{bio,tools}[foss/2022a] ProTstab2 v2.0.2, rpy2 v3.5.15 by smoors · Pull Request #22302 · easybuilders/easybuild-easyconfigs

smoors · 2025-02-13T11:18:42Z

(created using eb --new-pr)

…022a.eb

github-actions · 2025-02-13T11:19:44Z

Updated software `rpy2-3.5.15-foss-2022a.eb`

Diff against rpy2-3.5.15-foss-2023a.eb

easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb

diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
index 452318ddc2..467e00dba3 100644
--- a/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb
+++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
@@ -10,19 +10,21 @@ version = '3.5.15'
 homepage = 'https://rpy2.github.io'
 description = """rpy2 is an interface to R running embedded in a Python process."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2022a'}
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('R', '4.3.2'),
-    ('R-bundle-CRAN', '2023.12'),
-    ('IPython', '8.14.0'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('R', '4.2.1'),
+    ('IPython', '8.5.0'),
     ('cffi', '1.15.1'),
 ]
 
+# newer setuptools is required for rpy2-3.5 to use setuptools.command.build
 exts_list = [
+    ('setuptools', '67.7.2', {
+        'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'],
+    }),
     ('coverage', '7.4.3', {
         'checksums': ['276f6077a5c61447a48d133ed13e759c09e62aff0dc84274a68dc18660104d52'],
     }),

Diff against rpy2-3.4.5-foss-2021a.eb

easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb

diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
index 7a5bbcea9b..467e00dba3 100644
--- a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb
+++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
@@ -1,59 +1,42 @@
 # Author: Pavel Grochal (INUITS)
-# Updated: Denis Kristak (INUITS)
+# Updated: Denis Kristak, Pavel Tománek (INUITS)
 # License: GPLv2
 
 easyblock = 'PythonBundle'
 
 name = 'rpy2'
-version = '3.4.5'
+version = '3.5.15'
 
-homepage = 'https://rpy2.bitbucket.io/'
+homepage = 'https://rpy2.github.io'
 description = """rpy2 is an interface to R running embedded in a Python process."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2022a'}
 
 dependencies = [
-    ('Python', '3.9.5'),
-    ('R', '4.1.0'),
-    ('IPython', '7.25.0'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('R', '4.2.1'),
+    ('IPython', '8.5.0'),
+    ('cffi', '1.15.1'),
 ]
 
+# newer setuptools is required for rpy2-3.5 to use setuptools.command.build
 exts_list = [
-    ('simplegeneric', '0.8.1', {
-        'source_tmpl': '%(name)s-%(version)s.zip',
-        'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'],
+    ('setuptools', '67.7.2', {
+        'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'],
     }),
-    # stick to tzlocal < 3.0 to avoid test errors in rpy2 like
-    # AttributeError: 'NoneType' object has no attribute 'total_seconds'
-    ('tzlocal', '2.1', {
-        'checksums': ['643c97c5294aedc737780a49d9df30889321cbe1204eac2c2ec6134035a92e44'],
+    ('coverage', '7.4.3', {
+        'checksums': ['276f6077a5c61447a48d133ed13e759c09e62aff0dc84274a68dc18660104d52'],
     }),
-    ('cffi', '1.15.1', {
-        'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'],
+    ('pytest-cov', '4.1.0', {
+        'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'],
     }),
-    ('tzdata', '2023.3', {
-        'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'],
-    }),
-    ('backports-zoneinfo', '0.2.1', {
-        'modulename': 'backports.zoneinfo',
-        'source_tmpl': 'backports.zoneinfo-%(version)s.tar.gz',
-        'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'],
-    }),
-    ('pytz-deprecation-shim', '0.1.0.post0', {
-        'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz',
-        'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'],
+    ('tzlocal', '5.2', {
+        'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'],
     }),
     (name, version, {
-        'patches': ['rpy2-3.4.5_disable_gui_tests.patch'],
-        'checksums': [
-            {'rpy2-3.4.5.tar.gz': '5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3'},
-            {'rpy2-3.4.5_disable_gui_tests.patch': '7424fed4bc9edb246944ad54fcb434a1ae5f2db086679b1a53d44cf5d3b98d8b'},
-        ],
+        'checksums': ['444fae4a84dc7f233b70eaab0aa81398ee0147c4e1ae38dd4524d779d6f25b2b'],
     }),
 ]
 
