use proper release of MATES v0.1.5 #21998

boegel · 2024-12-10T13:30:11Z

(created using eb --new-pr)

follow-up for #21919, where a commit was used because there was no proper release of 0.1.5 yet (but there is now)

github-actions · 2024-12-10T13:30:39Z

Updated software `MATES-0.1.5-foss-2023b.eb`

Diff against MATES-0.1.5-20241121-foss-2023b.eb

easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb

diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
index 2c87d3d09b..d142586c26 100644
--- a/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
@@ -1,8 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'MATES'
-version = '0.1.5-20241121'
-local_commit = '3846ad5'
+version = '0.1.5'
 
 homepage = 'https://github.com/mcgilldinglab/MATES'
 description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data."
@@ -36,12 +35,12 @@ exts_list = [
         'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
     }),
     (name, version, {
-        'modulename': 'MATES',
+        'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['be0170d83bf1d039c9de278791e2ad5a61476581c59c245f53ba087b3a5a3407'],
         # unpin exact versions of dependencies
         'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """,
-        'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
-        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'],
+        'modulename': 'MATES',
     }),
 ]

Diff against MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
index dbba96ddf2..d142586c26 100644
--- a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
@@ -1,27 +1,24 @@
 easyblock = 'PythonBundle'
 
 name = 'MATES'
-version = '0.1.2-20240813'
-local_commit = 'd5ee15b'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '0.1.5'
 
 homepage = 'https://github.com/mcgilldinglab/MATES'
 description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('matplotlib', '3.7.2'),
-    ('anndata', '0.10.5.post1'),
-    ('SAMtools', '1.18'),
-    ('pybedtools', '0.9.1'),
-    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('anndata', '0.11.1'),
+    ('pybedtools', '0.10.0'),
+    ('PyTorch', '2.1.2'),
     ('Pysam', '0.22.0'),
-    ('tqdm', '4.66.1'),
+    ('tqdm', '4.66.2'),
+    ('SAMtools', '1.19.2'),
 ]
 
 use_pip = True
@@ -34,19 +31,16 @@ exts_list = [
     ('ncls', '0.0.68', {
         'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
     }),
-    ('natsort', '8.4.0', {
-        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
-    }),
     ('pyranges', '0.0.129', {
         'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
     }),
     (name, version, {
-        'modulename': 'MATES',
-        # unpin exact versions of dependencies
-        'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ",
         'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
-        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['be0170d83bf1d039c9de278791e2ad5a61476581c59c245f53ba087b3a5a3407'],
+        # unpin exact versions of dependencies
+        'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """,
+        'modulename': 'MATES',
     }),
 ]

Diff against MATES-0.1.2-20240813-foss-2023a.eb

easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb

diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
index e7e73a89e8..d142586c26 100644
--- a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-foss-2023b.eb
@@ -1,25 +1,24 @@
 easyblock = 'PythonBundle'
 
 name = 'MATES'
-version = '0.1.2-20240813'
-local_commit = 'd5ee15b'
+version = '0.1.5'
 
 homepage = 'https://github.com/mcgilldinglab/MATES'
 description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('Python-bundle-PyPI', '2023.06'),
-    ('SciPy-bundle', '2023.07'),
-    ('matplotlib', '3.7.2'),
-    ('anndata', '0.10.5.post1'),
-    ('SAMtools', '1.18'),
-    ('pybedtools', '0.9.1'),
-    ('PyTorch-bundle', '2.1.2'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('matplotlib', '3.8.2'),
+    ('anndata', '0.11.1'),
+    ('pybedtools', '0.10.0'),
+    ('PyTorch', '2.1.2'),
     ('Pysam', '0.22.0'),
-    ('tqdm', '4.66.1'),
+    ('tqdm', '4.66.2'),
+    ('SAMtools', '1.19.2'),
 ]
 
 use_pip = True
@@ -32,19 +31,16 @@ exts_list = [
     ('ncls', '0.0.68', {
         'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'],
     }),
-    ('natsort', '8.4.0', {
-        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
-    }),
     ('pyranges', '0.0.129', {
         'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'],
     }),
     (name, version, {
-        'modulename': 'MATES',
-        # unpin exact versions of dependencies
-        'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ",
         'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'],
-        'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['be0170d83bf1d039c9de278791e2ad5a61476581c59c245f53ba087b3a5a3407'],
+        # unpin exact versions of dependencies
+        'preinstallopts': """sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && """,
+        'modulename': 'MATES',
     }),
 ]

boegel · 2024-12-10T13:31:56Z

@boegelbot please test @ generoso

boegelbot · 2024-12-10T13:35:12Z

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

PR test command 'EB_PR=21998 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21998 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14849

Test results coming soon (I hope)...

- notification for comment with ID 2531648538 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).

boegel · 2024-12-10T13:35:27Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3102.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/4ea073bff4d537061d694d0a52105260 for a full test report.

boegelbot · 2024-12-10T13:40:48Z

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/2d6ac0d35af49f7680ab50bf6760e99c for a full test report.

boegel · 2024-12-10T16:08:47Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-12-10T16:10:09Z

@boegel: 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=21998 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21998 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5426

Test results coming soon (I hope)...

- notification for comment with ID 2532168189 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 · 2024-12-10T16:14:01Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/b5c9acb18aab869ac4e97e5c8f94f7d6 for a full test report.

use proper release of MATES v0.1.5

5b7c849

boegel added update bug fix change and removed update labels Dec 10, 2024

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

boegel mentioned this pull request Dec 10, 2024

{bio}[foss/2023b] MATES v0.1.5-20241121, anndata v0.11.1, pybedtools v0.10.0, ... #21919

Merged

hajgato approved these changes Dec 10, 2024

View reviewed changes

hajgato merged commit e148286 into easybuilders:develop Dec 10, 2024
10 checks passed

boegel deleted the 20241210143005_new_pr_MATES015 branch December 10, 2024 16:26

boegel mentioned this pull request Dec 11, 2024

MATES vscentrum/vsc-software-stack#463

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use proper release of MATES v0.1.5 #21998

use proper release of MATES v0.1.5 #21998

boegel commented Dec 10, 2024 •

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boegelbot commented Dec 10, 2024

use proper release of MATES v0.1.5 #21998

use proper release of MATES v0.1.5 #21998

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github-actions bot commented Dec 10, 2024

Updated software MATES-0.1.5-foss-2023b.eb

boegel commented Dec 10, 2024

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boegel commented Dec 10, 2024 •

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Updated software `MATES-0.1.5-foss-2023b.eb`

boegel commented Dec 10, 2024 •

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