{bio}[foss/2023b] purge_dups v1.2.6 by akesandgren · Pull Request #21991 · easybuilders/easybuild-easyconfigs

akesandgren · 2024-12-09T15:16:33Z

(created using eb --new-pr)

github-actions · 2024-12-09T15:17:47Z

Updated software `purge_dups-1.2.6-foss-2023b.eb`

Diff against purge_dups-1.2.5-foss-2021b.eb

easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb

diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb
index c2a1fcd985..a407a2ec4b 100644
--- a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb
@@ -1,18 +1,23 @@
 easyblock = 'PythonBundle'
 
 name = 'purge_dups'
-version = '1.2.5'
+version = '1.2.6'
 
 homepage = 'https://github.com/dfguan/purge_dups'
 description = "purge haplotigs and overlaps in an assembly based on read depth"
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('pybind11', '2.11.1'),
+]
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('matplotlib', '3.4.3'),
-    ('minimap2', '2.22'),
-    ('zlib', '1.2.11'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('Python', '3.11.5'),
+    ('matplotlib', '3.8.2'),
+    ('minimap2', '2.28'),
 ]
 
 use_pip = True
@@ -21,18 +26,25 @@ default_easyblock = 'MakeCp'
 
 components = [
     (name, version, {
-        'source_urls': ['https://github.com/dfguan/purge_dups/archive/refs/tags/'],
+        'source_urls': ['https://github.com/dfguan/purge_dups/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['7879a8ecc26e5de1eaaf4b4633cb240ed2802d648068b193652477317a3e2645'],
+        'checksums': ['75b20df834d28410858ccd4e2d65b6c70849f3cbe5fc05959f38bfc2d041c704'],
         'start_dir': 'purge_dups-%(version)s',
         'prebuildopts': "cd src && ",
         'buildopts': 'CC="$CC" CFLAGS="$CFLAGS"',
         'files_to_copy': ['bin', 'scripts'],
     }),
     ('KMC', '20190629', {
-        'source_urls': ['https://github.com/dfguan/KMC/archive/'],
+        'source_urls': ['https://github.com/dfguan/KMC/archive'],
         'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4'],
+        'patches': [{
+            'name': 'KMC-dfguan-c05a5f9_use_EB_pybind11_and_libs.patch',
+            'sourcepath': 'KMC-c05a5f9fd94683248ebe04484a60f86792cf328f',
+        }],
+        'checksums': [
+            '7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4',
+            '2f54971aae26787777d0e4b638a9682bd4bc22cbf3fda170c7baf4c610808ac9',
+        ],
         'prebuildopts': 'cd KMC-* && ',
         'buildopts': 'CC="$CXX"',
         'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'],
@@ -41,6 +53,7 @@ components = [
 
 exts_list = [
     ('runner', '20191220', {
+        'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && ",
         'sources': [{
             'git_config': {
                 'url': 'https://github.com/dfguan/',
@@ -50,7 +63,6 @@ exts_list = [
             'filename': 'runner-%(version)s.tar.gz',
         }],
         'checksums': [None],
-        'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && "
     }),
 ]

akesandgren · 2024-12-09T15:25:03Z

Test report by @akesandgren
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-cn1611.hpc2n.umu.se - Linux Ubuntu 22.04, x86_64, AMD EPYC 7313 16-Core Processor, 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.58.02, Python 3.10.12
See https://gist.github.com/akesandgren/97bf47ae1f4ffc1f167608b27db74cd3 for a full test report.

bedroge · 2024-12-10T09:15:23Z

@boegelbot please test @ generoso

boegelbot · 2024-12-10T09:20:09Z

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

PR test command 'EB_PR=21991 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21991 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14842

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 · 2024-12-10T09:23:53Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/a1f82243040fdc1d8ceced6046d73cb8 for a full test report.

bedroge · 2024-12-10T10:14:35Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-12-10T10:20:22Z

@bedroge: 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=21991 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21991 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5421

Test results coming soon (I hope)...

Details

- notification for comment with ID 2531109503 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 · 2024-12-10T10:23:34Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 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 3.9.19
See https://gist.github.com/boegelbot/eef4d45f1044c17ba52d6de3f880f8ae for a full test report.

bedroge · 2024-12-10T10:44:36Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.1 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/05eabb465cb30417e26ce5654099c16e for a full test report.

bedroge · 2024-12-10T10:58:10Z

Test report by @bedroge
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/af62a66b7006dfe296167332e8508802 for a full test report.

easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb

bedroge · 2024-12-16T10:20:41Z

@boegelbot please test @ generoso

bedroge · 2024-12-16T10:23:18Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.1 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/a6e68e69851b00e442892d37f86f5582 for a full test report.

bedroge

Lgtm

boegelbot · 2024-12-16T10:25:09Z

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

PR test command 'EB_PR=21991 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21991 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14869

Test results coming soon (I hope)...

Details

- notification for comment with ID 2545177107 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 · 2024-12-16T10:28:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/566d27d3cfbc8065cd8f49ebb82d6735 for a full test report.

bedroge · 2024-12-16T11:00:56Z

Going in, thanks @akesandgren!

Flamefire · 2025-06-13T15:33:04Z

This fails for me because it tries to run the test step (make) in purge_dups-1.2.6 instead of the src subdir

Any idea why this didn't fail before?

Edit: Tests steps for bundle are only run recently

ocaisa · 2025-06-14T06:20:16Z

@Flamefire I think I have a general fix for this in easybuilders/easybuild-easyblocks#3775

adding easyconfigs: purge_dups-1.2.6-foss-2023b.eb

e26bc12

akesandgren added the update label Dec 9, 2024

purge_dups: Add KMC patch to use EB pybind11 and libs

7b61829

bedroge added this to the release after 4.9.4 milestone Dec 10, 2024

bedroge reviewed Dec 10, 2024

View reviewed changes

easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb Outdated Show resolved Hide resolved

purge_dups: Rename KMC patch to better show where it belongs

9c32130

bedroge approved these changes Dec 16, 2024

View reviewed changes

bedroge merged commit 6b89819 into easybuilders:develop Dec 16, 2024
10 checks passed

akesandgren deleted the 20241209161623_new_pr_purge_dups126 branch December 16, 2024 11:02

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

Flamefire mentioned this pull request Jun 13, 2025

enhance Bundle generic easyblock to also run test step for each bundle component easybuilders/easybuild-easyblocks#3748

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Updated software `purge_dups-1.2.6-foss-2023b.eb`

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