{vis}[foss/2023a] micro-sam v1.0.1, torch_em v0.7.1, affogato v0.3.3, ...

easybuild/easyconfigs/a/affogato/affogato-0.3.3-foss-2023a.eb

@@ -0,0 +1,40 @@
+easyblock = 'CMakeMakeCp'
+
+name = 'affogato'
+version = '0.3.3'
+
+homepage = 'https://github.com/constantinpape/affogato/'
+description = """Affinity based segmentation algorithms and tools."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/constantinpape/affogato/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['ad3bb1aca50ce9311d4e88e97e701237bce94faa6e79460f0bc2d2061f1484d2']
+
+builddependencies = [('CMake', '3.26.3')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Boost', '1.82.0'),
+    ('SciPy-bundle', '2023.07'),
+    ('vigra', '1.11.2'),
+    ('xtensor', '0.24.7'),
+    ('h5py', '3.9.0'),
+]
+
+configopts = '-DBUILD_PYTHON=ON '
+# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" '
+
+files_to_copy = [(['python/affogato'], 'lib/python%(pyshortver)s/site-packages')]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/affogato'],
+}
+sanity_check_commands = ["python -c 'import affogato'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'

easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.82.0-GCC-12.3.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.Python'
+version = '1.82.0'
+
+homepage = 'https://boostorg.github.io/python'
+description = """Boost.Python is a C++ library which enables seamless interoperability between C++
+ and the Python programming language."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_1_82_0.tar.gz']
+checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c']
+
+dependencies = [
+    ('Boost', version),
+    ('Python', '3.11.3'),
+]
+
+only_python_bindings = True
+
+moduleclass = 'lib'

easybuild/easyconfigs/m/micro-sam/micro-sam-1.0.1-foss-2023a.eb

@@ -0,0 +1,43 @@
+easyblock = 'PythonBundle'
+
+name = 'micro-sam'
+version = '1.0.1'
+
+homepage = 'https://github.com/computational-cell-analytics/micro-sam/'
+description = "Tools for segmentation and tracking in microscopy build on top of SegmentAnything."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('torchvision', '0.16.0'),
+    ('napari', '0.4.18'),
+    ('zarr', '2.17.1'),
+    ('vigra', '1.11.2'),
+    ('python-elf', '0.5.1'),
+    ('z5py', '2.0.17'),
+    ('python-xxhash', '3.4.1'),
+    ('segment-anything', '1.0'),
+    ('torch-em', '0.7.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/computational-cell-analytics/micro-sam/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['5b7cc562a639d68de4f9462f3696f17b479ea0d669eaedb34687b65ceac715e9'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import affogato'",
+    "python -c 'import napari.viewer'",
+    "micro_sam.annotator_2d -h",
+    "micro_sam.annotator_3d -h",
+]
+
+moduleclass = 'vis'

easybuild/easyconfigs/n/nifty/nifty-1.2.1-foss-2023a.eb

@@ -0,0 +1,54 @@
+easyblock = 'CMakeMakeCp'
+
+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')]
+
+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'),
+    ('xtensor', '0.24.7'),
+    ('zlib', '1.2.13'),
+    ('HDF5', '1.14.0'),
+]
+
+# Add flags (nifty/.github/workflows/build_unix.sh)
+configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH_CPLEX=OFF -DWITH_GUROBI=OFF '
+# Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
+configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON '
+
+# export PYTHON_MODULE_INSTALL_DIR to fix make install
+preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" && '
+
+files_to_copy = [(['python/nifty'], 'lib/python%(pyshortver)s/site-packages')]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/nifty'],
+}
+
+sanity_check_commands = [
+    "python -c 'import nifty'",
+    "python -c 'from nifty.graph import UndirectedGraph'",
+    "python -c 'import nifty.tools'",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'

easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.7-foss-2023a.eb

@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'pycocotools'
+version = '2.0.7'
+
+homepage = 'https://pypi.org/project/pycocotools'
+description = "Official APIs for the MS-COCO dataset"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['da8b7815196eebf0adabf67fcc459126cbc6498bbc6ab1fd144c371465d86879']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'data'

