#314 pre PR version + 327 clean comment

314_napari_microsam/affogato.eb

@@ -29,29 +29,15 @@ dependencies = [
     ('Boost', '1.82.0'),
     ('SciPy-bundle', '2023.07'),
     ('vigra', '1.11.2'),
-#     ('bzip2', '1.0.8'),
-#     ('lz4', '1.9.4'),
-#     ('XZ', '5.4.2'),
-#     ('zlib', '1.2.13'),
     ('xtensor', '0.24.7'),
-#     ('python-blosc', '1.11.0'),
-#     ('imageio', '2.33.1'),
     ('h5py', '3.9.0'),
-#     ('nlohmann_json', '3.11.2'),
-#     ('zarr', '2.17.1'),
-#     ('pybind11', '2.11.1'),
 ]
 
-# Add flags
 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" '
 
-# # export PYTHON_MODULE_INSTALL_DIR to fix make install
-# preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
-
 files_to_copy = [(['python/affogato'], 'lib/python%(pyshortver)s/site-packages')]
-# files_to_copy = ['*']
 
 sanity_check_paths = {
     'files': [],

314_napari_microsam/elf.eb

@@ -41,21 +41,12 @@ use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('structsvm', '0.1.1', {
-        'checksums': ['3f0c83f33656ebe13516b6dde2911469b6d8f805e024fa7069972a8bcf081f79'],
-    }),
-    ('ilpy', '0.4.0', {
-        'checksums': ['5cee3c0e5fe6e48cbb4686a8d8362b5e5fa407ab242c480b3981beb7b3429f0c'],
-    }),
     ('nose2', '0.14.1', {
         'checksums': ['7f8f03a21c9de2c33015933afcef72bf8e4a2d5dfec3b40092287de6e41b093a'],
     }),
     ('intern', '1.4.1', {
         'checksums': ['7cdc6caa66716760f93dbbadaa67cc8a03866d6c5f33a6a3285cb9e5f4994315'],
     }),
-    ('motile', '0.2.1', {
-        'checksums': ['c2cd61e8566198b5a3fdbcb11355837fdcfe82f415bd6d3358ff7acec877ff12'],
-    }),
     ('skan', '0.11.1', {
         'checksums': ['d5439c17fbf5f86386a7548acb6ab11482961164a6284047b9bdc6652a0d1faf'],
     }),
@@ -67,14 +58,6 @@ exts_list = [
     }),
 ]
 
-# postinstallcmds = [
-#     'sed -i "s/np.float/float/g" %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2/predictQuality.py',
-#     '%(installdir)s/bin/checkm2 database --download --path %(installdir)s',
-#     # 'export CHECKM2DB="$EBROOTCHECKM2/CheckM2_database/uniref100.KO.1.dmnd"',
-# ]
-
-# modextrapaths = {'CHECKM2DB': 'CheckM2_database/uniref100.KO.1.dmnd', 'PYTHONPATH': ''}
-
 sanity_check_commands = [
     "python -c 'import elf.segmentation.multicut'",
     "python -c 'import elf.segmentation.features'",
@@ -86,7 +69,7 @@ sanity_check_commands = [
     "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.motile_tracking'",
+    "python -c 'import elf.tracking.tracking_utils'",
     "python -c 'import elf.transformation'",
     "python -c 'import elf.util'",
 ]

314_napari_microsam/napari_microsam-1.0.0.eb → 314_napari_microsam/napari_microsam-1.0.1.eb

@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'micro-sam'
-version = '1.0.0'
+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."
@@ -11,7 +11,6 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 # DEPS:
 # napari OK
 # pyqt OK (in napari)
-# $ micro_sam.annotator -> GUI needs more deps:
 # zarr OK 
 # torch OK - torchvision
 # vigra NO (not in EB) -> created OK
@@ -20,7 +19,7 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 # z5py -> created OK
 # python-xxhash OK
 # segment_anything -> created OK
-# torch_em >=0.7.0
+# torch_em >=0.7.0 -> created OK
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -33,6 +32,7 @@ dependencies = [
     ('z5py', '2.0.17'),
     ('python-xxhash', '3.4.1'),
     ('segment-anything', '1.0'),
+    ('torch_em', '0.7.1'),
 ]
 
 use_pip = True
@@ -42,18 +42,15 @@ exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/computational-cell-analytics/micro-sam/archive/'],
         'sources': ['v%(version)s.tar.gz'],
-        'checksums': ['c9bdf7d141911a56062e4df4e0d23a094848a70381b8e09ba9013eea53bbdadd'],
+        'checksums': ['5b7cc562a639d68de4f9462f3696f17b479ea0d669eaedb34687b65ceac715e9'],
     }),
 ]
 
