{bio}[foss/2022a] Omnipose v0.4.4

easybuild/easyconfigs/m/mahotas/mahotas-1.4.13-foss-2022a.eb

@@ -0,0 +1,23 @@
+easyblock = 'PythonPackage'
+
+name = 'mahotas'
+version = '1.4.13'
+
+homepage = 'https://mahotas.readthedocs.io/'
+description = "Mahotas is a computer vision and image processing library for Python"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['a78dfe15045a20a0d9e01538b80f874580cd3525ae3eaa2c83ced51eb455879c']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05')
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

easybuild/easyconfigs/m/mgen/mgen-1.2.1-foss-2022a.eb

@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'mgen'
+version = '1.2.1'
+
+homepage = 'https://github.com/NOhs/mgen/tree/master'
+description = "Convenient matrix generation functions"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3caa56fc85ee71250cc55f484832af52d48c0cb84c945e1a32859b458a85ab39']
+
+# also requires pbr, which is an extension in Python already
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05')
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb

@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'ncolor'
+version = '1.2.1'
+
+homepage = 'https://github.com/kevinjohncutler/ncolor'
+description = """Fast remapping of instance labels 1,2,3,...,M to
+a smaller set of repeating, disjoint labels, 1,2,...,N."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# also requires pbr, which is an extension in Python already
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('numba', '0.56.4'),
+    ('mahotas', '1.4.13'),
+    ('scikit-image', '0.19.3'),
+]
+
+exts_list = [
+    ('edt', '2.3.1', {
+        'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'],
+    }),
+    ('fastremap', '1.13.5', {
+        'preinstallopts': "export PBR_VERSION=1.2.3 && ",
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/seung-lab/fastremap/archive/'],
+        'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'],
+    }),
+    (name, version, {
+        'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ",
+        'sources': ['%(name)s-%(version)s.tar.gz'],
+        'checksums': ['f05bfc75b8f1ea3ba9ee61c353e13146064bd63503a1655accee00a602ae2797'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a.eb

@@ -0,0 +1,117 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'PythonBundle'
+
+name = 'Omnipose'
+version = '0.4.4'
+
+homepage = 'https://omnipose.readthedocs.io'
+description = """
+Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways
+described in our paper. It works for both 2D and 3D images and on any imaging modality or
+cell shape, so long as you train it on representative images.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyQt5', '5.15.5'),
+    ('PyTorch', '1.12.0'),
+    ('PyQtGraph', '0.13.3'),
+    ('numba', '0.56.4'),
+    ('scikit-image', '0.19.3'),
+    ('scikit-learn', '1.1.2'),
+    ('matplotlib', '3.5.2'),
+    ('igraph', '0.10.3'),
+    ('MXNet', '1.9.1'),
+    ('mgen', '1.2.1'),
+    ('ncolor', '1.2.1'),
+    ('mahotas', '1.4.13'),
+    ('peakdetect', '1.2'),
+    ('python-igraph', '0.10.3'),
+    ('torchvf', '0.1.3'),
+    ('OpenCV', '4.6.0', '-contrib'),
+    ('tqdm', '4.64.0'),
+    ('imagecodecs', '2022.9.26'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('edt', '2.3.1', {
+        'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'],
+    }),
+    ('tifffile', '2023.4.12', {
+        'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'],
+    }),
+    ('natsort', '8.3.1', {
+        'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'],
+    }),
+    ('fastremap', '1.13.5', {
+        'source_urls': ['https://github.com/seung-lab/fastremap/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'],
+        'preinstallopts': "export PBR_VERSION=1.2.3 && ",
+    }),
+    ('roifile', '2023.5.12', {
+        'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'],
+    }),
+    ('pyasn1-modules', '0.2.8', {
+        'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'],
+    }),
+    ('rsa', '4.9', {
+        'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'],
+    }),
+    ('googleapis-common-protos', '1.59.1', {
+        'checksums': ['b35d530fe825fb4227857bc47ad84c33c809ac96f312e13182bdeaa2abe1178a'],
+        'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ',
+        'modulename': 'google.api',
+    }),
+    ('cachetools', '5.3.1', {
+        'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'],
+    }),
+    ('google-crc32c', '1.5.0', {
+        'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'],
+        'modulename': 'google_crc32c',
+    }),
+    ('google-auth', '2.22.0', {
+        'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'],
+        'modulename': 'google.auth',
+    }),
+    ('google-cloud-core', '2.3.3', {
+        'checksums': ['37b80273c8d7eee1ae816b3a20ae43585ea50506cb0e60f3cf5be5f87f1373cb'],
+        'modulename': 'google.api',
+    }),
+    ('google-api-core', '2.11.1', {
+        'checksums': ['25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a'],
+        'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ',
+        'modulename': 'google.api_core',
+    }),
+    ('google-resumable-media', '2.5.0', {
+        'checksums': ['218931e8e2b2a73a58eb354a288e03a0fd5fb1c4583261ac6e4c078666468c93'],
+        'modulename': 'google.resumable_media',
+    }),
+    ('google-cloud-storage', '2.10.0', {
+        'checksums': ['934b31ead5f3994e5360f9ff5750982c5b6b11604dc072bc452c25965e076dc7'],
+        'modulename': 'google.cloud.storage',
+    }),
+    ('cellpose-omni', '0.9.1', {
+        'patches': ['%(name)s-%(version)s_fix_deps_and_scm.patch'],
+        'checksums': [
+            {'cellpose-omni-0.9.1.tar.gz': '84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e'},
+            {'cellpose-omni-0.9.1_fix_deps_and_scm.patch':
+             'a1c42309d1a39297744a8505b45b9bff2e0f9ef738680349cc4adf8f663c4be0'},
+        ],
+    }),
+    ('omnipose', version, {
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'checksums': ['0bf1c333359504b0af511c36cc8db60ba5edba92d22c6aff183d9b858d269fe1'],
+        'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ",
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/o/Omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch

