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

pavelToman · 2024-11-27T15:41:09Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#463

…1-foss-2023b.eb, pybedtools-0.10.0-foss-2023b.eb, BEDTools-2.31.1-GCC-13.2.0.eb

github-actions · 2024-11-27T15:41:50Z

Updated software `anndata-0.11.1-foss-2023b.eb`

Diff against anndata-0.9.2-foss-2021b.eb

easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
index f5f7d79dad..cb2317d16c 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
@@ -1,29 +1,37 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.9.2'
+version = '0.11.1'
 
 homepage = 'https://github.com/scverse/anndata'
 description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
  positioned between pandas and xarray"""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('h5py', '3.6.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
+    ('array_api_compat', '1.9.1', {
+        'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'],
+    }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
     (name, version, {
-        'checksums': ['e5b8383d09723af674cae7ad0c2ef53eb1f8c73949b7f4c182a6e30f42196327'],
+        'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'],
     }),
 ]

Diff against anndata-0.10.5.post1-foss-2023a.eb

easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
index 8c520bf7d0..cb2317d16c 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
@@ -1,39 +1,37 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.10.5.post1'
+version = '0.11.1'
 
 homepage = 'https://github.com/scverse/anndata'
 description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
  positioned between pandas and xarray"""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 builddependencies = [
     ('hatchling', '1.18.0'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('h5py', '3.9.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('packaging', '23.2', {
-        'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'],
-    }),
-    ('array_api_compat', '1.4.1', {
-        'checksums': ['053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0'],
+    ('array_api_compat', '1.9.1', {
+        'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'],
     }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
     (name, version, {
-        'checksums': ['9a17c6eda9fc40759b3f5f81742f5d18c1a0a1acdf02f13e1646700ec082c155'],
+        'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'],
     }),
 ]

Diff against anndata-0.9.2-foss-2021a.eb

easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
index 62b7466587..cb2317d16c 100644
--- a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb
@@ -1,32 +1,37 @@
 easyblock = 'PythonBundle'
 
 name = 'anndata'
-version = '0.9.2'
+version = '0.11.1'
 
 homepage = 'https://github.com/scverse/anndata'
 description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
  positioned between pandas and xarray"""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
 
 dependencies = [
-    ('Python', '3.9.5'),
-    ('SciPy-bundle', '2021.05'),
-    ('h5py', '3.2.1'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    # more recent setuptools required because scib-metrics uses pyproject.toml
-    ('setuptools', '68.1.2', {
-        'checksums': ['3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d'],
+    ('array_api_compat', '1.9.1', {
+        'checksums': ['17bab828c93c79a5bb8b867145b71fcb889686607c5672b060aef437e0359ea8'],
     }),
     ('natsort', '8.4.0', {
         'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
     }),
     (name, version, {
-        'checksums': ['e5b8383d09723af674cae7ad0c2ef53eb1f8c73949b7f4c182a6e30f42196327'],
+        'checksums': ['36bff9a85276fc5f1b9fd01f15aff9aa49408129985f42e0fca4e2c5b7fa909f'],
     }),
 ]
 
@@ -37,6 +42,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ["natsort --help"]
 
-sanity_pip_check = True
-
 moduleclass = 'bio'

Updated software `BEDTools-2.31.1-GCC-13.2.0.eb`

Diff against BEDTools-2.31.1-GCC-13.3.0.eb

easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
index 8503277b57..ee6ee7885e 100644
--- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
@@ -16,32 +16,25 @@ The BEDTools utilities allow one to address common genomics tasks such as findin
 computing coverage.
 The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
 
-toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e']
 
 builddependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.11.5'),
 ]
 dependencies = [
-    ('XZ', '5.4.5'),
-    ('zlib', '1.3.1'),
+    ('XZ', '5.4.4'),
+    ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('BamTools', '2.5.2'),
 ]
 
 buildopts = 'CXX="$CXX"'
 
