{astro,cae,math,vis}[foss/2025a] SPAM v0.8.1.4, emcee v3.1.6, ... by pavelToman · Pull Request #25156 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-01-26T17:29:52Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#614
based on: #24887

…a.eb, meshio-5.3.5-foss-2025a.eb, PyAMG-5.3.0-gfbf-2025a.eb and patches: SPAM-0.8.1.4_filterout-NaNs.patch, SPAM-0.8.1.4_spambind_typo_fix.patch

github-actions · 2026-01-26T17:30:21Z

Updated software `emcee-3.1.6-foss-2025a.eb`

Diff against emcee-3.1.4-foss-2022a.eb

easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.6-foss-2025a.eb
index f2e7eca4aa..7c45cb3eca 100644
--- a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.6-foss-2025a.eb
@@ -1,28 +1,29 @@
 easyblock = 'PythonPackage'
 
 name = 'emcee'
-version = '3.1.4'
+version = '3.1.6'
 
 homepage = 'https://emcee.readthedocs.io/'
 description = """Emcee is an extensible, pure-Python implementation of
 Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.
 It's designed for Bayesian parameter estimation and it's really sweet! """
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['8e0e19dc8bcef9c6d02f860bef8ddc6c876b8878a6ce666943e2c5cfd9317fed']
+checksums = ['11af4daf6ab8f9ca69681e3c29054665db7bbd87fd4eb8e437d2c3a1248c637d']
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
 ]
 
+testinstall = True
+runtest = 'pytest'
+
 sanity_check_paths = {
     'files': [],
     'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'],
 }
 
-sanity_check_commands = [('pytest')]
-
 moduleclass = 'astro'

Diff against emcee-3.1.4-foss-2021b.eb

easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb

diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.6-foss-2025a.eb
index 76e9b128ca..7c45cb3eca 100644
--- a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb
+++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.6-foss-2025a.eb
@@ -1,28 +1,29 @@
 easyblock = 'PythonPackage'
 
 name = 'emcee'
-version = '3.1.4'
+version = '3.1.6'
 
 homepage = 'https://emcee.readthedocs.io/'
 description = """Emcee is an extensible, pure-Python implementation of
 Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.
 It's designed for Bayesian parameter estimation and it's really sweet! """
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['8e0e19dc8bcef9c6d02f860bef8ddc6c876b8878a6ce666943e2c5cfd9317fed']
+checksums = ['11af4daf6ab8f9ca69681e3c29054665db7bbd87fd4eb8e437d2c3a1248c637d']
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
 ]
 
+testinstall = True
+runtest = 'pytest'
+
 sanity_check_paths = {
     'files': [],
     'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'],
 }
 
-sanity_check_commands = [('pytest')]
-
 moduleclass = 'astro'

Updated software `PyAMG-5.3.0-gfbf-2025a.eb`

Diff against PyAMG-5.3.0-gfbf-2024a.eb

easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2024a.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
index 1f5eee9a9c..8ad5c25d38 100644
--- a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
@@ -6,18 +6,15 @@ version = '5.3.0'
 homepage = 'https://pyamg.github.io'
 description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface."""
 
-toolchain = {'name': 'gfbf', 'version': '2024a'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['5323d0f1a4cd999be246a90d580c9e1e9b584b98887f6298d397611087ef860b']
 
-builddependencies = [
-    ('pybind11', '2.12.0'),
-]
-
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('pybind11', '2.13.6'),
 ]
 
 options = {'modulename': 'pyamg'}

Diff against PyAMG-5.2.1-gfbf-2023b.eb

easybuild/easyconfigs/p/PyAMG/PyAMG-5.2.1-gfbf-2023b.eb

diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.2.1-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
index 8813590cab..8ad5c25d38 100644
--- a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.2.1-gfbf-2023b.eb
+++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
@@ -1,19 +1,20 @@
 easyblock = "PythonPackage"
 
 name = 'PyAMG'
-version = '5.2.1'
+version = '5.3.0'
 
 homepage = 'https://pyamg.github.io'
 description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface."""
 
-toolchain = {'name': 'gfbf', 'version': '2023b'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f449d934224e503401ee72cd2eece1a29d893b7abe35f62a44d52ba831198efa']
+checksums = ['5323d0f1a4cd999be246a90d580c9e1e9b584b98887f6298d397611087ef860b']
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('pybind11', '2.13.6'),
 ]
 
 options = {'modulename': 'pyamg'}

Diff against PyAMG-5.1.0-foss-2023a.eb

easybuild/easyconfigs/p/PyAMG/PyAMG-5.1.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.1.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
index 157107ae14..8ad5c25d38 100644
--- a/easybuild/easyconfigs/p/PyAMG/PyAMG-5.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-5.3.0-gfbf-2025a.eb
@@ -1,19 +1,20 @@
 easyblock = "PythonPackage"
 
 name = 'PyAMG'
-version = '5.1.0'
+version = '5.3.0'
 
 homepage = 'https://pyamg.github.io'
 description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2025a'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f90f9de795b4e29589edd2eb446d11ddb466678ebe823ed329fcf35759ea390c']
+checksums = ['5323d0f1a4cd999be246a90d580c9e1e9b584b98887f6298d397611087ef860b']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('pybind11', '2.13.6'),
 ]
 
 options = {'modulename': 'pyamg'}

pavelToman · 2026-01-26T17:31:35Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-01-26T17:40:13Z

@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=25156 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25156 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9496

Test results coming soon (I hope)...

