#458 to update deps ecs

458_bin2cell/bin2cell.eb

@@ -0,0 +1,38 @@
+# should be compatible with Single-cell-python-bundle/2024.02-foss-2023a
+easyblock = 'PythonBundle'
+
+name = 'bin2cell'
+version = '0.3.2'
+
+homepage = 'https://github.com/Teichlab/bin2cell'
+description = """Bin2cell proposes 2um bin to cell groupings based on segmentation,
+which can be done on the morphology image and/or a visualisation of the gene expression."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+# DEPS:
+    # ok build_backend: flit_core >=3.2,<4
+    # OK "numpy < 2",
+    # OK "scanpy",
+    # UPDATE - "stardist",
+    # OK? "opencv-python",
+    # UPDATE - "fastparquet"
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scanpy', '1.9.8'),
+    ('OpenCV', '4.8.1', '-contrib'),
+]
+
+exts_list = [
+    ('flit_core', '3.9.0', {
+        'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'],
+    }),
+    (name, version),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'bio'

458_bin2cell/fastparquet.eb

@@ -0,0 +1,103 @@
+easyblock = 'CargoPythonBundle'
+
+name = 'fastparquet'
+version = '2023.4.0'
+
+homepage = "https://fastparquet.readthedocs.io/"
+description = """fastparquet is a python implementation of the parquet format, aiming to integrate
+into python-based big data work-flows. It is used implicitly by the projects
+Dask, Pandas and intake-parquet."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+builddependencies = [
+    ('patchelf', '0.17.2'),
+    ('maturin', '1.1.0'),  # for cramjam
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+crates = [
+    ('adler', '1.0.2'),
+    ('ahash', '0.7.6'),
+    ('alloc-no-stdlib', '2.0.4'),
+    ('alloc-stdlib', '0.2.2'),
+    ('autocfg', '1.1.0'),
+    ('bitflags', '1.3.2'),
+    ('brotli', '3.3.4'),
+    ('brotli-decompressor', '2.3.2'),
+    ('bzip2', '0.4.3'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cc', '1.0.73'),
+    ('cfg-if', '1.0.0'),
+    ('crc32fast', '1.3.2'),
+    ('flate2', '1.0.23'),
+    ('getrandom', '0.2.8'),
+    ('indoc', '1.0.6'),
+    ('jobserver', '0.1.24'),
+    ('libc', '0.2.126'),
+    ('libmimalloc-sys', '0.1.25'),
+    ('lock_api', '0.4.7'),
+    ('lz4', '1.23.3'),
+    ('lz4-sys', '1.9.4'),
+    ('matrixmultiply', '0.3.2'),
+    ('memoffset', '0.6.5'),
+    ('mimalloc', '0.1.29'),
+    ('miniz_oxide', '0.5.1'),
+    ('ndarray', '0.15.4'),
+    ('num-complex', '0.4.1'),
+    ('num-integer', '0.1.45'),
+    ('num-traits', '0.2.15'),
+    ('numpy', '0.17.2'),
+    ('once_cell', '1.10.0'),
+    ('parking_lot', '0.12.0'),
+    ('parking_lot_core', '0.9.3'),
+    ('pkg-config', '0.3.25'),
+    ('proc-macro2', '1.0.39'),
+    ('pyo3', '0.17.3'),
+    ('pyo3-build-config', '0.17.3'),
+    ('pyo3-ffi', '0.17.3'),
+    ('pyo3-macros', '0.17.3'),
+    ('pyo3-macros-backend', '0.17.3'),
+    ('quote', '1.0.18'),
+    ('rawpointer', '0.2.1'),
+    ('redox_syscall', '0.2.13'),
+    ('scopeguard', '1.1.0'),
+    ('smallvec', '1.8.0'),
+    ('snap', '1.0.5'),
+    ('syn', '1.0.95'),
+    ('target-lexicon', '0.12.3'),
+    ('unicode-ident', '1.0.0'),
+    ('unindent', '0.1.9'),
+    ('version_check', '0.9.4'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('windows-sys', '0.36.1'),
+    ('windows_aarch64_msvc', '0.36.1'),
+    ('windows_i686_gnu', '0.36.1'),
+    ('windows_i686_msvc', '0.36.1'),
+    ('windows_x86_64_gnu', '0.36.1'),
+    ('windows_x86_64_msvc', '0.36.1'),
+    ('zstd', '0.11.2+zstd.1.5.2'),
+    ('zstd-safe', '5.0.2+zstd.1.5.2'),
+    ('zstd-sys', '2.0.1+zstd.1.5.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('thrift', '0.16.0', {
+        'checksums': ['2b5b6488fcded21f9d312aa23c9ff6a0195d0f6ae26ddbd5ad9e3e25dfc14408'],
+    }),
+    ('cramjam', '2.6.2', {
+        'checksums': ['1ffdc8d1381b5fee57b33b537e38fa7fd29e8d8f3b544dbab1d71dbfaaec3bef'],
+    }),
+    (name, version, {
+        'checksums': ['917e6d288ea07e10b28b5fa4b4c0b70f60b14971ece3ba5bf30690320a53aa70'],
+    }),
+]
+
+moduleclass = 'tools'

458_bin2cell/stardist.eb

@@ -0,0 +1,50 @@
+easyblock = 'PythonBundle'
+
+name = 'stardist'
+version = '0.8.3'
+
+homepage = 'https://github.com/stardist/stardist'
+description = "Object Detection with Star-convex Shapes."
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('TensorFlow', '2.7.1'),
+    ('numba', '0.54.1'),
+    ('imageio', '2.13.5'),
+    ('scikit-image', '0.19.1'),
+    ('tqdm', '4.62.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('tifffile', '2022.10.10', {
+        'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'],
+    }),
+    ('csbdeep', '0.7.2', {
+        'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'],
+    }),
+    ('edt', '2.3.0', {
+        'checksums': ['220e2086fdf32bbd8964df76b3e1a42061ece1f4b9ea95ec83a094d24d258664'],
+    }),
+    (name, version, {
+        'checksums': ['8ac1f6165ca8e8496651c6e2b49ce57d6d574dfb22bf6f63ddaec1f64b8868d1'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "stardist-predict2d --help",
+    "stardist-predict3d --help",
+]
+
+moduleclass = 'vis'