-files_to_copy = [
-    'bin',
-    'docs',
-    'data',
-    'genomes',
-    'scripts',
-    'test',
-]
+files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test']
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],

Diff against BEDTools-2.31.0-GCC-12.3.0.eb

easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
index 184e7f7b83..ee6ee7885e 100644
--- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
@@ -8,7 +8,7 @@
 easyblock = 'MakeCp'
 
 name = 'BEDTools'
-version = '2.31.0'
+version = '2.31.1'
 
 homepage = 'https://bedtools.readthedocs.io/'
 description = """BEDTools: a powerful toolset for genome arithmetic.
@@ -16,17 +16,17 @@ The BEDTools utilities allow one to address common genomics tasks such as findin
 computing coverage.
 The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec']
+checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e']
 
 builddependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '3.11.5'),
 ]
 dependencies = [
-    ('XZ', '5.4.2'),
+    ('XZ', '5.4.4'),
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('BamTools', '2.5.2'),
@@ -34,14 +34,7 @@ dependencies = [
 
 buildopts = 'CXX="$CXX"'
 
-files_to_copy = [
-    'bin',
-    'docs',
-    'data',
-    'genomes',
-    'scripts',
-    'test',
-]
+files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test']
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],

Diff against BEDTools-2.30.0-GCC-12.2.0.eb

easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
index e85979fa03..ee6ee7885e 100644
--- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.1-GCC-13.2.0.eb
@@ -8,38 +8,39 @@
 easyblock = 'MakeCp'
 
 name = 'BEDTools'
-version = '2.30.0'
+version = '2.31.1'
 
-homepage = "https://bedtools.readthedocs.io/"
+homepage = 'https://bedtools.readthedocs.io/'
 description = """BEDTools: a powerful toolset for genome arithmetic.
 The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
 computing coverage.
 The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
 
-source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8']
-
-builddependencies = [('Python', '3.10.8')]
+source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e']
 
+builddependencies = [
+    ('Python', '3.11.5'),
+]
 dependencies = [
-    ('XZ', '5.2.7'),
-    ('zlib', '1.2.12'),
+    ('XZ', '5.4.4'),
+    ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),
     ('BamTools', '2.5.2'),
 ]
 
 buildopts = 'CXX="$CXX"'
 
-files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test']
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
     'dirs': files_to_copy,
 }
 
-sanity_check_commands = ['bedtools --help']
+sanity_check_commands = ['%(namelower)s --help']
 
 moduleclass = 'bio'

Updated software `MATES-0.1.5-20241121-foss-2023b.eb`

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-0.1.5-20241121-foss-2023b.eb
index dbba96ddf2..2c87d3d09b 100644
--- a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb
@@ -1,27 +1,25 @@
 easyblock = 'PythonBundle'
 
 name = 'MATES'
-version = '0.1.2-20240813'
-local_commit = 'd5ee15b'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '0.1.5-20241121'
+local_commit = '3846ad5'
 
 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 +32,16 @@ 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 && ",
+        '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': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+        'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'],
     }),
 ]

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-0.1.5-20241121-foss-2023b.eb
index e7e73a89e8..2c87d3d09b 100644
--- a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb
+++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.5-20241121-foss-2023b.eb
@@ -1,25 +1,25 @@
 easyblock = 'PythonBundle'
 
 name = 'MATES'
-version = '0.1.2-20240813'
-local_commit = 'd5ee15b'
+version = '0.1.5-20241121'
+local_commit = '3846ad5'
 
 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 +32,16 @@ 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 && ",
+        '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': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'],
+        'checksums': ['40fbb87dd72ca4c9e5347f2e984f9c0a0caa817d4eee692476be71e733e76f61'],
     }),
 ]