Details

- notification for comment with ID 3800793745 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 · 2026-01-26T17:58:47Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 18 mins 18 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 3.9.23
See https://gist.github.com/boegelbot/64562e5e2067f70116b9934884ec590c for a full test report.

pavelToman · 2026-01-26T18:22:32Z

Test report by @pavelToman
SUCCESS
Build succeeded for 5 out of 5 (total: 48 mins 14 secs) (4 easyconfigs in total)
node4007.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/610007c52bfd754f01f55c4a9b9468ea for a full test report.

pavelToman · 2026-01-26T18:25:07Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (total: 52 mins 56 secs) (4 easyconfigs in total)
node4236.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/d28830daa71348b5da0b74dc18c17e02 for a full test report.

pavelToman · 2026-01-27T17:39:57Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-01-27T17:40:08Z

@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=25156 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25156 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9503

Test results coming soon (I hope)...

Details

- notification for comment with ID 3806567342 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 · 2026-01-27T17:57:45Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 4 (total: 17 mins 17 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 3.9.23
See https://gist.github.com/boegelbot/2518bd7d17bd4717fe15f5cfadf4cdd7 for a full test report.

pavelToman · 2026-01-27T18:08:53Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (total: 28 mins 2 secs) (4 easyconfigs in total)
node4007.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/91df7a9ec27e258392695a758c8187b7 for a full test report.

pavelToman · 2026-01-27T18:21:33Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (total: 41 mins 34 secs) (4 easyconfigs in total)
node4236.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/9f2c0eb20bcc9c980200c2393c679f94 for a full test report.

pavelToman · 2026-01-28T10:42:31Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-01-28T10:50:22Z

@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=25156 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25156 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9515

Test results coming soon (I hope)...

Details

- notification for comment with ID 3810532677 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 · 2026-01-28T11:09:21Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 18 mins 43 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 3.9.23
See https://gist.github.com/boegelbot/7ddf16bf433d04213730cd196988d1eb for a full test report.

…asyconfigs into 20260126182948_new_pr_SPAM0814

Micket · 2026-03-21T00:39:55Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-03-21T00:40:08Z

@Micket: 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=25156 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25156 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10072

Test results coming soon (I hope)...

Details

- notification for comment with ID 4101639594 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 · 2026-03-21T00:57:02Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (total: 16 mins 36 secs) (3 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/d8a83ee72ade929e6a234d410e62a783 for a full test report.

Micket · 2026-03-21T03:39:51Z

Test report by @Micket
SUCCESS
Build succeeded for 12 out of 12 (total: 2 hours 59 mins 19 secs) (3 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/02c57fdf7844ae6fc29403195e179957 for a full test report.

Micket

lgtm

resolved

adding easyconfigs: SPAM-0.8.1.4-foss-2025a.eb, emcee-3.1.6-foss-2025…

de2df00

…a.eb, meshio-5.3.5-foss-2025a.eb, PyAMG-5.3.0-gfbf-2025a.eb and patches: SPAM-0.8.1.4_filterout-NaNs.patch, SPAM-0.8.1.4_spambind_typo_fix.patch

pavelToman added new update labels Jan 26, 2026

github-actions Bot added the 2025a issues & PRs related to 2025a common toolchains label Jan 26, 2026

pavelToman mentioned this pull request Jan 26, 2026

{astro,cae,math,vis}[foss/2025a] SPAM v0.8.1.4, meshio v5.3.5, PyAMG v5.3.0, ... #24887

Closed

pavelToman mentioned this pull request Jan 27, 2026

SPAM vscentrum/vsc-software-stack#614

Open

boegel requested a review from laraPPr January 27, 2026 12:27

update the SPAM-NaNs patch

1228a89

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

c300792

…asyconfigs into 20260126182948_new_pr_SPAM0814

boegel previously requested changes Mar 9, 2026

View reviewed changes

Comment thread easybuild/easyconfigs/s/SPAM/SPAM-0.8.1.4_spambind_typo_fix.patch

Comment thread easybuild/easyconfigs/s/SPAM/SPAM-0.8.1.4_filterout-NaNs.patch

pavelToman added 2 commits March 10, 2026 10:42

patch links

90afb39

patch links2

04e817c

Micket changed the title ~~{astro,cae,math,vis}[foss/2025a] SPAM v0.8.1.4, emcee v3.1.6, meshio v5.3.5, ...~~ {astro,cae,math,vis}[foss/2025a] SPAM v0.8.1.4, emcee v3.1.6, ... Mar 21, 2026

Micket reviewed Mar 21, 2026

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Comment thread easybuild/easyconfigs/e/emcee/emcee-3.1.6-foss-2025a.eb Outdated

Apply suggestion from @Micket

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Micket approved these changes Mar 21, 2026

View reviewed changes

Micket merged commit 0f97e8f into easybuilders:develop Mar 21, 2026
6 checks passed

Micket added this to the next release (5.2.2?) milestone Mar 21, 2026

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Updated software emcee-3.1.6-foss-2025a.eb

Updated software PyAMG-5.3.0-gfbf-2025a.eb

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pavelToman commented Jan 26, 2026 •

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Updated software `emcee-3.1.6-foss-2025a.eb`

Updated software `PyAMG-5.3.0-gfbf-2025a.eb`