{bio}[foss/2021b] Vamb v3.0.9 w/ Python 3.9.6

easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Vamb'
+version = '3.0.9'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/RasmussenLab/vamb'
+description = """Vamb is a metagenomic binner which feeds sequence
+composition information from a contig catalogue and co-abundance
+information from BAM files into a variational autoencoder and clusters
+the latent representation."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('CUDA', '11.5.2', '', SYSTEM),
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('Pysam', '0.17.0'),
+    ('PyTorch', '1.12.1', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('setuptools', '59.6.0', {
+        'source_tmpl': 'setuptools-%(version)s.tar.gz',
+        'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'],
+    }),
+    (name, version, {
+        'patches': ['%(name)s-%(version)s_allow_pytorch_1.12.patch'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/RasmussenLab/vamb/archive'],
+        'checksums': [
+            {'v3.0.9.tar.gz': '3a9025ddc3e9e54e3debe65855ac2367335f920efbcb9e5ecc671a1036455d1e'},
+            {'Vamb-3.0.9_allow_pytorch_1.12.patch': '52f909a91d7d63ead3dfa1314c66efb2918a3606212a8f3d8e3a9f7ee7b33c86'},
+        ],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch

@@ -0,0 +1,15 @@
+Drop requirement of pytorch to 1.12 to allow the use of foss/2021b toolchain
+
+Åke Sandgren, 2023-03-01
+diff -ru vamb-3.0.9.orig/setup.py vamb-3.0.9/setup.py
+--- vamb-3.0.9.orig/setup.py	2022-11-24 11:02:48.000000000 +0100
++++ vamb-3.0.9/setup.py	2023-03-01 08:26:12.432734868 +0100
+@@ -22,7 +22,7 @@
+     "ext_modules": [Extension("vamb._vambtools",
+                                sources=["src/_vambtools.pyx"],
+                                language="c")],
+-    "install_requires": ["numpy>=1.20", "torch>=1.13", "pysam>=0.14"],
++    "install_requires": ["numpy>=1.20", "torch>=1.12", "pysam>=0.14"],
+     "setup_requires": ['Cython>=0.29', "setuptools>=58.0"],
+     "python_requires": ">=3.5",
+     "classifiers":[