{bio}[gfbf/2025a] pyrho v0.2.1, LDpop v1.0.2, msprime v1.4.1, cyvcf2 v0.32.1 by JarneRenders · Pull Request #25517 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-03-06T09:51:24Z

(created using eb --new-pr)

….eb, msprime-1.4.1-gfbf-2025a.eb, cyvcf2-0.32.1-gfbf-2025a.eb

github-actions · 2026-03-06T09:51:57Z

Updated software `cyvcf2-0.32.1-gfbf-2025a.eb`

Diff against cyvcf2-0.31.1-gfbf-2023a.eb

easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.32.1-gfbf-2025a.eb
index 0f07fe6476..ab8ef75836 100644
--- a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.31.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.32.1-gfbf-2025a.eb
@@ -3,21 +3,21 @@
 easyblock = 'PythonBundle'
 
 name = 'cyvcf2'
-version = '0.31.1'
+version = '0.32.1'
 
 homepage = 'https://github.com/brentp/cyvcf2'
 description = "cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files."
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
+
+builddependencies = [('Cython', '3.1.1')]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('HTSlib', '1.18'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('HTSlib', '1.22.1'),
 ]
 
-fix_python_shebang_for = ['bin/*']
-
 exts_list = [
     ('humanfriendly', '10.0', {
         'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
@@ -27,7 +27,7 @@ exts_list = [
     }),
     (name, version, {
         'preinstallopts': 'CYVCF2_HTSLIB_MODE=EXTERNAL',
-        'checksums': ['00bd0e09a3719d29fbc02bc8a40a690ac2c475e91744648750907d1816558fc5'],
+        'checksums': ['34f3f4464f27794a4956413481e9c08a00dbf87d998b8cc72d33560de874f263'],
     }),
 ]

Updated software `msprime-1.4.1-gfbf-2025a.eb`

Diff against msprime-1.2.0-foss-2022a.eb

easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/m/msprime/msprime-1.4.1-gfbf-2025a.eb
index 28cfe29db0..fcec2b6557 100644
--- a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/msprime/msprime-1.4.1-gfbf-2025a.eb
@@ -1,42 +1,42 @@
 easyblock = 'PythonBundle'
 
 name = 'msprime'
-version = '1.2.0'
+version = '1.4.1'
 
 homepage = 'https://msprime.readthedocs.io'
-description = "msprime is a coalescent simulator and library for processing tree-based genetic data."
+description = """
+msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral
+histories for a sample of individuals (consistent with a given demographic model) under a range of
+different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral
+history (which can be produced by msprime or other programs supporting tskit) under a variety of
+genome sequence evolution models.
+"""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
+
+builddependencies = [('setuptools', '80.9.0')]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),  # for numpy
-    ('GSL', '2.7'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),  # for numpy
+    ('GSL', '2.8'),
 ]
 
 exts_list = [
-    ('svgwrite', '1.4.3', {
-        'source_tmpl': '%(name)s-%(version)s.zip',
-        'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'],
-    }),
-    ('tskit', '0.5.4', {
-        'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'],
-    }),
-    ('ruamel.yaml.clib', '0.2.7', {
-        'modulename': False,
-        'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'],
+    ('tskit', '1.0.1', {
+        'checksums': ['2bcf811e420d28a52f4994f72cb3b6900d31865ca0deaefce0aec4ee26021581'],
     }),
     ('ruamel.yaml', '0.17.21', {
         'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'],
     }),
-    ('demes', '0.2.2', {
-        'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'],
+    ('demes', '0.2.3', {
+        'checksums': ['9e613b65b475dba277bca751de1f37a89fd5eb4d856ba27733a2099c8a823617'],
     }),
-    ('newick', '1.9.0', {
-        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
+    ('newick', '1.11.0', {
+        'checksums': ['b8bf81f88dbc0e1cb85928e6f4c7e0e29062c3739e27216aae76c3065a297186'],
     }),
     (name, version, {
-        'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'],
+        'checksums': ['68a7208eaea30ca473365287c833078f654af1e186b24fc0105e7717c93bb967'],
     }),
 ]

Diff against msprime-1.2.0-foss-2021b.eb

easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb

diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb b/easybuild/easyconfigs/m/msprime/msprime-1.4.1-gfbf-2025a.eb
index 7225bf2fb3..fcec2b6557 100644
--- a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/m/msprime/msprime-1.4.1-gfbf-2025a.eb
@@ -1,42 +1,42 @@
 easyblock = 'PythonBundle'
 
 name = 'msprime'
-version = '1.2.0'
+version = '1.4.1'
 
 homepage = 'https://msprime.readthedocs.io'
-description = "msprime is a coalescent simulator and library for processing tree-based genetic data."
+description = """
+msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral
+histories for a sample of individuals (consistent with a given demographic model) under a range of
+different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral
+history (which can be produced by msprime or other programs supporting tskit) under a variety of
+genome sequence evolution models.
+"""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
+
+builddependencies = [('setuptools', '80.9.0')]
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),  # for numpy
-    ('GSL', '2.7'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),  # for numpy
+    ('GSL', '2.8'),
 ]
 
