{bio}[foss/2023a] fastStructure v1.0 w/ Python 2.7.18 by PetrKralCZ · Pull Request #22423 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-02-28T13:38:55Z

resolves vscentrum/vsc-software-stack#506
needs

add back easyblock for fastStructure, ported to run_shell_cmd and module_load_environment easybuild-easyblocks#3642

github-actions · 2025-02-28T13:39:25Z

Updated software `Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb`

Diff against Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

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

diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
index 8cc129c05c..3f844e477a 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '0.29.37'
+version = '0.27.3'
 versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://cython.org/'
@@ -16,8 +16,8 @@ docurls = [
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
-sources = [SOURCE_WHL]
-checksums = ['95f1d6a83ef2729e67b3fa7318c829ce5b07ac64c084cd6af11c228e0364662c']
+sources = [SOURCE_TAR_GZ]
+checksums = ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64']
 
 builddependencies = [
     ('binutils', '2.40'),

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-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
index 9a5300d65a..3f844e477a 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.0.10'
+version = '0.27.3'
+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']
+checksums = ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64']
 
 builddependencies = [
-    ('binutils', '2.42'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '2.7.18'),
 ]
 
 sanity_check_paths = {

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-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
index d8269cf28b..3f844e477a 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.0.10'
+version = '0.27.3'
+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']
+checksums = ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64']
 
 builddependencies = [
     ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.11.5'),
+    ('Python', '2.7.18'),
 ]
 
 sanity_check_paths = {

PetrKralCZ · 2025-02-28T13:43:43Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr 3642"

boegelbot · 2025-02-28T13:50:09Z

@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=22423 EB_ARGS="--include-easyblocks-from-pr 3642" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22423 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5817

Test results coming soon (I hope)...

Details

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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).

boegel · 2025-03-03T13:48:29Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr 3642"
EB_BRANCH=5.0.x

boegelbot · 2025-03-03T13:50:15Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ "5.0.x" != 'develop' ]]; then EB_BRANCH="5.0.x" ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/"5.0.x" source init_env_easybuild_develop.sh; fi; EB_PR=22423 EB_ARGS="--include-easyblocks-from-pr 3642" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH="5.0.x" /opt/software/slurm/bin/sbatch --job-name test_PR_22423 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5828

Test results coming soon (I hope)...

Details

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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 · 2025-03-03T13:51:41Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3642
FAILED
Build succeeded for 0 out of 1 (1 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/79cade691a7ffa95251024da36fd2ee4 for a full test report.

PetrKralCZ · 2025-03-11T12:48:01Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr 3642"
EB_BRANCH=5.0.x

boegelbot · 2025-03-11T12:50:16Z

@PetrKralCZ: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ "5.0.x" != 'develop' ]]; then EB_BRANCH="5.0.x" ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/"5.0.x" source init_env_easybuild_develop.sh; fi; EB_PR=22423 EB_ARGS="--include-easyblocks-from-pr 3642" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH="5.0.x" /opt/software/slurm/bin/sbatch --job-name test_PR_22423 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5911

Test results coming soon (I hope)...

Details

- notification for comment with ID 2714075033 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 · 2025-03-11T12:54:15Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3642
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/9f84b90467cf7b9d92cdfc417e710e9a for a full test report.

…ructure10

PetrKralCZ · 2025-03-28T10:38:22Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--include-easyblocks-from-pr 3642"

boegelbot · 2025-03-28T10:40:08Z

@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=22423 EB_ARGS="--include-easyblocks-from-pr 3642" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22423 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6046

Test results coming soon (I hope)...

Details

- notification for comment with ID 2760921811 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 · 2025-03-28T10:43:56Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3642
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/b37cb94208bd84b97a0179bd6cc6974f for a full test report.

easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb

…syconfig Co-authored-by: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com>

PetrKralCZ · 2025-04-08T09:27:17Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-04-08T09:30:08Z

@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=22423 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22423 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6130

Test results coming soon (I hope)...

Details

- notification for comment with ID 2785811394 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 · 2025-04-08T09:34:10Z

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/e30fdd7165767691f6487fa0a1f8fec7 for a full test report.

laraPPr · 2025-04-08T13:21:49Z

Test report by @laraPPr
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3642
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3505.doduo.os - Linux RHEL 9.4 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.18
See https://gist.github.com/laraPPr/0646884f85e9952cb0d88de17d3e95bb for a full test report.

laraPPr

style changes

easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb

laraPPr

lgtm

laraPPr · 2025-04-08T13:49:25Z

Going in, thanks @PetrKralCZ!

PetrKralCZ marked this pull request as draft February 28, 2025 13:39

github-actions bot added the update label Feb 28, 2025

boegel changed the base branch from develop to 5.0.x March 3, 2025 13:44

adding easyconfigs: fastStructure-1.0-foss-2023a-Python-2.7.18.eb

924a510

boegel force-pushed the 20250228143532_new_pr_fastStructure10 branch from 32a0561 to 924a510 Compare March 3, 2025 13:47

github-actions bot added new and removed update labels Mar 3, 2025

boegel mentioned this pull request Mar 3, 2025

add back easyblock for fastStructure, ported to run_shell_cmd and module_load_environment easybuilders/easybuild-easyblocks#3642

Merged

PetrKralCZ mentioned this pull request Mar 3, 2025

fastStructure vscentrum/vsc-software-stack#506

Closed

use compatible version of Cython

6945940

github-actions bot added the update label Mar 11, 2025

Merge branch 'easybuilders:develop' into 20250228143532_new_pr_fastSt…

e1d522d

…ructure10

github-actions bot added change workflow labels Mar 28, 2025

PetrKralCZ changed the base branch from 5.0.x to develop March 28, 2025 09:49

remove comments

561fb37

github-actions bot removed change workflow labels Mar 28, 2025

PetrKralCZ marked this pull request as ready for review March 28, 2025 10:48

laraPPr requested changes Apr 1, 2025

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easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb Outdated Show resolved Hide resolved

don't explicitly set use_pip and sanity_pip_check in fastStructure ea…

db02dac

…syconfig Co-authored-by: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com>

laraPPr requested changes Apr 8, 2025

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easybuild/easyconfigs/c/Cython/Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb Show resolved Hide resolved

remove extra white line

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laraPPr approved these changes Apr 8, 2025

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

laraPPr merged commit dfe9f94 into easybuilders:develop Apr 8, 2025
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Updated software `Cython-0.27.3-GCCcore-12.3.0-Python-2.7.18.eb`