{bio,lib}[gfbf/2024a] MACS3 v3.0.3, hmmlearn v0.3.3 by PetrKralCZ · Pull Request #23312 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-07-04T08:38:27Z

(created using eb --new-pr)

…24a.eb

github-actions · 2025-07-04T08:38:52Z

Updated software `hmmlearn-0.3.3-gfbf-2024a.eb`

Diff against hmmlearn-0.3.0-gfbf-2023a.eb

easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.3-gfbf-2024a.eb
index 54d9ee216f..1e5272327a 100644
--- a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.3-gfbf-2024a.eb
@@ -1,19 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'hmmlearn'
-version = '0.3.0'
+version = '0.3.3'
 
 homepage = 'https://github.com/hmmlearn/hmmlearn'
 description = "hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models"
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f']
+checksums = ['1d3c5dc4c5257e0c238dc1fe5387700b8cb987eab808edb3e0c73829f1cc44ec']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('scikit-learn', '1.3.1'),
+    ('Python', '3.12.3'),
+    ('scikit-learn', '1.5.2'),
+    ('pybind11', '2.12.0'),
 ]
 
 moduleclass = 'lib'

Diff against hmmlearn-0.3.0-foss-2022b.eb

easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.3-gfbf-2024a.eb
index 52ab42b89b..1e5272327a 100644
--- a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.3-gfbf-2024a.eb
@@ -1,19 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'hmmlearn'
-version = '0.3.0'
+version = '0.3.3'
 
 homepage = 'https://github.com/hmmlearn/hmmlearn'
 description = "hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models"
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f']
+checksums = ['1d3c5dc4c5257e0c238dc1fe5387700b8cb987eab808edb3e0c73829f1cc44ec']
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('scikit-learn', '1.2.1'),
+    ('Python', '3.12.3'),
+    ('scikit-learn', '1.5.2'),
+    ('pybind11', '2.12.0'),
 ]
 
 moduleclass = 'lib'

Updated software `MACS3-3.0.3-gfbf-2024a.eb`

Diff against MACS3-3.0.1-foss-2022b.eb

easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-foss-2022b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
index d78b223e7f..eced8a93e0 100644
--- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
@@ -1,31 +1,31 @@
 easyblock = 'PythonBundle'
 
 name = 'MACS3'
-version = '3.0.1'
+version = '3.0.3'
 
 homepage = 'https://macs3-project.github.io/MACS/'
 description = """Model Based Analysis for ChIP-Seq data"""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 builddependencies = [
-    ('pybind11', '2.10.3'),
+    ('pybind11', '2.12.0'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('SciPy-bundle', '2023.02'),
-    ('matplotlib', '3.7.0'),
-    ('hmmlearn', '0.3.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('matplotlib', '3.9.2'),
+    ('hmmlearn', '0.3.3'),
 ]
 
 exts_list = [
     ('cykhash', '2.0.1', {
         'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'],
     }),
-    (name, version, {
-        'checksums': ['b07ca6e84a71aab29589f63e3dff96049aa6739e055a629125b31c788c877016'],
-        'preinstallopts': "sed -i 's/scipy>=1.11.4/scipy>=1.10/g' setup.py && ",
+    ('%(namelower)s', version, {
+        'checksums': ['ee1c892901c4010ff9e201b433c0623cbd747a3058300322386a7185623b1684'],
         'modulename': 'MACS3',
     }),
 ]

Diff against MACS3-3.0.1-gfbf-2023a.eb

easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
index dcb58af9d1..eced8a93e0 100644
--- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
@@ -1,31 +1,31 @@
 easyblock = 'PythonBundle'
 
 name = 'MACS3'
-version = '3.0.1'
+version = '3.0.3'
 
 homepage = 'https://macs3-project.github.io/MACS/'
 description = """Model Based Analysis for ChIP-Seq data"""
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 builddependencies = [
-    ('pybind11', '2.11.1'),
+    ('pybind11', '2.12.0'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('matplotlib', '3.7.2'),
-    ('hmmlearn', '0.3.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('matplotlib', '3.9.2'),
+    ('hmmlearn', '0.3.3'),
 ]
 
 exts_list = [
     ('cykhash', '2.0.1', {
         'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'],
     }),
-    (name, version, {
-        'checksums': ['b07ca6e84a71aab29589f63e3dff96049aa6739e055a629125b31c788c877016'],
-        'preinstallopts': "sed -i 's/scipy>=1.11.4/scipy>=1.11/g' setup.py && ",
+    ('%(namelower)s', version, {
+        'checksums': ['ee1c892901c4010ff9e201b433c0623cbd747a3058300322386a7185623b1684'],
         'modulename': 'MACS3',
     }),
 ]

