{bio}[foss/2023b] purge_dups v1.2.6

[akesandgren]

(created using eb --new-pr)

[github-actions]

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..6848c4131d 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_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]

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]

@boegelbot please test @ generoso

[boegelbot]

@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)...

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Message to humans: this is just bookkeeping information for me,
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[boegelbot]

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]

@boegelbot please test @ jsc-zen3

[boegelbot]

@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)...

- 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]

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]

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]

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.

[bedroge]

Shouldn't this include the KMC version (and may some comment or other name like KMC-dfguan to indicate that this is for a fork of KMC, as it confused me for a while when I saw your other KMC PR 😄)?