-sanity_check_commands = [
-    "pytest --pyargs rpy2 "
-]
-
 moduleclass = 'tools'

Diff against rpy2-3.4.5-foss-2021b.eb

easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb

diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
index 14da024620..467e00dba3 100644
--- a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb
+++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2022a.eb
@@ -1,57 +1,42 @@
 # Author: Pavel Grochal (INUITS)
-# Updated: Denis Kristak (INUITS)
+# Updated: Denis Kristak, Pavel Tománek (INUITS)
 # License: GPLv2
 
 easyblock = 'PythonBundle'
 
 name = 'rpy2'
-version = '3.4.5'
+version = '3.5.15'
 
-homepage = 'https://rpy2.bitbucket.io/'
+homepage = 'https://rpy2.github.io'
 description = """rpy2 is an interface to R running embedded in a Python process."""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2022a'}
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('R', '4.1.2'),
-    ('IPython', '7.26.0'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('R', '4.2.1'),
+    ('IPython', '8.5.0'),
+    ('cffi', '1.15.1'),
 ]
 
+# newer setuptools is required for rpy2-3.5 to use setuptools.command.build
 exts_list = [
-    ('simplegeneric', '0.8.1', {
-        'source_tmpl': '%(name)s-%(version)s.zip',
-        'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'],
+    ('setuptools', '67.7.2', {
+        'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'],
     }),
-    ('tzlocal', '2.1', {
-        'checksums': ['643c97c5294aedc737780a49d9df30889321cbe1204eac2c2ec6134035a92e44'],
+    ('coverage', '7.4.3', {
+        'checksums': ['276f6077a5c61447a48d133ed13e759c09e62aff0dc84274a68dc18660104d52'],
     }),
-    ('cffi', '1.15.0', {
-        'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'],
+    ('pytest-cov', '4.1.0', {
+        'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'],
     }),
-    ('tzdata', '2021.5', {
-        'checksums': ['68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21'],
-    }),
-    ('backports-zoneinfo', '0.2.1', {
-        'modulename': 'backports.zoneinfo',
-        'source_tmpl': 'backports.zoneinfo-%(version)s.tar.gz',
-        'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'],
-    }),
-    ('pytz-deprecation-shim', '0.1.0.post0', {
-        'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz',
-        'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'],
+    ('tzlocal', '5.2', {
+        'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'],
     }),
     (name, version, {
-        'patches': ['rpy2-%(version)s_disable_gui_tests.patch'],
-        'checksums': [
-            '5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3',  # rpy2-3.4.5.tar.gz
-            '7424fed4bc9edb246944ad54fcb434a1ae5f2db086679b1a53d44cf5d3b98d8b',  # rpy2-3.4.5_disable_gui_tests.patch
-        ],
+        'checksums': ['444fae4a84dc7f233b70eaab0aa81398ee0147c4e1ae38dd4524d779d6f25b2b'],
     }),
 ]
 
-sanity_check_commands = [
-    "pytest --pyargs rpy2 "
-]
-
 moduleclass = 'tools'

smoors · 2025-04-05T14:23:19Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-04-05T14:30:08Z

@smoors: 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=22302 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22302 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6114

Test results coming soon (I hope)...

Details

- notification for comment with ID 2780749553 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 · 2025-04-05T14:36:43Z

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/a09cc3c7baece067373d7e2123436258 for a full test report.

lexming

LGTM

lexming · 2025-04-08T13:54:12Z

Merging, thanks @smoors !

adding easyconfigs: ProTstab2-2.0.2-foss-2022a.eb, rpy2-3.5.15-foss-2…

cae785a

…022a.eb

smoors added new update labels Feb 13, 2025

update for EB 5 and add missing patch

a6ad015

lexming approved these changes Apr 8, 2025

View reviewed changes

lexming added this to the release after 5.0.0 milestone Apr 8, 2025

lexming merged commit 028a16d into easybuilders:develop Apr 8, 2025
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{bio,tools}[foss/2022a] ProTstab2 v2.0.2, rpy2 v3.5.15#22302

{bio,tools}[foss/2022a] ProTstab2 v2.0.2, rpy2 v3.5.15#22302
lexming merged 2 commits intoeasybuilders:developfrom
smoors:20250213121838_new_pr_ProTstab2202

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smoors commented Feb 13, 2025

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Updated software rpy2-3.5.15-foss-2022a.eb

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Updated software `rpy2-3.5.15-foss-2022a.eb`