{bio,devel}[GCCcore/14.2.0] intervaltree-python v3.2.1, wurlitzer v3.1.1 by JarneRenders · Pull Request #25894 · easybuilders/easybuild-easyconfigs

JarneRenders · 2026-04-30T09:04:01Z

(created using eb --new-pr)

…itzer-3.1.1-GCCcore-14.2.0.eb

github-actions · 2026-04-30T09:04:42Z

Updated software `intervaltree-python-3.2.1-GCCcore-14.2.0.eb`

Diff against intervaltree-python-3.1.0-GCCcore-13.3.0.eb

easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
index 1bd175a8d3..eda7bab503 100644
--- a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
@@ -2,30 +2,33 @@
 # Update: Petr Král (INUITS)
 # Update: Loris Bennett (FU Berlin)
 
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'intervaltree-python'
-_modname = 'intervaltree'
-version = '3.1.0'
+version = '3.2.1'
 
 homepage = 'https://github.com/chaimleib/intervaltree'
 description = """A mutable, self-balancing interval tree. Queries may be by
  point, by range overlap, or by range containment.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
-source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname]
-sources = ['%s-%s.tar.gz' % (_modname, version)]
-checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d']
-
-builddependencies = [('binutils', '2.42')]
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.27.0'),
+]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
-options = {'modulename': _modname}
+exts_list = [
+    ('intervaltree', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['f3f7e8baeb7dd75b9f7a6d33cf3ec10025984a8e66e3016d537e52130c73cfe2'],
+    }),
+]
 
 moduleclass = 'bio'

Diff against intervaltree-python-3.1.0-GCCcore-12.3.0.eb

easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
index f38b8b49f8..eda7bab503 100644
--- a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
@@ -1,30 +1,34 @@
 # Author: Jasper Grimm (UoY)
 # Update: Petr Král (INUITS)
+# Update: Loris Bennett (FU Berlin)
 
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'intervaltree-python'
-_modname = 'intervaltree'
-version = '3.1.0'
+version = '3.2.1'
 
 homepage = 'https://github.com/chaimleib/intervaltree'
 description = """A mutable, self-balancing interval tree. Queries may be by
  point, by range overlap, or by range containment.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
-source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname]
-sources = ['%s-%s.tar.gz' % (_modname, version)]
-checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d']
-
-builddependencies = [('binutils', '2.40')]
+builddependencies = [
+    ('binutils', '2.42'),
+    ('hatchling', '1.27.0'),
+]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
-options = {'modulename': _modname}
+exts_list = [
+    ('intervaltree', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['f3f7e8baeb7dd75b9f7a6d33cf3ec10025984a8e66e3016d537e52130c73cfe2'],
+    }),
+]
 
 moduleclass = 'bio'

Diff against intervaltree-python-3.1.0-GCCcore-12.2.0.eb

easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
index ba9b7b5eff..eda7bab503 100644
--- a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.2.1-GCCcore-14.2.0.eb
@@ -1,30 +1,34 @@
 # Author: Jasper Grimm (UoY)
+# Update: Petr Král (INUITS)
+# Update: Loris Bennett (FU Berlin)
 
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'intervaltree-python'
-_modname = 'intervaltree'
-version = '3.1.0'
+version = '3.2.1'
 
 homepage = 'https://github.com/chaimleib/intervaltree'
 description = """A mutable, self-balancing interval tree. Queries may be by
  point, by range overlap, or by range containment.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
-
-source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname]
-sources = ['%s-%s.tar.gz' % (_modname, version)]
-checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d']
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 builddependencies = [
-    ('binutils', '2.39'),
+    ('binutils', '2.42'),
+    ('hatchling', '1.27.0'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
+    ('Python', '3.13.1'),
+    ('Python-bundle-PyPI', '2025.04'),
 ]
 
-options = {'modulename': _modname}
+exts_list = [
+    ('intervaltree', version, {
+        'sources': [SOURCE_TAR_GZ],
+        'checksums': ['f3f7e8baeb7dd75b9f7a6d33cf3ec10025984a8e66e3016d537e52130c73cfe2'],
+    }),
+]
 
 moduleclass = 'bio'

Updated software `wurlitzer-3.1.1-GCCcore-14.2.0.eb`

Diff against wurlitzer-3.1.1-GCCcore-13.2.0.eb

easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-14.2.0.eb
index 3cc7226a63..d2d83ca1fc 100644
--- a/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-14.2.0.eb
@@ -10,13 +10,13 @@ For more details on why this is needed, please read this blog post:
 https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python
 """
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['bfb9144ab9f02487d802b9ff89dbd3fa382d08f73e12db8adc4c2fb00cd39bd9']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
-dependencies = [('Python', '3.11.5')]
+dependencies = [('Python', '3.13.1')]
 
 moduleclass = 'devel'

Diff against wurlitzer-3.1.1-GCCcore-12.3.0.eb

easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-14.2.0.eb
index f4ca75c0c5..d2d83ca1fc 100644
--- a/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/w/wurlitzer/wurlitzer-3.1.1-GCCcore-14.2.0.eb
@@ -10,13 +10,13 @@ For more details on why this is needed, please read this blog post:
 https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python
 """
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['bfb9144ab9f02487d802b9ff89dbd3fa382d08f73e12db8adc4c2fb00cd39bd9']
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [('binutils', '2.42')]
 
-dependencies = [('Python', '3.11.3')]
+dependencies = [('Python', '3.13.1')]
 
 moduleclass = 'devel'

JarneRenders · 2026-04-30T12:43:56Z

Test report by @JarneRenders
SUCCESS
Build succeeded for 2 out of 2 (total: 32 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/9b8645cd9d90613b16c7cfcb5da36563 for a full test report.

verdurin · 2026-05-01T15:41:04Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (total: 1 min 6 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/005f4b5aeed690b578dd451e8efa510a for a full test report.

verdurin · 2026-05-01T16:53:55Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-05-01T17:00:08Z

@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=25894 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25894 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10338

Test results coming soon (I hope)...

Details

- notification for comment with ID 4360494146 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 · 2026-05-01T17:01:57Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 1 min 34 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/dbb47d129310eb30a029fe1c2db68ad7 for a full test report.

adding easyconfigs: intervaltree-python-3.2.1-GCCcore-14.2.0.eb, wurl…

5fe14f4

…itzer-3.1.1-GCCcore-14.2.0.eb

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

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JarneRenders marked this pull request as draft April 30, 2026 11:50

Change to PythonBundle to pass pip list check

08720ac

JarneRenders marked this pull request as ready for review April 30, 2026 12:43

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{bio,devel}[GCCcore/14.2.0] intervaltree-python v3.2.1, wurlitzer v3.1.1#25894

{bio,devel}[GCCcore/14.2.0] intervaltree-python v3.2.1, wurlitzer v3.1.1#25894
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Updated software intervaltree-python-3.2.1-GCCcore-14.2.0.eb

Updated software wurlitzer-3.1.1-GCCcore-14.2.0.eb

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Updated software `intervaltree-python-3.2.1-GCCcore-14.2.0.eb`

Updated software `wurlitzer-3.1.1-GCCcore-14.2.0.eb`