easybuild/easyconfigs/p/python-blosc/python-blosc-1.11.0-foss-2023a.eb

@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'python-blosc'
+version = '1.11.0'
+
+homepage = 'https://github.com/Blosc/python-blosc/'
+description = "A Python wrapper for the extremely fast Blosc compression library."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('scikit-build', '0.17.6'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Blosc', '1.21.5'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+local_preinstallopts = 'export USE_SYSTEM_BLOSC=1 && '
+local_preinstallopts += 'export Blosc_ROOT=$EBROOTBLOSC && '
+
+exts_list = [
+    ('blosc', version, {
+        'preinstallopts': local_preinstallopts,
+        'checksums': ['c985b8f435dbc49b190fe88947539ed710ad0e9aaaf83778acc506a71ada7bd2'],
+    }),
+]
+
+sanity_check_commands = ["python -m blosc.test"]
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/python-elf/python-elf-0.5.1-foss-2023a.eb

@@ -0,0 +1,72 @@
+easyblock = 'PythonBundle'
+
+name = 'python-elf'
+version = '0.5.1'
+
+homepage = 'https://github.com/constantinpape/elf'
+description = "Utils and convenience functions for large-scale bio-image analysis."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [
+    ('scikit-build', '0.17.6'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('imageio', '2.33.1'),
+    ('scikit-image', '0.22.0'),
+    ('scikit-learn', '1.3.1'),
+    ('h5py', '3.9.0'),
+    ('zarr', '2.17.1'),
+    ('mrcfile', '1.5.0'),
+    ('numba', '0.58.1'),
+    ('tqdm', '4.66.1'),
+    ('vigra', '1.11.2'),
+    ('python-blosc', '1.11.0'),
+    ('openpyxl', '3.1.2'),
+    ('nifty', '1.2.1'),
+    ('z5py', '2.0.17'),
+    ('affogato', '0.3.3'),
+    ('napari', '0.4.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('nose2', '0.14.1', {
+        'checksums': ['7f8f03a21c9de2c33015933afcef72bf8e4a2d5dfec3b40092287de6e41b093a'],
+    }),
+    ('intern', '1.4.1', {
+        'checksums': ['7cdc6caa66716760f93dbbadaa67cc8a03866d6c5f33a6a3285cb9e5f4994315'],
+    }),
+    ('skan', '0.11.1', {
+        'checksums': ['d5439c17fbf5f86386a7548acb6ab11482961164a6284047b9bdc6652a0d1faf'],
+    }),
+    (name, version, {
+        'modulename': 'elf',
+        'source_urls': ['https://github.com/constantinpape/elf/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['29c542dfb953a1975e2d45f72c84b8f8a2f79fcb0cb2d855dae5493cadbbaa9d'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import elf.segmentation.multicut'",
+    "python -c 'import elf.segmentation.features'",
+    "python -c 'import elf.segmentation.embeddings'",
+    "python -c 'from elf.segmentation.mutex_watershed import mutex_watershed_clustering'",
+    "python -c 'from elf.segmentation.utils import load_mutex_watershed_problem'",
+    "python -c 'import elf.htm'",
+    "python -c 'from elf.parallel.label import label'",
+    "python -c 'from elf.evaluation import rand_index'",
+    "python -c 'from elf.io import open_file'",
+    "python -c 'from elf.visualisation import visualise_edges'",
+    "python -c 'import elf.tracking.tracking_utils'",
+    "python -c 'import elf.transformation'",
+    "python -c 'import elf.util'",
+]
+
+moduleclass = 'vis'

easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2023a.eb

@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'segment-anything'
+version = '1.0'
+
+homepage = 'https://github.com/facebookresearch/segment-anything'
+description = """The Segment Anything Model (SAM) produces high quality object masks from input prompts
+ such as points or boxes, and it can be used to generate masks for all objects in an image.
+ It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot
+ performance on a variety of segmentation tasks."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = ['segment_anything-%(version)s.tar.gz']
+checksums = ['ed0c9f6fb07bbef9c6238a7028a13c8272f1ba6b6305ca73e3e064266503736b']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('torchvision', '0.16.0'),
+    ('OpenCV', '4.8.1', '-contrib'),
+    ('pycocotools', '2.0.7'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'ai'