Merge pull request #21026 from lexming/20240720122935_new_pr_Biotite0410

{lib}[foss/2023a] Biotite v0.41.0, ESM3 v3.0.0.post2 w/ CUDA 12.1.1

easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb

@@ -0,0 +1,32 @@
+easyblock = 'PythonBundle'
+
+name = 'Biotite'
+version = '0.41.0'
+
+homepage = 'https://www.biotite-python.org/'
+description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to
+identify homologous sequence regions in a protein family or you would like to
+find disulfide bonds in a protein structure: Biotite has the right tool for
+you. This package bundles popular tasks in computational molecular biology into
+a uniform Python library."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('networkx', '3.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biotite', version, {
+        'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,53 @@
+easyblock = 'PythonBundle'
+
+name = 'ESM3'
+version = '3.0.0.post2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.evolutionaryscale.ai/'
+description = """ESM3 is a frontier generative model for biology, able to jointly reason across
+three fundamental biological properties of proteins: sequence, structure, and
+function. These three data modalities are represented as tracks of discrete
+tokens at the input and output of ESM3. You can present the model with a
+combination of partial inputs across the tracks, and ESM3 will provide output
+predictions for all the tracks.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('Transformers', '4.39.3'),
+    ('Biopython', '1.83'),
+    ('Biotite', '0.41.0'),
+    ('Brotli-python', '1.0.9'),
+    ('einops', '0.7.0'),
+    ('IPython', '8.14.0'),
+    ('scikit-learn', '1.3.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('msgpack-numpy', '0.4.8', {
+        'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
+    }),
+    ('cloudpathlib', '0.16.0', {
+        'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
+    }),
+    ('esm', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = [
+    "python -c 'import esm'",
+    "python -c 'from esm.models.esm3 import ESM3'",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb

@@ -0,0 +1,51 @@
+easyblock = 'PythonBundle'
+
+name = 'ESM3'
+version = '3.0.0.post2'
+
+homepage = 'https://www.evolutionaryscale.ai/'
+description = """ESM3 is a frontier generative model for biology, able to jointly reason across
+three fundamental biological properties of proteins: sequence, structure, and
+function. These three data modalities are represented as tracks of discrete
+tokens at the input and output of ESM3. You can present the model with a
+combination of partial inputs across the tracks, and ESM3 will provide output
+predictions for all the tracks.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('PyTorch-bundle', '2.1.2'),
+    ('Transformers', '4.39.3'),
+    ('Biopython', '1.83'),
+    ('Biotite', '0.41.0'),
+    ('Brotli-python', '1.0.9'),
+    ('einops', '0.7.0'),
+    ('IPython', '8.14.0'),
+    ('scikit-learn', '1.3.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('msgpack-numpy', '0.4.8', {
+        'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
+    }),
+    ('cloudpathlib', '0.16.0', {
+        'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
+    }),
+    ('esm', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = [
+    "python -c 'import esm'",
+    "python -c 'from esm.models.esm3 import ESM3'",
+]
+
+moduleclass = 'bio'