{lib}[foss/2022a] CPC2 v0.1 w/ Python 3.10.4 by deniskristak · Pull Request #17849 · easybuilders/easybuild-easyconfigs

deniskristak · 2023-05-03T11:42:19Z

(created using eb --new-pr)

…libsvm_path_and_python2.patch

deniskristak · 2023-05-03T11:42:36Z

one of dependencies for vscentrum/vsc-software-stack#106

boegel · 2023-05-04T09:53:22Z

@boegelbot please test @ generoso

boegel · 2023-05-04T09:53:54Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3144.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/acb6f615d59e01d20ca613dc745e4918 for a full test report.

boegelbot · 2023-05-04T09:55:12Z

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

PR test command 'EB_PR=17849 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17849 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10742

Test results coming soon (I hope)...

Details

- notification for comment with ID 1534442982 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 · 2023-05-04T09:55:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b3f8d97db2bd55d75315350b9c79df5b for a full test report.

Micket · 2023-05-04T22:45:27Z

+# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available
+# download from github mirror
+source_urls = ['https://github.com/lucventurini/CPC2/archive/']


This seems to be available? https://github.com/gao-lab/CPC2_standalone/releases
I was directed here by going to the old website, which redirected to the new gao-lab website, which redirected here.
This seems much much newer as well compared to the version 0.1 in the lucventurini repo, and this one has been ported to python 3 already.

@deniskristak @smoors Thoughts on going with a more recent version available via https://github.com/gao-lab/CPC2_standalone/releases ?

@boegel just pushed an updated version using the newer source. I had to change version too, so I'm removing the original files.

thanks, didnt notice Co-authored-by: Mikael Öhman <[email protected]>

unnecessary, as source files for python3 were found

removing, as src files for py3 were found (and version change was necessary, renaming the file)

verdurin · 2023-05-16T09:04:13Z

Test report by @verdurin
SUCCESS
Build succeeded for 2 out of 2 (1 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/51b1e5c1dea6603423446b90806c93c8 for a full test report.

verdurin · 2023-05-16T09:06:41Z

@boegelbot please test @ generoso

boegelbot · 2023-05-16T09:10:09Z

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

PR test command 'EB_PR=17849 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17849 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10784

Test results coming soon (I hope)...

Details

- notification for comment with ID 1549283662 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 · 2023-05-16T09:10:57Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/467e43ef67b8cd47bee8ec60f3cfd4c4 for a full test report.

verdurin · 2023-05-16T09:14:05Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-16T09:17:07Z

@verdurin: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=17849 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17849 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2599

Test results coming soon (I hope)...

Details

- notification for comment with ID 1549295559 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 · 2023-05-16T09:17:37Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/2d2c90b91a4f1d845f7590c6446e169e for a full test report.

verdurin · 2023-05-16T09:36:09Z

Looks okay to me now.
Agreed @Micket ?

Co-authored-by: Mikael Öhman <[email protected]>

verdurin · 2023-05-18T13:03:37Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 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/09582f73c530fd6a234e28410a396999 for a full test report.

verdurin · 2023-05-18T13:04:34Z

@boegelbot please test @ generoso

boegelbot · 2023-05-18T13:05:12Z

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

PR test command 'EB_PR=17849 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17849 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10801

Test results coming soon (I hope)...

Details

- notification for comment with ID 1553026231 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 · 2023-05-18T13:06:02Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/ce906c515d8973948508767882d7fc64 for a full test report.

Changes addressed.

verdurin · 2023-05-18T13:09:04Z

Going in, thanks @deniskristak!

adding easyconfigs: CPC2-0.1-foss-2022a.eb and patches: CPC2-0.1_fix_…

9f29798

…libsvm_path_and_python2.patch

deniskristak added the new label May 3, 2023

code style

7d9fcc0

boegel requested changes May 4, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb Outdated

also check for 'data' in sanity check for CPC2

28b35d2

boegel added this to the next release (4.7.2) milestone May 4, 2023

boegel previously approved these changes May 4, 2023

View reviewed changes

Micket requested changes May 4, 2023

View reviewed changes

deniskristak dismissed boegel’s stale review via 69e3e59 May 6, 2023 12:29

deniskristak and others added 4 commits May 6, 2023 14:29

Update easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb

69e3e59

thanks, didnt notice Co-authored-by: Mikael Öhman <[email protected]>

using cpc2 made for python3

7f62900

Delete CPC2-0.1_fix_libsvm_path_and_python2.patch

8a93adc

unnecessary, as source files for python3 were found

Delete CPC2-0.1-foss-2022a.eb

9b71436

removing, as src files for py3 were found (and version change was necessary, renaming the file)

deniskristak mentioned this pull request May 15, 2023

{bio}[foss/2022a] Annocript 2.0, BioPerl 1.7.8 w/ Python 3.10.4 #17910

Merged

Micket previously requested changes May 16, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb Outdated

Comment thread easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb Outdated

deniskristak and others added 2 commits May 16, 2023 12:16

Update easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb

d455e47

Co-authored-by: Mikael Öhman <[email protected]>

Update easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb

7d1ab24

Co-authored-by: Mikael Öhman <[email protected]>

verdurin approved these changes May 18, 2023

View reviewed changes

verdurin merged commit 851e8b7 into easybuilders:develop May 18, 2023

Conversation

deniskristak commented May 3, 2023

Uh oh!

deniskristak commented May 3, 2023

Uh oh!

Uh oh!

boegel commented May 4, 2023

Uh oh!

boegel commented May 4, 2023

Uh oh!

boegelbot commented May 4, 2023

Uh oh!

boegelbot commented May 4, 2023

Uh oh!

Uh oh!

Micket May 4, 2023

Choose a reason for hiding this comment

Uh oh!

boegel May 5, 2023

Choose a reason for hiding this comment

Uh oh!

deniskristak May 15, 2023

Choose a reason for hiding this comment

Uh oh!

verdurin commented May 16, 2023

Uh oh!

verdurin commented May 16, 2023

Uh oh!

boegelbot commented May 16, 2023

Uh oh!

boegelbot commented May 16, 2023

Uh oh!

verdurin commented May 16, 2023

Uh oh!

boegelbot commented May 16, 2023

Uh oh!

boegelbot commented May 16, 2023

Uh oh!

verdurin commented May 16, 2023

Uh oh!

Uh oh!

Uh oh!

verdurin commented May 18, 2023

Uh oh!

verdurin commented May 18, 2023

Uh oh!

boegelbot commented May 18, 2023

Uh oh!

boegelbot commented May 18, 2023

Uh oh!

verdurin commented May 18, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants