edited

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Updated software `parasail-2.6.2-GCC-14.2.0.eb`

Updated software `python-parasail-1.3.4-gfbf-2025a.eb`