Merge pull request #20551 from pavelToman/20240517134249_new_pr_CellB…

…ender030 {tools}[foss/2023a] CellBender v0.3.0, jupyter-contrib-nbextensions v0.7.0, pyro-ppl v1.9.0
easybuilders · Jun 4, 2024 · 62af27c · 62af27c
2 parents b962b77 + c5b7f04
commit 62af27c
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diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,72 @@
+easyblock = 'PythonBundle'
+
+name = 'CellBender'
+version = '0.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://github.com/broadinstitute/CellBender'
+description = """
+CellBender is a software package for eliminating technical artifacts from
+high-throughput single-cell RNA sequencing (scRNA-seq) data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('IPython', '8.14.0'),
+    ('anndata', '0.10.5.post1'),
+    ('jupyter-contrib-nbextensions', '0.7.0'),
+    ('pyro-ppl', '1.9.0', versionsuffix),
+    ('loompy', '3.0.7'),
+    ('PyTables', '3.8.0'),
+    ('Qtconsole', '5.5.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
+    ('traitlets', '5.14.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'],
+    }),
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('notebook', '6.5.7', {
+        'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'],
+    }),
+    ('mistune', '0.8.4', {
+        'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
+    }),
+    ('nbconvert', '6.5.4', {
+        'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'],
+    }),
+    ('cellbender', version, {
+        'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cellbender'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cellbender --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.0-foss-2023a.eb
@@ -0,0 +1,70 @@
+easyblock = 'PythonBundle'
+
+name = 'CellBender'
+version = '0.3.0'
+
+homepage = 'http://github.com/broadinstitute/CellBender'
+description = """
+CellBender is a software package for eliminating technical artifacts from
+high-throughput single-cell RNA sequencing (scRNA-seq) data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('PyTorch', '2.1.2'),
+    ('IPython', '8.14.0'),
+    ('anndata', '0.10.5.post1'),
+    ('jupyter-contrib-nbextensions', '0.7.0'),
+    ('pyro-ppl', '1.9.0'),
+    ('loompy', '3.0.7'),
+    ('PyTables', '3.8.0'),
+    ('Qtconsole', '5.5.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
+    ('traitlets', '5.14.1', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'],
+    }),
+    ('jupyter_console', '6.6.3', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('notebook', '6.5.7', {
+        'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'],
+    }),
+    ('mistune', '0.8.4', {
+        'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
+    }),
+    ('nbconvert', '6.5.4', {
+        'checksums': ['9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1'],
+    }),
+    ('cellbender', version, {
+        'checksums': ['94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/cellbender'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cellbender --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/...nfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb b/...nfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-12.3.0.eb
@@ -0,0 +1,62 @@
+easyblock = "PythonBundle"
+
+name = 'jupyter-contrib-nbextensions'
+version = '0.7.0'
+
+homepage = 'https://github.com/ipython-contrib/jupyter_contrib_nbextensions'
+description = 'A collection of various notebook extensions for Jupyter'
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('nodejs', '18.17.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('IPython', '8.14.0'),
+    ('PyYAML', '6.0'),
+    ('jupyter-server', '2.7.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('entrypoints', '0.4', {
+        'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'],
+    }),
+    ('nbclassic', '1.0.0', {
+        'checksums': ['0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'],
+    }),
+    # need jupyter_client in v7 - notebook 6.5.7 has requirement jupyter-client<8,>=5.3.4
+    ('jupyter_client', '7.4.9', {
+        'checksums': ['52be28e04171f07aed8f20e1616a5a552ab9fee9cbbe6c1896ae170c3880d392'],
+    }),
+    # use notebook v6, in v7 the extension are moved to jupyter lab
+    ('notebook', '6.5.7', {
+        'checksums': ['04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4'],
+    }),
+    ('jupyter_contrib_core', '0.4.2', {
+        'checksums': ['1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb'],
+    }),
+    ('jupyter_highlight_selected_word', '0.2.0', {
+        'checksums': ['9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b'],
+    }),
+    ('jupyter_nbextensions_configurator', '0.6.3', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['cece496f3f62cf80bb0b04867ea463c32ed5db19ff5814fe18a3a7f1bb9da95b'],
+    }),
+    ('jupyter_contrib_nbextensions', version, {
+        'checksums': ['06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/jupyter-contrib', 'bin/jupyter-contrib-nbextension', 'bin/jupyter-nbextensions_configurator'],
+    'dirs': ['lib64/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,47 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'pyro-ppl'
+version = '1.9.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/pyro-ppl/pyro'
+description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2', versionsuffix),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('opt-einsum', '3.3.0', {
+        'source_tmpl': 'opt_einsum-%(version)s.tar.gz',
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    ('pyro-api', '0.1.2', {
+        'modulename': 'pyroapi',
+        'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'],
+    }),
+    (name, version, {
+        'modulename': 'pyro',
+        'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = [
+    "python -c 'from pyroapi import distributions as dist'",
+    "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'",
+    "python -c 'from pyro import infer, nn, distributions'",
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.9.0-foss-2023a.eb
@@ -0,0 +1,45 @@
+# Author: Denis Krišťák (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'pyro-ppl'
+version = '1.9.0'
+
+homepage = 'https://github.com/pyro-ppl/pyro'
+description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('PyTorch', '2.1.2'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('opt-einsum', '3.3.0', {
+        'source_tmpl': 'opt_einsum-%(version)s.tar.gz',
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    ('pyro-api', '0.1.2', {
+        'modulename': 'pyroapi',
+        'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'],
+    }),
+    (name, version, {
+        'modulename': 'pyro',
+        'checksums': ['41f4c005159568280fbc511648960a98a2b1a410027d8bd0a43220ac9b102cdf'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = [
+    "python -c 'from pyroapi import distributions as dist'",
+    "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'",
+    "python -c 'from pyro import infer, nn, distributions'",
+]
+
+moduleclass = 'tools'