Diff against MACS3-3.0.0-foss-2022b.eb

easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
index f73f083082..eced8a93e0 100644
--- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.3-gfbf-2024a.eb
@@ -1,33 +1,32 @@
 easyblock = 'PythonBundle'
 
 name = 'MACS3'
-version = '3.0.0'
+version = '3.0.3'
 
 homepage = 'https://macs3-project.github.io/MACS/'
 description = """Model Based Analysis for ChIP-Seq data"""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2024a'}
 
 builddependencies = [
-    ('pybind11', '2.10.3'),
+    ('pybind11', '2.12.0'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    # MACS3 3.0 requires Cython 3.x
-    ('Cython', '3.0.8'),
-    ('SciPy-bundle', '2023.02'),
-    ('matplotlib', '3.7.0'),
-    ('hmmlearn', '0.3.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('matplotlib', '3.9.2'),
+    ('hmmlearn', '0.3.3'),
 ]
 
 exts_list = [
     ('cykhash', '2.0.1', {
         'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'],
     }),
-    (name, version, {
+    ('%(namelower)s', version, {
+        'checksums': ['ee1c892901c4010ff9e201b433c0623cbd747a3058300322386a7185623b1684'],
         'modulename': 'MACS3',
-        'checksums': ['57271e060c0f2c41f3aa6de44245c6db7fd0b1945ebfba115a6841628f75770e'],
     }),
 ]

PetrKralCZ · 2025-07-04T08:51:05Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-07-04T09:00:12Z

@PetrKralCZ: 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=23312 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23312 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7137

Test results coming soon (I hope)...

Details

- notification for comment with ID 3035035461 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 · 2025-07-04T09:00:57Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/ca8b6cb7a3ac4000c42af20804e0e16f for a full test report.

PetrKralCZ · 2025-07-04T13:07:19Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-07-04T13:10:09Z

@PetrKralCZ: 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=23312 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23312 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7140

Test results coming soon (I hope)...

Details

- notification for comment with ID 3036231934 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 · 2025-07-04T13:17:59Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/cd0fdd33bc961e8fcc38e8445f682b75 for a full test report.

verdurin · 2025-07-04T14:52:16Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10 (Green Obsidian), x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.11.11
See https://gist.github.com/verdurin/a5fc2dbddb51e4ef777172a28db621a9 for a full test report.

verdurin

Looks fine.

verdurin · 2025-07-04T16:09:30Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: MACS3-3.0.3-gfbf-2024a.eb, hmmlearn-0.3.3-gfbf-20…

91c818d

…24a.eb

PetrKralCZ added the update label Jul 4, 2025

This was referenced Jul 4, 2025

SnapATAC2 vscentrum/vsc-software-stack#547

Closed

{bio,lib,math,tools}[foss/2024a] SnapATAC2 v2.9.0-dev0-20250630, anndata v0.10.9, rustworkx v0.16.0, ... #23314

Merged

add pybind11 as a dependency

de6d414

verdurin approved these changes Jul 4, 2025

View reviewed changes

verdurin added this to the release after 5.1.1 milestone Jul 4, 2025

verdurin merged commit 7e142e6 into easybuilders:develop Jul 4, 2025
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{bio,lib}[gfbf/2024a] MACS3 v3.0.3, hmmlearn v0.3.3#23312

{bio,lib}[gfbf/2024a] MACS3 v3.0.3, hmmlearn v0.3.3#23312
verdurin merged 2 commits intoeasybuilders:developfrom
PetrKralCZ:20250704103824_new_pr_MACS3303

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PetrKralCZ commented Jul 4, 2025

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Updated software hmmlearn-0.3.3-gfbf-2024a.eb

Updated software MACS3-3.0.3-gfbf-2024a.eb

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Updated software `hmmlearn-0.3.3-gfbf-2024a.eb`

Updated software `MACS3-3.0.3-gfbf-2024a.eb`