{bio,lang}[GCC/12.3.0,GCCcore/12.3.0] Pysam v0.20.0, Cython v0.29.37 w/ Python 2.7.18 by PetrKralCZ · Pull Request #22354 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-02-21T10:04:33Z

(created using eb --new-pr)

…0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

github-actions · 2025-02-21T10:09:48Z

Updated software `Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb`

Diff against Cython-3.0.10-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
index c9e419d570..0e787707e9 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.0.10'
+version = '0.29.37'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,17 +14,17 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99']
+sources = [SOURCE_WHL]
+checksums = ['95f1d6a83ef2729e67b3fa7318c829ce5b07ac64c084cd6af11c228e0364662c']
 
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '2.7.18'),
 ]
 
 download_dep_fail = True

Diff against Cython-3.0.10-GCCcore-13.2.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
index 194048d611..0e787707e9 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.0.10'
+version = '0.29.37'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,17 +14,17 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99']
+sources = [SOURCE_WHL]
+checksums = ['95f1d6a83ef2729e67b3fa7318c829ce5b07ac64c084cd6af11c228e0364662c']
 
 builddependencies = [
     ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
+    ('Python', '2.7.18'),
 ]
 
 download_dep_fail = True

Diff against Cython-3.0.8-GCCcore-12.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
index ac694119eb..0e787707e9 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.0.8'
+version = '0.29.37'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://cython.org/'
 description = """
@@ -15,15 +16,15 @@ docurls = [
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['8333423d8fd5765e7cceea3a9985dd1e0a5dfeb2734629e1a2ed2d6233d39de6']
+sources = [SOURCE_WHL]
+checksums = ['95f1d6a83ef2729e67b3fa7318c829ce5b07ac64c084cd6af11c228e0364662c']
 
 builddependencies = [
     ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '2.7.18'),
 ]
 
 download_dep_fail = True

Updated software `Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb`

Diff against Pysam-0.22.1-GCC-13.3.0.eb

easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
index 2920aeda78..6f30d071e1 100644
--- a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
@@ -1,28 +1,26 @@
 easyblock = 'PythonPackage'
 
 name = 'Pysam'
-version = '0.22.1'
+version = '0.20.0'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/pysam-developers/pysam'
-description = """Pysam is a python module for reading and manipulating Samfiles.
+description = """Pysam is a python module for reading and manipulating Samfiles. 
  It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."""
 
-toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/pysam-developers/pysam/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6']
-
-builddependencies = [
-    ('Cython', '3.0.10')
-]
+checksums = ['5a25d95b986c2cb9f5040b9df4e1d93ce9a8bc3af5a956b1317416ed05269f60']
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
-    ('ncurses', '6.5'),
-    ('cURL', '8.7.1'),
-    ('XZ', '5.4.5'),
+    ('Python', '2.7.18'),
+    ('Cython', '0.29.37', versionsuffix),
+    ('ncurses', '6.4'),
+    ('cURL', '8.0.1'),
+    ('XZ', '5.4.2'),
 ]
 
 download_dep_fail = True

Diff against Pysam-0.22.0-GCC-13.2.0.eb

easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-13.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
index 41ccf5a345..6f30d071e1 100644
--- a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-13.2.0.eb
+++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
@@ -1,24 +1,26 @@
 easyblock = 'PythonPackage'
 
 name = 'Pysam'
-version = '0.22.0'
+version = '0.20.0'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/pysam-developers/pysam'
-description = """Pysam is a python module for reading and manipulating Samfiles.
+description = """Pysam is a python module for reading and manipulating Samfiles. 
  It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."""
 
-toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/pysam-developers/pysam/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f']
+checksums = ['5a25d95b986c2cb9f5040b9df4e1d93ce9a8bc3af5a956b1317416ed05269f60']
 
 dependencies = [
-    ('Python', '3.11.5'),
-    ('Python-bundle-PyPI', '2023.10'),
+    ('Python', '2.7.18'),
+    ('Cython', '0.29.37', versionsuffix),
     ('ncurses', '6.4'),
-    ('cURL', '8.3.0'),
-    ('XZ', '5.4.4'),
+    ('cURL', '8.0.1'),
+    ('XZ', '5.4.2'),
 ]
 
 download_dep_fail = True

Diff against Pysam-0.22.0-GCC-12.3.0.eb

easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
index 684f680624..6f30d071e1 100644
--- a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb
@@ -1,21 +1,23 @@
 easyblock = 'PythonPackage'
 
 name = 'Pysam'
-version = '0.22.0'
+version = '0.20.0'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/pysam-developers/pysam'
-description = """Pysam is a python module for reading and manipulating Samfiles.
+description = """Pysam is a python module for reading and manipulating Samfiles. 
  It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix."""
 
 toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/pysam-developers/pysam/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f']
+checksums = ['5a25d95b986c2cb9f5040b9df4e1d93ce9a8bc3af5a956b1317416ed05269f60']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
+    ('Python', '2.7.18'),
+    ('Cython', '0.29.37', versionsuffix),
     ('ncurses', '6.4'),
     ('cURL', '8.0.1'),
     ('XZ', '5.4.2'),

PetrKralCZ · 2025-02-21T11:10:46Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-02-21T11:20:09Z

@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=22354 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22354 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5754

Test results coming soon (I hope)...

Details

- notification for comment with ID 2674268401 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 · 2025-02-21T11:24:37Z

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/3d9b4d3862bacde8ce52864ccfc66158 for a full test report.

verdurin · 2025-02-24T10:16:43Z

@PetrKralCZ assume this is also for compatibility with checkM?

verdurin · 2025-02-24T10:21:45Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/3ab0d44db816a3c61ea4d4567ee74a80 for a full test report.

PetrKralCZ · 2025-02-24T10:23:21Z

@PetrKralCZ assume this is also for compatibility with checkM?

Yes, it is needed for CheckM with Python 2. Which is needed for CONCOCT which is needed for MetaWRAP (vscentrum/vsc-software-stack#494)

boegel · 2025-02-24T14:18:27Z

easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_WHL]


@PetrKralCZ Any reason why we're not building from source here, using SOURCE_TAR_GZ?

Whenever there is none-any wheel available, I use that. Is that wrong?

It should be fine, I mostly wondered why the SOURCE_TAR_GZ is no longer used as it was before

boegel

lgtm

boegel · 2025-02-24T18:13:14Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb, Cython-…

10b61a5

…0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

PetrKralCZ added the update label Feb 21, 2025

PetrKralCZ mentioned this pull request Feb 21, 2025

MetaWRAP vscentrum/vsc-software-stack#494

Closed

PetrKralCZ mentioned this pull request Feb 21, 2025

{bio}[GCCcore/12.3.0,foss/2023a] CheckM v1.0.18, DendroPy v4.5.2 w/ Python 2.7.18 #22362

Merged

boegel requested changes Feb 24, 2025

View reviewed changes

boegel added this to the release after 4.9.4 milestone Feb 24, 2025

boegel approved these changes Feb 24, 2025

View reviewed changes

boegel merged commit eb09c5e into easybuilders:develop Feb 24, 2025
10 checks passed

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

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{bio,lang}[GCC/12.3.0,GCCcore/12.3.0] Pysam v0.20.0, Cython v0.29.37 w/ Python 2.7.18#22354

{bio,lang}[GCC/12.3.0,GCCcore/12.3.0] Pysam v0.20.0, Cython v0.29.37 w/ Python 2.7.18#22354
boegel merged 1 commit intoeasybuilders:developfrom
PetrKralCZ:20250221110429_new_pr_Pysam0200

PetrKralCZ commented Feb 21, 2025

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		toolchain = {'name': 'GCCcore', 'version': '12.3.0'}

		sources = [SOURCE_WHL]

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PetrKralCZ commented Feb 21, 2025

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github-actions bot commented Feb 21, 2025

Updated software Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

Updated software Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb

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PetrKralCZ commented Feb 21, 2025

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Updated software `Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb`

Updated software `Pysam-0.20.0-GCC-12.3.0-Python-2.7.18.eb`