 exts_list = [
-    ('svgwrite', '1.4.3', {
-        'source_tmpl': '%(name)s-%(version)s.zip',
-        'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'],
-    }),
-    ('tskit', '0.5.4', {
-        'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'],
-    }),
-    ('ruamel.yaml.clib', '0.2.7', {
-        'modulename': False,
-        'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'],
+    ('tskit', '1.0.1', {
+        'checksums': ['2bcf811e420d28a52f4994f72cb3b6900d31865ca0deaefce0aec4ee26021581'],
     }),
     ('ruamel.yaml', '0.17.21', {
         'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'],
     }),
-    ('demes', '0.2.2', {
-        'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'],
+    ('demes', '0.2.3', {
+        'checksums': ['9e613b65b475dba277bca751de1f37a89fd5eb4d856ba27733a2099c8a823617'],
     }),
-    ('newick', '1.6.0', {
-        'checksums': ['5610335826c0afd35afe66ebbacba0881e69f25097418c2f08456be629be6eac'],
+    ('newick', '1.11.0', {
+        'checksums': ['b8bf81f88dbc0e1cb85928e6f4c7e0e29062c3739e27216aae76c3065a297186'],
     }),
     (name, version, {
-        'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'],
+        'checksums': ['68a7208eaea30ca473365287c833078f654af1e186b24fc0105e7717c93bb967'],
     }),
 ]

lexming · 2026-03-06T13:55:51Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-03-06T14:00:13Z

@lexming: 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=25517 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25517 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9969

Test results coming soon (I hope)...

Details

- notification for comment with ID 4011890913 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 · 2026-03-06T14:08:16Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 7 mins 32 secs) (4 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/3f8b8ca2db5225121b6476b6ed002012 for a full test report.

Co-authored-by: Alex Domingo <[email protected]>

lexming · 2026-03-06T14:33:52Z

@boegelbot please test @ jsc-zen3

lexming

LGTM

boegelbot · 2026-03-06T14:40:18Z

@lexming: 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=25517 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25517 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9972

Test results coming soon (I hope)...

Details

- notification for comment with ID 4012106615 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 · 2026-03-06T14:49:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 9 mins 24 secs) (4 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/abe8830cfd15f699eb1d9a635b5bea44 for a full test report.

lexming · 2026-03-06T14:54:37Z

Merging, thanks @JarneRenders !

adding easyconfigs: pyrho-0.2.1-foss-2025a.eb, LDpop-1.0.2-gfbf-2025a…

1acba15

….eb, msprime-1.4.1-gfbf-2025a.eb, cyvcf2-0.32.1-gfbf-2025a.eb

github-actions Bot added 2025a issues & PRs related to 2025a common toolchains new update labels Mar 6, 2026

Fix capitalisation of LDpop dependency

3db4cef

Micket modified the milestone: next release (5.2.2?) Mar 6, 2026

lexming reviewed Mar 6, 2026

View reviewed changes

Comment thread easybuild/easyconfigs/p/pyrho/pyrho-0.2.1-foss-2025a.eb Outdated

Comment thread easybuild/easyconfigs/l/LDpop/LDpop-1.0.2-gfbf-2025a.eb Outdated

Use local var for commit in more places

0aa65d2

Co-authored-by: Alex Domingo <[email protected]>

lexming approved these changes Mar 6, 2026

View reviewed changes

lexming merged commit 92f5b88 into easybuilders:develop Mar 6, 2026
6 checks passed

JarneRenders deleted the 20260306105116_new_pr_pyrho021 branch March 6, 2026 14:58

boegel changed the title ~~{bio}[gfbf/2025a] pyrho v0.2.1, LDpop v1.0.2, msprime v1.4.1, ...~~ {bio}[gfbf/2025a] pyrho v0.2.1, LDpop v1.0.2, msprime v1.4.1, cyvcf2 v0.32.1 Apr 9, 2026

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{bio}[gfbf/2025a] pyrho v0.2.1, LDpop v1.0.2, msprime v1.4.1, cyvcf2 v0.32.1#25517

{bio}[gfbf/2025a] pyrho v0.2.1, LDpop v1.0.2, msprime v1.4.1, cyvcf2 v0.32.1#25517
lexming merged 3 commits intoeasybuilders:developfrom
JarneRenders:20260306105116_new_pr_pyrho021

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JarneRenders commented Mar 6, 2026

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Updated software cyvcf2-0.32.1-gfbf-2025a.eb

Updated software msprime-1.4.1-gfbf-2025a.eb

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Updated software `cyvcf2-0.32.1-gfbf-2025a.eb`

Updated software `msprime-1.4.1-gfbf-2025a.eb`