Updated software `pybedtools-0.10.0-foss-2023b.eb`

Diff against pybedtools-0.9.1-foss-2023a.eb

easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.1-foss-2023a.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
index ac4c03a4f6..2f643966cd 100644
--- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
@@ -1,27 +1,25 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'pybedtools'
-version = '0.9.1'
+version = '0.10.0'
 
 homepage = 'https://daler.github.io/pybedtools'
 description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('BEDTools', '2.31.0'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('BEDTools', '2.31.1'),
     ('Pysam', '0.22.0'),
 ]
 
 use_pip = True
+download_dep_fail = True
 sanity_pip_check = True
 
-exts_list = [
-    (name, version, {
-        'checksums': ['586a626895b1b7215aef877e985c03fd8a908fd6c636e5b9ff8a1a1d09a1d514'],
-    }),
-]
-
 moduleclass = 'bio'

Diff against pybedtools-0.9.0-GCC-12.2.0.eb

easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
index d7062b3aad..2f643966cd 100644
--- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
@@ -1,26 +1,25 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'pybedtools'
-version = '0.9.0'
+version = '0.10.0'
 
 homepage = 'https://daler.github.io/pybedtools'
 description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python."
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161']
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('BEDTools', '2.30.0'),
-    ('Pysam', '0.21.0'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('BEDTools', '2.31.1'),
+    ('Pysam', '0.22.0'),
 ]
 
 use_pip = True
+download_dep_fail = True
 sanity_pip_check = True
 
-exts_list = [
-    (name, version, {
-        'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'],
-    }),
-]
-
 moduleclass = 'bio'

Diff against pybedtools-0.9.0-GCC-11.3.0.eb

easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
index 4b4c5f4002..2f643966cd 100644
--- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.10.0-foss-2023b.eb
@@ -1,28 +1,25 @@
-easyblock = 'PythonBundle'
+easyblock = 'PythonPackage'
 
 name = 'pybedtools'
-version = '0.9.0'
+version = '0.10.0'
 
 homepage = 'https://daler.github.io/pybedtools'
 description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python."
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161']
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('BEDTools', '2.30.0'),
-    ('Pysam', '0.19.1'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('BEDTools', '2.31.1'),
+    ('Pysam', '0.22.0'),
 ]
 
 use_pip = True
+download_dep_fail = True
 sanity_pip_check = True
 
-exts_list = [
-    (name, version, {
-        'source_urls': ['https://daler.github.io/pybedtools/archive'],
-        'sources': [SOURCE_TAR_GZ],
-        'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'],
-    }),
-]
-
 moduleclass = 'bio'

pavelToman · 2024-11-27T15:47:03Z

@boegelbot please test @ generoso

boegelbot · 2024-11-27T15:50:05Z

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

PR test command 'EB_PR=21919 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21919 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14771

Test results coming soon (I hope)...

- notification for comment with ID 2504208393 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).

pavelToman · 2024-11-27T15:59:24Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4003.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/2916bb46de060aa6f038817972aaea5c for a full test report.

boegelbot · 2024-11-27T16:01:07Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/48aa1d1617fddb175ae6035e41e1228d for a full test report.

pavelToman · 2024-11-27T16:06:35Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-27T16:10:09Z

@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=21919 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21919 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5343

Test results coming soon (I hope)...

- notification for comment with ID 2504257437 processed

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boegelbot · 2024-11-27T16:17:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/ad88ce291da06e4a6896e16902c84497 for a full test report.

pavelToman · 2024-11-27T16:18:15Z

Test report by @pavelToman
SUCCESS
Build succeeded for 5 out of 5 (4 easyconfigs in total)
node4202.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/327ec414d50e27aac22df1af4b576ce9 for a full test report.

easybuild/easyconfigs/a/anndata/anndata-0.11.1-foss-2023b.eb

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

pavelToman · 2024-11-28T13:50:54Z

@boegelbot please test @ generoso

boegelbot · 2024-11-28T13:55:10Z

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

PR test command 'EB_PR=21919 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21919 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14775

Test results coming soon (I hope)...