-# postinstallcmds = [
-#     'sed -i "s/np.float/float/g" %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2/predictQuality.py',
-#     '%(installdir)s/bin/checkm2 database --download --path %(installdir)s',
-#     # 'export CHECKM2DB="$EBROOTCHECKM2/CheckM2_database/uniref100.KO.1.dmnd"',
-# ]
-
-# modextrapaths = {'CHECKM2DB': 'CheckM2_database/uniref100.KO.1.dmnd', 'PYTHONPATH': ''}
-
-# sanity_check_commands = ["pyscenic --help"]
+sanity_check_commands = [
+    "python -c 'import affogato'",
+    "python -c 'import napari.viewer'",
+    "micro_sam.annotator_2d -h",
+    "micro_sam.annotator_3d -h",
+]
 
 moduleclass = 'vis'

314_napari_microsam/nifty.eb

@@ -33,47 +33,31 @@ dependencies = [
     ('nlohmann_json', '3.11.2'),
     ('scikit-image', '0.22.0'),
     ('vigra', '1.11.2'),
-    # ('zarr', '2.17.1'),
     ('xtensor', '0.24.7'),
     ('zlib', '1.2.13'),
     ('HDF5', '1.14.0'),
 ]
 
-# # Print out _NUMPY_VALUES - not working
-# preconfigopts = "pwd && cd %(builddir)s && pwd && "
-# preconfigopts += "sed -i '62 a\message(\"${_NUMPY_VALUES}\")' nifty-1.2.1/cmake/modules/FindNUMPY.cmake && "
-# preconfigopts += "cd /tmp/vsc47063/easybuild/build/nifty/1.2.1/foss-2023a/easybuild_obj &&"
-
-# Try find_package (Python3 COMPONENTS Interpreter) - ok, do not help - still python 3.6.8
-# preconfigopts = "pwd && cd %(builddir)s && pwd && "
-# preconfigopts += "sed -i 's/PythonInterp/Python3 COMPONENTS Interpreter/g' nifty-1.2.1/cmake/modules/FindNUMPY.cmake && "
-# preconfigopts += "cd /tmp/vsc47063/easybuild/build/nifty/1.2.1/foss-2023a/easybuild_obj &&"
-
 # Add flags (nifty/.github/workflows/build_unix.sh)
 configopts = '-DWITH_QPBO=OFF -DWITH_HDF5=ON -DWITH_Z5=OFF -DWITH_ZLIB=ON -DWITH_CPLEX=OFF -DWITH_GUROBI=OFF '
 # Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
 configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" -DBUILD_NIFTY_PYTHON=ON '
 
-# # Fix python files path in make install step -> maybe better to export PYTHON_MODULE_INSTALL_DIR
-# path = "%(builddir)s/nifty-1.2.1/src/python/CMakeList.txt"
-# preinstallopts = "sed -i '44 s/${PYTHON_MODULE_INSTALL_DIR}/\"%(installdir)s/lib/python%(pyshortver)s/site-packages\/"' %s && " % path
-
-# # export PYTHON_MODULE_INSTALL_DIR to fix make install
-# preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages" '
-# easybuild_obj/python/
+# export PYTHON_MODULE_INSTALL_DIR to fix make install
 preinstallopts = 'export PYTHON_MODULE_INSTALL_DIR="%(builddir)s/easybuild_obj/python/" '
 
-# separate_build_dir = False
-
 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'"]
-# from nifty.graph import UndirectedGraph
+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'}
 

314_napari_microsam/torch_em.eb

@@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 # DEPS:
 # "torch", OK
 # "h5py" OK
-# - affogato NO - should be version from constantinpape
+# - affogato ok created
 # - bioimageio.spec >=0.5.0 OK exts
 # - bioimageio.core >=0.6.0 OK exts
 # - cpuonly ??? no
@@ -46,6 +46,12 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 # email-validator 2.1.1 requires dnspython, ok exts
 # fire 0.6.0 requires termcolor, ok exts
 # bioimageio-spec 0.5.2.post5 has requirement pydantic<3,>=2.6.3, but you have pydantic 2.5.3. -> unpin by preinstallopts
+    # imports to torch_em from bioimageio.spec:
+    # bioimageio.spec.model.v0_5
+    # from bioimageio.spec import save_bioimageio_package
+# skimage -> scikit-image (in elf, nifty)
+    # import skimage.measure
+    # import skimage.segmentation
 
