From 0ad69ecb6ba5bdf0080a0ebeca53a6f9a2d839de Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 5 Jun 2024 10:38:33 +0200 Subject: [PATCH] #331 cleanup --- 331_CellBender/CellBender_cpu.eb | 70 ------------------ 331_CellBender/CellBender_gpu.eb | 72 ------------------- .../jupyter-contrib-nbextensions.eb | 62 ---------------- 331_CellBender/pyro-ppl_cpu.eb | 45 ------------ 331_CellBender/pyro-ppl_gpu.eb | 47 ------------ 5 files changed, 296 deletions(-) delete mode 100644 331_CellBender/CellBender_cpu.eb delete mode 100644 331_CellBender/CellBender_gpu.eb delete mode 100644 331_CellBender/jupyter-contrib-nbextensions.eb delete mode 100644 331_CellBender/pyro-ppl_cpu.eb delete mode 100644 331_CellBender/pyro-ppl_gpu.eb diff --git a/331_CellBender/CellBender_cpu.eb b/331_CellBender/CellBender_cpu.eb deleted file mode 100644 index 5fb9920f..00000000 --- a/331_CellBender/CellBender_cpu.eb +++ /dev/null @@ -1,70 +0,0 @@ -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/331_CellBender/CellBender_gpu.eb b/331_CellBender/CellBender_gpu.eb deleted file mode 100644 index 94c6fc2c..00000000 --- a/331_CellBender/CellBender_gpu.eb +++ /dev/null @@ -1,72 +0,0 @@ -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/331_CellBender/jupyter-contrib-nbextensions.eb b/331_CellBender/jupyter-contrib-nbextensions.eb deleted file mode 100644 index 1e0ea2bd..00000000 --- a/331_CellBender/jupyter-contrib-nbextensions.eb +++ /dev/null @@ -1,62 +0,0 @@ -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/331_CellBender/pyro-ppl_cpu.eb b/331_CellBender/pyro-ppl_cpu.eb deleted file mode 100644 index 28ed959d..00000000 --- a/331_CellBender/pyro-ppl_cpu.eb +++ /dev/null @@ -1,45 +0,0 @@ -# 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' diff --git a/331_CellBender/pyro-ppl_gpu.eb b/331_CellBender/pyro-ppl_gpu.eb deleted file mode 100644 index 4add431b..00000000 --- a/331_CellBender/pyro-ppl_gpu.eb +++ /dev/null @@ -1,47 +0,0 @@ -# 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'