{lib}[foss/2024a] CheckM2 v1.1.0, TensorFlow v2.18.1, Bazel v6.5.0, ...

easybuild/easyconfigs/b/Bazel/Bazel-6.5.0-GCCcore-13.3.0-Java-11.eb

@@ -0,0 +1,31 @@
+name = 'Bazel'
+version = '6.5.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://bazel.io/'
+description = """Bazel is a build tool that builds code quickly and reliably.
+It is used to build the majority of Google's software."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s']
+sources = ['%(namelower)s-%(version)s-dist.zip']
+patches = ['Bazel-6.3.1_add-symlinks-in-runfiles.patch']
+checksums = [
+    {'bazel-6.5.0-dist.zip': 'fc89da919415289f29e4ff18a5e01270ece9a6fe83cb60967218bac4a3bb3ed2'},
+    {'Bazel-6.3.1_add-symlinks-in-runfiles.patch': '81db53aa87229557480b6f719c99a0f1af9c69dfec12185451e520b0128c3ae2'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+    ('Zip', '3.0'),
+]
+
+dependencies = [('Java', '11', '', SYSTEM)]
+
+runtest = True
+pretestopts = "sed -i 's/assertEquals/assertEqual/g' examples/py_native/test.py examples/py_native/fail.py && "
+testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..."
+
+moduleclass = 'devel'

easybuild/easyconfigs/c/CheckM2/CheckM2-1.1.0-foss-2024a.eb

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+easyblock = 'PythonPackage'
+
+name = 'CheckM2'
+version = '1.1.0'
+
+homepage = 'https://github.com/chklovski/CheckM2/'
+description = "Assessing the quality of metagenome-derived genome bins using machine learning"
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+source_urls = ['https://github.com/chklovski/CheckM2/archive/']
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['7978e4ca08ae8ea3285931b955d1a4818684f9f955995837e98e6ab7ff90674f']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('scikit-build-core', '0.10.6'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('SciPy-bundle', '2024.05'),
+    ('DIAMOND', '2.1.11'),
+    ('TensorFlow', '2.18.1'),
+    ('prodigal', '2.6.3'),
+    ('tqdm', '4.66.5'),
+    ('scikit-learn', '1.6.1'),
+    ('LightGBM', '4.6.0'),
+]
+
+# Fix undefined variable from https://github.com/chklovski/CheckM2/commit/6144f70
+postinstallcmds = [
+    "cd %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2 && "
+    "sed -i 's/format(f)/format(bin)/' main.py",
+]
+
+modloadmsg = """
+You need to download a Diamond database and setup a path to this db now:
+
+1) Download the database (/CheckM2_database/uniref100.KO.1.dmnd will be created):
+$ checkm2 database --download --path /path/to/database --no_write_json_db
+- for example: $ checkm2 database --download --path $HOME/DB_CHECKM2 --no_write_json_db
+
+2) Setup $CHECKM2DB:
+$ export CHECKM2DB="/path/to/database/CheckM2_database/uniref100.KO.1.dmnd"
+- for example: $ export CHECKM2DB="$HOME/DB_CHECKM2/CheckM2_database/uniref100.KO.1.dmnd"
+Unset it by: $ unset CHECKM2DB
+
+You can check the path to the database:
+$ checkm2 database --current
+
+You can test if everything is setup properly:
+$ checkm2 testrun
+"""
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/LightGBM/LightGBM-4.6.0-foss-2024a.eb

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+easyblock = 'PythonBundle'
+
+name = "LightGBM"
+version = "4.6.0"
+
+homepage = "https://lightgbm.readthedocs.io"
+description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM
+or MART) framework based on decision tree algorithms, used for ranking,
+classification and many other machine learning tasks."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('scikit-build-core', '0.10.6'),
+    ('wget', '1.25.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('Arrow', '17.0.0'),  # optional
+    ('dask', '2024.9.1'),  # optional
+    ('scikit-learn', '1.6.1'),  # optional
+]
+
+# example files are not distributed with the sources
+_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples"
+_test_cmds_pre = " && ".join([
+    "mkdir regression",
+    "wget -P regression %s/regression/regression.test" % _test_repo_url,
+    "wget -P regression %s/regression/regression.train" % _test_repo_url,
+    "mkdir test",
+    "cd test",
+    "wget %s/python-guide/simple_example.py" % _test_repo_url,
+    "",
+])
+
+exts_list = [
+    ('lightgbm', version, {
+        'checksums': ['cb1c59720eb569389c0ba74d14f52351b573af489f230032a1c9f314f8bab7fe'],
+        'installopts': "--config-settings=cmake.define.USE_MPI=ON",
+        'use_pip_extras': "arrow,dask,pandas,scikit-learn",
+        'pretestopts': _test_cmds_pre,
+        'runtest': 'python',
+        'testopts': "simple_example.py",
+        'testinstall': True,
+    }),
+]
+
+moduleclass = 'ai'

easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.6.1-gfbf-2024a.eb

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+easyblock = 'PythonBundle'
+
+name = 'scikit-learn'
+version = '1.6.1'
+
+homepage = 'https://scikit-learn.org/stable/index.html'
+description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world,
+building upon numpy, scipy, and matplotlib. As a machine-learning module,
+it provides versatile tools for data mining and analysis in any field of science and engineering.
+It strives to be simple and efficient, accessible to everybody, and reusable in various contexts."""
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+
+builddependencies = [
+    ('meson-python', '0.16.0'),
+    ('Cython', '3.0.10'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('SciPy-bundle', '2024.05'),
+]
+
+exts_list = [
+    (name, version, {
+        'modulename': 'sklearn',
+        'sources': ['scikit_learn-%(version)s.tar.gz'],
+        'checksums': ['b4fc2525eca2c69a59260f583c56a7557c6ccdf8deafdba6e060f94c1c59738e'],
+    }),
+    ('sklearn', '0.0', {
+        'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'],
+    }),
+]
+
+moduleclass = 'data'