@@ -0,0 +1,33 @@
+Making dependencies more flexible, adding version, disabling SCM (not working with EasyBuild)
+--- setup_orig.py	2023-07-24 15:21:02.016292082 +0200
++++ setup.py	2023-07-24 15:45:57.822276166 +0200
+@@ -1,10 +1,10 @@
+ import setuptools
+ from setuptools import setup
+
+-install_deps = ['numpy>=1.22.4', 'scipy', 'natsort',
++install_deps = ['numpy>=1.22.3', 'scipy', 'natsort',
+                 'tifffile', 'tqdm', 'numba', 
+                 'torch>=1.6',
+-                'opencv-python-headless', # headless not working with pyinstaller 
++                'opencv-contrib-python', # headless not working with pyinstaller 
+                 'fastremap', 'imagecodecs'
+                 ]
+
+@@ -57,6 +57,7 @@
+
+ setup(
+     name="cellpose-omni",
++    version='0.9.1',
+     license="BSD",
+     author="Kevin Cutler",
+     author_email="kevinjohncutler@outlook.com",
+@@ -69,7 +70,7 @@
+       'setuptools_scm',
+     ],
+     packages=setuptools.find_packages(),
+-    use_scm_version=True,
++    use_scm_version=False,
+     install_requires = install_deps,
+     tests_require=[
+       'pytest'

easybuild/easyconfigs/p/peakdetect/peakdetect-1.2-foss-2022a.eb

@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'peakdetect'
+version = '1.2'
+
+homepage = 'https://github.com/avhn/peakdetect'
+description = "Simple peak detection library for Python based on Billauer's work and this gist."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/avhn/peakdetect/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['8f64a1fd6717ecaaec64fca6c16cb15698caa6aa8d6bc83bba3a22090a63e94f']
+
+# also requires pbr, which is an extension in Python already
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05')
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb

@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'torchvf'
+version = '0.1.3'
+
+homepage = 'https://github.com/ryanirl/torchvf'
+description = """
+TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# also requires pbr, which is an extension in Python already
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('OpenCV', '4.6.0', '-contrib'),
+    ('torchvision', '0.13.1'),
+    ('PyYAML', '6.0'),
+    ('scikit-learn', '1.1.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('edt', '2.3.1', {
+        'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'],
+    }),
+    (name, version, {
+        'preinstallopts': r"""sed -i 's/opencv-python-headless = "\*"//g' pyproject.toml && """,
+        'sources': ['%(namelower)s-%(version)s.tar.gz'],
+        'checksums': ['b2603ed660009ada68751fa507e02f297119e7180b3549098f4fdfe8242b8699'],
+    }),
+]
+
+
+moduleclass = 'ai'