 builddependencies = [
     ('maturin', '1.1.0'),
@@ -54,27 +60,25 @@ builddependencies = [
 ]
 dependencies = [
     ('Python', '3.11.3'),
-#     ('Python-bundle-PyPI', '2023.06'),
     ('torchvision', '0.16.0'),
     ('h5py', '3.9.0'),
-    ('imagecodecs', '2023.1.23'), # from empanada-dl
+    ('imagecodecs', '2023.1.23'),
     ('tensorboard', '2.15.1'),
     ('tqdm', '4.66.1'),
-#     ('napari', '0.4.18'),
-#     ('zarr', '2.17.1'),
-#     ('vigra', '1.11.2'),
+    ('napari', '0.4.18'),
+    ('vigra', '1.11.2'),
     ('python-elf', '0.5.1'),
-#     ('z5py', '2.0.17'),
-#     ('python-xxhash', '3.4.1'),
-#     ('segment-anything', '1.0'),
+    ('z5py', '2.0.17'),
     ('pydantic', '2.5.3'),
     ('xarray', '2023.9.0'),
+    ('affogato', '0.3.3'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 # avoid using hatchling as build backend (since installing it for this old Python version is a nightmare)
+# copied from MONAI-1.0.1-foss-2022a.eb
 local_preinstallopts_termcolor = ' '.join([
     r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """,
     r"""-e 's/^requires = \[/requires = \["setuptools"/g' """,
@@ -129,6 +133,7 @@ exts_list = [
         'checksums': ['3b2851e44a2b074536c36fe3bb05b28dc1413ed358d3edd0eb272b75e6c9ca2b'],
     }),
     ('bioimageio.spec', '0.5.2.post5', {
+        # delete pin of pydantic version
         'preinstallopts': "sed -i 's/pydantic>=2.6.3,<3/pydantic/' setup.py && ",
         'checksums': ['3007aedc4da9f77f4fb46f72c134c8367bd469f05f6dd275db1a93f0fff48e97'],
     }),
@@ -139,14 +144,18 @@ exts_list = [
     }),
 ]
 
-# # postinstallcmds = [
-# #     'sed -i "s/np.float/float/g" %(installdir)s/lib/python%(pyshortver)s/site-packages/checkm2/predictQuality.py',
-# #     '%(installdir)s/bin/checkm2 database --download --path %(installdir)s',
-# #     # 'export CHECKM2DB="$EBROOTCHECKM2/CheckM2_database/uniref100.KO.1.dmnd"',
-# # ]
-
-# # modextrapaths = {'CHECKM2DB': 'CheckM2_database/uniref100.KO.1.dmnd', 'PYTHONPATH': ''}
-
-# # sanity_check_commands = ["pyscenic --help"]
+sanity_check_commands = [
+    "python -c 'import torch_em.data.datasets.util'",
+    "python -c 'import torch_em.transform.label'",
+    "python -c 'import torch_em.data.sampler'",
+    "python -c 'import torch_em.segmentation'",
+    "python -c 'import torch_em.data.datasets.neurips_cell_seg'",
+    "python -c 'import torch_em.model'",
+    "python -c 'import torch_em.loss'",
+    "python -c 'import torch_em.trainer'",
+    # check if unpined pydantic version is woking 
+    "python -c 'import bioimageio.spec.model.v0_5'",
+    "python -c 'from bioimageio.spec import save_bioimageio_package'",
+]
 
 moduleclass = 'vis'

314_napari_microsam/vigra_v2.eb

@@ -32,11 +32,11 @@ dependencies = [
 ]
 
 # 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)
+_py_path = "%(builddir)s/%(name)s-Version-1-11-2/config/FindVIGRANUMPY_DEPENDENCIES.cmake"
+_py_add = "SET(VIGRANUMPY_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/python%(pyshortver)s/site-packages)"
+preinstallopts = "sed -i '90,91d' %s && " % _py_path
+preinstallopts += "sed -i '94d' %s && " % _py_path
+preinstallopts += "sed -i '89 a\%s' %s && " % (_py_add, _py_path)
 
 sanity_check_paths = {
     'files': ['bin/vigra-config'],

314_napari_microsam/z5py.eb

@@ -50,7 +50,6 @@ dependencies = [
     ('pybind11', '2.11.1'),
 ]
 
-# Add flags
 configopts = '-DWITH_ZLIB=ON -DWITH_BZIP2=ON '
 # Fix path to python executable - it finds v3.6.8 from /usr/bin/ without this fix
 configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python" '

327_RoseTTAFold-All-Atom/libgcrypt-1.10.3-GCCcore-12.3.0.eb

@@ -14,7 +14,7 @@ checksums = ['8b0870897ac5ac67ded568dcfadf45969cfa8a6beb0fd60af2a9eadc2a3272aa']
 
 builddependencies = [('binutils', '2.40')]
 
-dependencies = [('libgpg-error', '1.48')] # not for 12.3.0 -> ctreated
+dependencies = [('libgpg-error', '1.48')]
 
 sanity_check_paths = {
     'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT],