progress on #472 Geneformer

472_Geneformer/Geneformer-0.1.0-20241204-foss-2023a.eb

@@ -0,0 +1,76 @@
+easyblock = 'PythonBundle'
+
+name = 'Geneformer'
+version = '0.1.0-20241204'
+local_commit = '09de197'
+
+homepage = 'https://huggingface.co/ctheodoris/Geneformer'
+description = """Geneformer is a foundational transformer model pretrained on a large-scale
+corpus of single cell transcriptomes to enable context-aware predictions in settings
+with limited data in network biology."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('anndata', '0.10.5.post1'),
+    ('HF-Datasets', '2.18.0'),
+    ('loompy', '3.0.7'),
+    ('matplotlib', '3.7.2'),
+    ('Optuna', '3.5.0'),
+    ('Arrow', '14.0.1'),
+    ('Ray-project', '2.9.1'),
+    ('scanpy', '1.9.8'),
+    ('scikit-learn', '1.3.1'),
+    ('Seaborn', '0.13.2'),
+    ('statsmodels', '0.14.1'),
+    ('tensorboard', '2.15.1'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+    ('Transformers', '4.39.3'),
+    ('accelerate', '0.33.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('optuna_integration', '4.1.0', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d6ce0ffb650f7783e6cc4a4fd2f684fb1252db441414669b14c01f65b1556a2c'],
+    }),
+    ('peft', '0.13.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['d4e0951ec78eac11c45a051801c569913436888c578d48e5ce86996b715bc6ef'],
+    }),
+    ('accumulation_tree', '0.6.4', {
+        'checksums': ['5f907667e4106b5ba140b6b871e1902eb2a93d429b92f8a9f7ddb2bee7704334'],
+    }),
+    ('pyudorandom', '1.0.0', {
+        'checksums': ['f30a093a0170c15f9c7f87eb29f71f0f5fde995528b7c6dc4606d389e8c37755'],
+    }),
+    ('tdigest', '0.5.2.2', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['dd25f8d6e6be002192bba9e4b8c16491d36c10b389f50637818603d1f67c6fb2'],
+    }),
+    (name, version, {
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://huggingface.co/ctheodoris',
+                'repo_name': name,
+                'commit': local_commit,
+            },
+        }],
+        'checksums': [None],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+
+moduleclass = 'bio'

472_Geneformer/accelerate-0.33.0-foss-2023a.eb

@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'accelerate'
+version = '0.33.0'
+
+homepage = 'https://github.com/huggingface/accelerate'
+description = """A simple way to launch, train, and use PyTorch models on almost any device and 
+distributed configuration, automatic mixed precision (including fp8), 
+and easy-to-configure FSDP and DeepSpeed support."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch-bundle', '2.1.2'),
+    ('PyYAML', '6.0'),
+    ('Safetensors', '0.4.3'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('huggingface-hub', '0.24.5', {
+        'sources': ['huggingface_hub-%(version)s.tar.gz'],
+        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
+    }),
+    (name, version, {
+        'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'],
+    }),
+]
+
+sanity_check_commands = ['accelerate test']
+
+moduleclass = 'ai'