{bio,data,geo}[foss/2023a] Squidpy v1.4.1, PyGEOS v0.14, zarr v2.17.1

easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2023a.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'PyGEOS'
+version = '0.14'
+
+homepage = "https://pygeos.readthedocs.io"
+description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in
+ the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance
+ improvement when operating on arrays of geometries."""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['30fbc17f64844200b85133b885fcfb65541b8779531f6ef4f8fe467d3fba7623']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('GEOS', '3.12.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+moduleclass = 'geo'

easybuild/easyconfigs/s/Squidpy/Squidpy-1.4.1-foss-2023a.eb

@@ -0,0 +1,134 @@
+easyblock = 'PythonBundle'
+
+name = 'Squidpy'
+version = '1.4.1'
+
+homepage = 'https://squidpy.readthedocs.io'
+description = "Squidpy is a tool for the analysis and visualization of spatial molecular data."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.7.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('aiohttp', '3.8.5'),
+    ('anndata', '0.10.5.post1'),
+    ('dask', '2023.9.2'),
+    ('leidenalg', '0.10.2'),
+    ('matplotlib', '3.7.2'),
+    ('networkx', '3.1'),
+    ('numba', '0.58.1'),
+    ('Pillow', '10.0.0'),
+    ('scanpy', '1.9.8'),
+    ('scikit-image', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('statsmodels', '0.14.1'),
+    ('tqdm', '4.66.1'),
+    ('xarray', '2023.9.0'),
+    ('zarr', '2.17.1'),
+    ('geopandas', '0.14.2'),
+    ('Arrow', '14.0.1'),
+    ('PyGEOS', '0.14'),
+    ('Shapely', '2.0.1'),
+    ('wrapt', '1.15.0'),  # omnipath dep
+    ('pydantic', '2.5.3'),  # inflect dep
+]
+
+use_pip = True
+
+exts_list = [
+    ('pytest_socket', '0.7.0', {
+        'checksums': ['71ab048cbbcb085c15a4423b73b619a8b35d6a307f46f78ea46be51b1b7e11b3'],
+    }),
+    ('xarray_dataclasses', '1.7.0', {
+        'checksums': ['b82b454c5800bf9d488c188d6362428e6bc310d2fc35f96fa4063efa40d33267'],
+    }),
+    ('xarray-datatree', '0.0.13', {
+        'modulename': 'datatree',
+        'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'],
+    }),
+    ('multipledispatch', '1.0.0', {
+        'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'],
+    }),
+    ('colorcet', '3.1.0', {
+        'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'],
+    }),
+    ('pyct', '0.5.0', {
+        'checksums': ['dd9f4ac5cbd8e37c352c04036062d3c5f67efec76d404761ef16b0cbf26aa6a0'],
+    }),
+    ('param', '2.0.2', {
+        'checksums': ['785845a727a588eb94c7666d80551c7e2bb97d4309d3507beab66f95e57f7527'],
+    }),
+    ('slicerator', '1.1.0', {
+        'checksums': ['44010a7f5cd87680c07213b5cabe81d1fb71252962943e5373ee7d14605d6046'],
+    }),
+    ('datashader', '0.16.0', {
+        'checksums': ['ed4c111957578dcb3fcff972d954f77586dafd71a7345fd5cd069d9fb050d0d1'],
+    }),
+    ('typing_extensions', '4.8.0', {
+        'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'],
+    }),
+    ('inflect', '7.0.0', {
+        'checksums': ['63da9325ad29da81ec23e055b41225795ab793b4ecb483be5dc1fa363fd4717e'],
+    }),
+    ('PIMS', '0.6.1', {
+        'checksums': ['e2b704461d4ea9bce8b6a22ca35836fe67d6d34537736b405341ae5547194f3b'],
+    }),
+    ('xarray-spatial', '0.3.7', {
+        'modulename': 'xrspatial',
+        'preinstallopts': "sed -i 's/numpy <= 1.23.4/numpy/g' setup.cfg &&",
+        'checksums': ['21bef5f0f5a3cfe18d7a33f40d7c9eee459ed33f7e5674cfe1d156de56d47b2f'],
+    }),
+    ('xarray-schema', '0.0.3', {
+        'checksums': ['9c6c760489c0690a70394b2ad1368b32f8fa1333911c361b4adf249384212920'],
+    }),
+    ('spatial_image', '0.3.0', {
+        'checksums': ['508ed434d1cdba5147c1dd358aea0ea41a0f913b02a73e0fd36fcbdbee14b40d'],
+    }),
+    ('ome-zarr', '0.8.3', {
+        'checksums': ['e98762e6a3cc82e8f6ef50c938e23fc579498d94d1991f3476ccf9726209997b'],
+    }),
+    ('multiscale_spatial_image', '0.11.2', {
+        'checksums': ['07db47c3358bdfad9688a5ee8064a219ec72a43deb65e30bd4e591adfe35d10f'],
+    }),
+    ('spatialdata', '0.0.15', {
+        'checksums': ['7372b13b9fa84c0eadcbfca2f2cd354a9ae8dd370401745d55d572864eb4dc75'],
+    }),
+    ('validators', '0.22.0', {
+        'checksums': ['77b2689b172eeeb600d9605ab86194641670cdb73b60afd577142a9397873370'],
+    }),
+    ('tifffile', '2024.2.12', {
+        'checksums': ['4920a3ec8e8e003e673d3c6531863c99eedd570d1b8b7e141c072ed78ff8030d'],
+    }),
+    ('omnipath', '1.0.8', {
+        'checksums': ['3821b9ba11957412ff9e4932eb6d0c17242939661468064ad1ce28ee3e27394f'],
+    }),
+    ('matplotlib-scalebar', '0.8.1', {
+        'checksums': ['14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d'],
+    }),
+    ('fsspec', '2023.6.0', {
+        'checksums': ['d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af'],
+    }),
+    ('docrep', '0.3.2', {
+        'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'],
+    }),
+    ('dask-image', '2023.8.1', {
+        'checksums': ['5e9a8985b0527a1b5942c6a7e744e0e57d264e222c7058f05baeb81c374d04b6'],
+    }),
+    ('cycler', '0.12.1', {
+        'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'],
+    }),
+    ('squidpy', version, {
+        'preinstallopts': "sed -i 's/pandas>=2.1.0/pandas/g' pyproject.toml &&",
+        'checksums': ['485e48163b235af5b3d1cc06e3971ae848d0787c2958b5795200755a86dadf4f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/z/zarr/zarr-2.17.1-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = "PythonBundle"
+
+name = 'zarr'
+version = '2.17.1'
+
+homepage = 'https://zarr.readthedocs.io/en/stable/'
+description = """Zarr is a Python package providing an implementation of compressed, 
+chunked, N-dimensional arrays, designed for use in parallel computing."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('py-cpuinfo', '9.0.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('numcodecs', '0.12.1', {
+        'checksums': ['05d91a433733e7eef268d7e80ec226a0232da244289614a8f3826901aec1098e'],
+    }),
+    ('fasteners', '0.19', {
+        'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'],
+    }),
+    ('asciitree', '0.3.3', {
+        'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'],
+    }),
+    (name, version, {
+        'checksums': ['564b3aa072122546fe69a0fa21736f466b20fad41754334b62619f088ce46261'],
+    }),
+]
+
+moduleclass = 'data'