- notification for comment with ID 2506175208 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 · 2024-11-28T13:55:30Z

Test report by @boegelbot
FAILED
Failed during parsing of the easyconfigs, so no ecs were built (4 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/da6f2e018e7fe65685a3792f69550489 for a full test report.

pavelToman · 2024-11-28T13:58:10Z

@boegelbot please test @ generoso

boegelbot · 2024-11-28T14:00:10Z

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

PR test command 'EB_PR=21919 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21919 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14776

Test results coming soon (I hope)...

- notification for comment with ID 2506189443 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 · 2024-11-28T14:10:59Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/4f71d29dab34296212e3ef5bf198d06f for a full test report.

pavelToman · 2024-11-28T14:23:03Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-28T14:30:11Z

@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=21919 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21919 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5346

Test results coming soon (I hope)...

- notification for comment with ID 2506240124 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 · 2024-11-28T14:36:37Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/847e72a4cfda14e9f305b77749c8d5b0 for a full test report.

verdurin · 2024-11-28T14:47:58Z

@pavelToman thanks. See what you mean, but I think it's nice to keep an explicit check.

verdurin · 2024-11-28T15:10:43Z

Test report by @verdurin
FAILED
Build succeeded for 3 out of 5 (4 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/a4b9108d9db2bc341c38e87bc65b78f5 for a full test report.

verdurin · 2024-11-28T15:20:36Z

My build failed because PyTorch is already building for a different PR.

verdurin · 2024-11-28T19:38:15Z

Test report by @verdurin
SUCCESS
Build succeeded for 24 out of 24 (4 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/1f20c938dc1db326e7d9b26979fcedd7 for a full test report.

verdurin

Looks fine.

verdurin · 2024-11-29T09:34:32Z

Going in, thanks @pavelToman!

boegel · 2024-12-10T13:31:39Z

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

+
+name = 'MATES'
+version = '0.1.5-20241121'
+local_commit = '3846ad5'


changing this in #21998, since there's a proper 0.1.5 release tagged now: https://github.com/mcgilldinglab/MATES/releases/tag/v0.1.5 (commit 3661ef3)

adding easyconfigs: MATES-0.1.5-20241121-foss-2023b.eb, anndata-0.11.…

3b51546

…1-foss-2023b.eb, pybedtools-0.10.0-foss-2023b.eb, BEDTools-2.31.1-GCC-13.2.0.eb

github-actions bot added the update label Nov 27, 2024

pavelToman mentioned this pull request Nov 27, 2024

MATES vscentrum/vsc-software-stack#463

Open

2 tasks

update easyblock of pybedtools

c99da1e

verdurin requested changes Nov 28, 2024

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pavelToman added 2 commits November 28, 2024 14:47

Update anndata-0.11.1-foss-2023b.eb - add sanity_check_paths

e9d7220

Update MATES-0.1.5-20241121-foss-2023b.eb - add samtools dep

77487c1

Update MATES-0.1.5-20241121-foss-2023b.eb - typo

7345fe3

verdurin approved these changes Nov 29, 2024

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verdurin added this to the release after 4.9.4 milestone Nov 29, 2024

verdurin merged commit c81573c into easybuilders:develop Nov 29, 2024
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boegel mentioned this pull request Dec 10, 2024

use proper release of MATES v0.1.5 #21998

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

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

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

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

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pavelToman commented Nov 27, 2024 • edited Loading

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Updated software anndata-0.11.1-foss-2023b.eb

Updated software BEDTools-2.31.1-GCC-13.2.0.eb

Updated software MATES-0.1.5-20241121-foss-2023b.eb

Updated software pybedtools-0.10.0-foss-2023b.eb

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pavelToman commented Nov 27, 2024 •

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Updated software `anndata-0.11.1-foss-2023b.eb`

Updated software `BEDTools-2.31.1-GCC-13.2.0.eb`

Updated software `MATES-0.1.5-20241121-foss-2023b.eb`

Updated software `pybedtools-0.10.0-foss-2023b.eb`