{bio}[GCC/12.3.0,foss/2023a] ExpressBetaDiversity v1.0.10, Seqmagick v0.8.6 by pavelToman · Pull Request #19938 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-02-20T09:37:09Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#235

…ick-0.8.6-foss-2023a.eb

pavelToman · 2024-02-20T09:37:40Z

@boegelbot please test @ generoso

boegelbot · 2024-02-20T09:40:05Z

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12923

Test results coming soon (I hope)...

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boegelbot · 2024-02-20T09:41:10Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/4a0207c84e445e73eca20ace19bfe465 for a full test report.

boegelbot · 2024-02-20T10:25:39Z

@pavelToman: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/7971338385
Output from first failing test suite run:

FAIL: test_pr_python_packages (test.easyconfigs.easyconfigs.EasyConfigTest)
Several checks for easyconfigs that install (bundles of) Python packages.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1169, in test_pr_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in Seqmagick-0.8.6-foss-2023a.eb
'use_pip' should be set in Seqmagick-0.8.6-foss-2023a.eb
sanity_pip_check should be enabled in Seqmagick-0.8.6-foss-2023a.eb

======================================================================
FAIL: test_pr_sha256_checksums (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure changed easyconfigs have SHA256 checksums in place.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1051, in test_pr_sha256_checksums
    self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
AssertionError: False is not true : No checksum issues:
Checksums missing for one or more sources/patches in Seqmagick-0.8.6-foss-2023a.eb: found 1 sources + 0 patches vs 0 checksums

======================================================================
FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 97, in assertEqual
    super(TestCase, self).assertEqual(a, b)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/unittest/case.py", line 829, in assertEqual
    assertion_func(first, second, msg=msg)
AssertionError: 1 != 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 119, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 1:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb:25:27: W299 trailing whitespace

: 1 != 0:
DIFF:
- 1

----------------------------------------------------------------------
Ran 19177 tests in 768.925s

FAILED (failures=3)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

boegelbot · 2024-02-20T13:25:44Z

@pavelToman: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/7973918453
Output from first failing test suite run:

FAIL: test_pr_python_packages (test.easyconfigs.easyconfigs.EasyConfigTest)
Several checks for easyconfigs that install (bundles of) Python packages.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1169, in test_pr_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in Seqmagick-0.8.6-foss-2023a.eb
'use_pip' should be set in Seqmagick-0.8.6-foss-2023a.eb
sanity_pip_check should be enabled in Seqmagick-0.8.6-foss-2023a.eb

======================================================================
FAIL: test_pr_sha256_checksums (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure changed easyconfigs have SHA256 checksums in place.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1051, in test_pr_sha256_checksums
    self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
AssertionError: False is not true : No checksum issues:
Checksums missing for one or more sources/patches in Seqmagick-0.8.6-foss-2023a.eb: found 1 sources + 0 patches vs 0 checksums

----------------------------------------------------------------------
Ran 19180 tests in 751.523s

FAILED (failures=2)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

pavelToman · 2024-02-20T17:59:01Z

@boegelbot please test @ generoso

boegelbot · 2024-02-20T18:00:05Z

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12929

Test results coming soon (I hope)...

Details

- notification for comment with ID 1954774103 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 · 2024-02-20T18:01:20Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ecfe34791fb54e99f0c564a72fa9eb21 for a full test report.

boegelbot · 2024-02-20T18:25:35Z

@pavelToman: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/7977880131
Output from first failing test suite run:

FAIL: test_pr_python_packages (test.easyconfigs.easyconfigs.EasyConfigTest)
Several checks for easyconfigs that install (bundles of) Python packages.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1169, in test_pr_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in Seqmagick-0.8.6-foss-2023a.eb
'use_pip' should be set in Seqmagick-0.8.6-foss-2023a.eb
sanity_pip_check should be enabled in Seqmagick-0.8.6-foss-2023a.eb

----------------------------------------------------------------------
Ran 19180 tests in 760.939s

FAILED (failures=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

pavelToman · 2024-02-21T11:46:00Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-21T11:50:07Z

@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=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3644

Test results coming soon (I hope)...

Details

- notification for comment with ID 1956476270 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 · 2024-02-21T11:50:49Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/96c435da062f09af6a4e6433e0a4780d for a full test report.

pavelToman · 2024-02-21T14:48:17Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-21T14:50:07Z

@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=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3645

Test results coming soon (I hope)...

Details

- notification for comment with ID 1956816409 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 · 2024-02-21T14:50:52Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/cac53ed01b9482e66354e5c1cc503ed5 for a full test report.

pavelToman · 2024-02-21T15:21:55Z

Error discussed on Slack: https://easybuild.slack.com/archives/C34UA1HT7/p1708515423871799

pavelToman · 2024-02-22T14:51:18Z

@boegelbot please test @ generoso

boegelbot · 2024-02-22T14:55:09Z

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12945

Test results coming soon (I hope)...

Details

- notification for comment with ID 1959614708 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 · 2024-02-22T14:57:16Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/36dcf4c40231c317d67db4deb931832d for a full test report.

pavelToman · 2024-02-22T14:58:02Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-02-22T15:00:08Z

@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=19938 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19938 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 3655

Test results coming soon (I hope)...

Details

- notification for comment with ID 1959628097 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 · 2024-02-22T15:01:03Z

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 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/94fe384a98711c6c1095cbc9f7ea84e2 for a full test report.

verdurin · 2024-02-26T10:50:38Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/c26de5fb8f5f4a5f49ac7d925fc3b634 for a full test report.

verdurin

Looks fine.

verdurin · 2024-02-26T10:53:33Z

Going in, thanks @pavelToman!

adding easyconfigs: ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb, Seqmag…

cd63084

…ick-0.8.6-foss-2023a.eb

delete whitespace

ec225aa

pavelToman added 2 commits February 20, 2024 18:38

add fix_python_shebang_for

8745bee

add checksum

57d2df4

uupdate Seqmagick

d09970a

update Seqmagick to PythonBundle and add dep pygtrie

8f84b73

fix matching pattern in dep.py

184260c

verdurin added new update labels Feb 26, 2024

verdurin added this to the release after 4.9.0 milestone Feb 26, 2024

verdurin approved these changes Feb 26, 2024

View reviewed changes

verdurin merged commit ff8ea94 into easybuilders:develop Feb 26, 2024

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