#314 progress #305 update sklearn version

305_compass/compass-foss-2021b.eb

@@ -14,7 +14,7 @@ dependencies = [
     ('SciPy-bundle', '2021.10'),
     ('tqdm', '4.62.3'),
     ('python-libsbml', '5.20.2'),
-    ('scikit-learn', '1.0.2'),
+    ('scikit-learn', '1.0.1'),
     ('python-igraph', '0.9.8'),
     ('leidenalg', '0.8.8'),
     ('anndata', '0.9.2'),

314_napari_microsam/elf.eb

@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'python-elf'
-version = '0.5.0'
+version = '0.5.1'
 
 homepage = 'https://github.com/constantinpape/elf'
 description = "Utils and convenience functions for large-scale bio-image analysis."

314_napari_microsam/nifty.eb

@@ -0,0 +1,69 @@
+easyblock = 'CMakePythonPackage'
+
+name = 'nifty'
+version = '1.2.1'
+
+homepage = 'https://github.com/DerThorsten/nifty/'
+description = """A nifty library for 2D and 3D image segmentation, graph based segmentation an opt. 
+This library provided building blocks for segmentation algorithms and complex segmentation pipelines.."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/DerThorsten/nifty/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a5fd611463336ba18be828da3154da8828b6486603e2a04f14a4520cb357661a']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+# - boost-cpp>=1.63 OK Boost
+# - h5py OK
+# - nlohmann_json OK
+# - scikit-image OK
+# - xtensor>=0.21,<0.22 OK?
+# - xtensor-python>=0.24,<0.25 OK?
+# - vigra OK
+# - z5py -> NO -> zarr?
+# numpy
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Boost', '1.82.0'),
+    ('h5py', '3.9.0'),
+    ('nlohmann_json', '3.11.2'),
+    ('scikit-image', '0.22.0'),
+    ('vigra', '1.11.2'),
+    ('zarr', '2.17.1'),
+    ('xtensor', '0.21.10'),
+#     ('SciPy-bundle', '2023.07'),
+#     ('Boost.Python', '1.83.0'),
+#     ('libjpeg-turbo', '2.1.5.1'),
+#     ('OpenJPEG', '2.5.0'),
+#     ('LibTIFF', '4.5.0'),
+#     ('libpng', '1.6.39'),
+#     ('OpenEXR', '3.1.7'),
+#     ('HDF5', '1.14.0'),
+#     ('FFTW', '3.3.10'),
+#     ('nose3', '1.3.8'),
+]
+
+preconfigopts = "pwd && cd %(builddir)s && pwd && "
+preconfigopts += "sed -i '62 a\message(\"${_NUMPY_VALUES}\")' nifty-1.2.1/cmake/modules/FindNUMPY.cmake && "
+preconfigopts += "cd /tmp/vsc47063/easybuild/build/nifty/1.2.1/foss-2023a/easybuild_obj &&"
+# # Fix python files path in make install step
+# path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENCIES.cmake"
+# add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)"
+# preinstallopts = "sed -i '90,91d' %s && " % path
+# preinstallopts += "sed -i '94d' %s && " % path
+# preinstallopts += "sed -i '89 a\%s' %s && " % (add, path)
+
+# sanity_check_paths = {
+#     'files': ['bin/vigra-config'],
+#     'dirs': ['lib/python%(pyshortver)s/site-packages/vigra'],
+# }
+
+# sanity_check_commands = ["vigra-config --version", "python -c 'import vigra'"]
+
+moduleclass = 'vis'

314_napari_microsam/xtensor.eb

@@ -0,0 +1,49 @@
+easyblock = 'Bundle'
+
+name = 'xtensor'
+version = '0.21.10'
+
+homepage = 'https://github.com/xtensor-stack/xtensor'
+description = "xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+default_easyblock = 'CMakeMake'
+
+default_component_specs = {
+    'source_urls': ['https://github.com/xtensor-stack/%(name)s/archive/'],
+    'sources': ['%(version)s.tar.gz'],
+    'start_dir': '%(name)s-%(version)s',
+}
+
+components = [
+    ('xtl', '0.7.4', {
+        'checksums': ['3c88be0e696b64150c4de7a70f9f09c00a335186b0b0b409771ef9f56bca7d9a'],
+    }),
+    ('xsimd', '8.0.5', {
+        'checksums': ['0e1b5d973b63009f06a3885931a37452580dbc8d7ca8ad40d4b8c80d2a0f84d7'],
+    }),
+    ('xtensor', version, {
+        'checksums': ['0d1ff8c5f801b566891cfb5c68718f838be94a0b6e07e3fc6164f66e5ec6d3b5'],
+    }),
+    ('xtensor-python', '0.24.1', {
+        'checksums': ['e2e251721b9afd6f5229fec58be519179205b8d54bf0e2cd79aa97cacf0c9915'],
+        'configopts': '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['include/xtensor.hpp', 'lib/pkgconfig/xsimd.pc', 'lib/pkgconfig/xtensor.pc'],
+    'dirs': ['include/xsimd', 'include/xtensor', 'include/xtensor-python', 'include/xtl', 'lib/cmake'],
+}
+
+moduleclass = 'lib'