progress on #506 fastStructure

506_fastStructure/Cython-0.29.37-GCCcore-12.3.0-Python-2.7.18.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonPackage'
+
+name = 'Cython'
+version = '0.29.37'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://cython.org/'
+description = """
+Cython is an optimising static compiler for both the Python programming
+language and the extended Cython programming language (based on Pyrex).
+"""
+docurls = [
+    'https://cython.org/#documentation',
+    'https://github.com/cython/cython',
+]
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+sources = [SOURCE_WHL]
+checksums = ['95f1d6a83ef2729e67b3fa7318c829ce5b07ac64c084cd6af11c228e0364662c']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["cython --version"]
+
+moduleclass = 'lang'

506_fastStructure/SciPy-bundle-2024.06-foss-2023a-Python-2.7.18.eb

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+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2024.06'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [
+    ('hypothesis', '4.57.1', versionsuffix),
+    ('UnZip', '6.0'),
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('pybind11', '2.9.2', versionsuffix),  # required by scipy
+    ('numpy', '1.16.6', versionsuffix)
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.5', {
+        'checksums': ['5f4ae749ba7199034b6912af98f05b4058d6d48fc2f065037b241be819a22924'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('scipy', '1.2.3', {
+        'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'],
+        'prebuildopts': 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ',
+        'checksums': [
+            'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57',  # scipy-1.2.3.tar.gz
+            # scipy-1.2.3_fix_nan_problem_in_vi.patch
+            '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d',
+        ],
+    }),
+    ('mpi4py', '3.1.6', {
+        'checksums': ['c8fa625e0f92b082ef955bfb52f19fa6691d29273d7d71135d295aa143dee6cb'],
+    }),
+    ('numexpr', '2.7.3', {
+        'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'],
+    }),
+    ('Bottleneck', '1.3.2', {
+        'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
+    }),
+    ('python_dateutil', '2.9.0.post0', {
+        'modulename': 'dateutil',
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427'],
+    }),
+    ('pytz', '2025.1', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57'],
+    }),
+    ('pandas', '0.24.2', {
+        'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.3.1', {
+        'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

506_fastStructure/fastStructure-1.0-foss-2023a-Python-2.7.18.eb

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+easyblock = 'PythonBundle'
+
+name = 'fastStructure_new'
+version = '1.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://rajanil.github.io/fastStructure/'
+description = """
+fastStructure is a fast algorithm for inferring population structure
+from large SNP genotype data. It is based on a variational Bayesian
+framework for posterior inference and is written in Python2.x.
+"""
+docurls = ['https://github.com/rajanil/fastStructure']
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('Cython', '0.29.37', versionsuffix),
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('SciPy-bundle', '2024.06', versionsuffix),
+    ('matplotlib', '2.2.5', versionsuffix),
+    ('GSL', '2.7'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    # Needs Cython v0.27.3 see:
+    # https://github.com/rajanil/fastStructure/issues/39
+    ('Cython', '0.27.3', {
+        'checksums': ['6a00512de1f2e3ce66ba35c5420babaef1fe2d9c43a8faab4080b0dbcc26bc64'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/rajanil/fastStructure/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        # 'preinstallopts': 'cd vars && python -m pip install --prefix %(installdir)s --no-build-isolation . && cd - && ',
+        'preinstallopts': 'cd vars && python setup.py build_ext --inplace && cd - && ',
+        'install_cmd': 'python setup.py build_ext --inplace',
+        'checksums': ['f1bfb24bb5ecd108bc3a90145fad232012165c1e60608003f1c87d200f867b81'],
+    }),
+]
+
+fix_python_shebang_for = ['*.py']
+
+sanity_check_paths = {
+    'files': [
+        'fastStructure.%s' % SHLIB_EXT,
+        'parse_bed.%s' % SHLIB_EXT,
+        'parse_str.%s' % SHLIB_EXT,
+        'structure.py',
+    ],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    ('%(installdir)s/structure.py '
+     '-K 3 '
+     '--input=%(installdir)s/test/testdata '
+     '--output=%(builddir)s/testoutput_simple '
+     '--full '
+     '--seed=100'),
+]
+
+moduleclass = 'bio'
+
+# TODO https://github.com/easybuilders/easybuild-easyblocks/blob/develop/easybuild/easyblocks/f/faststructure.py
+# ERROR: More than one .egg-info directory found in /tmp/vsc45304/eb-b7wy4wzt/pip-pip-egg-info-r5KDqI

506_fastStructure/matplotlib-2.2.5-foss-2023a-Python-2.7.18.eb

@@ -0,0 +1,70 @@
+easyblock = 'PythonBundle'
+
+name = 'matplotlib'
+version = '2.2.5'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://matplotlib.org'
+description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
+ hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
+ and ipython shell, web application servers, and six graphical user interface toolkits."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('numpy', '1.16.6', versionsuffix),
+    ('libpng', '1.6.39'),
+    ('freetype', '2.13.0'),
+    ('Tkinter', '%(pyver)s', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('Cycler', '0.10.0', {
+        'modulename': 'cycler',
+        'source_tmpl': 'cycler-%(version)s.tar.gz',
+        'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'],
+    }),
+    ('kiwisolver', '1.1.0', {
+        'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'],
+    }),
+    ('python_dateutil', '2.9.0.post0', {
+        'modulename': 'dateutil',
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427'],
+    }),
+    ('pytz', '2025.1', {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['89dd22dca55b46eac6eda23b2d72721bf1bdfef212645d81513ef5d03038de57'],
+    }),
+    ('subprocess32', '3.5.4', {
+        'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'],
+    }),
+    (name, version, {
+        'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'],
+    }),
+]
+
+postinstallcmds = [
+    'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py',
+]
+
+sanity_check_commands = [
+    """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """,
+    "python -c 'from mpl_toolkits.mplot3d import Axes3D'",
+]
+
+# use non-interactive plotting backend as default
+# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend
+modextravars = {'MPLBACKEND': 'Agg'}
+
+moduleclass = 'vis'