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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"
[project]
name = "aind_exaspim_pipeline_utils"
description = "AIND exaSPIM pipeline utilities."
license = {text = "MIT"}
requires-python = ">=3.8"
authors = [
{name = "Allen Institute for Neural Dynamics"}
]
classifiers = [
"Programming Language :: Python :: 3"
]
readme = "README.md"
dynamic = ["version"]
dependencies = [
'argschema',
's3fs',
'pydantic',
'psutil',
'matplotlib',
'scipy',
'aind-data-schema==0.33.3',
'aind-codeocean-api',
'aind-ng-link>=1.0.15',
'numpy<2.0'
]
[project.optional-dependencies]
dev = [
'aind-exaspim-pipeline-utils[n5tozarr]',
'black',
'coverage',
'flake8',
'interrogate',
'isort',
'Sphinx',
'furo'
]
n5tozarr = [
# n5 to zarr conversion
'dask',
'distributed',
'zarr',
'numcodecs',
'aind-data-transfer[imaging]==0.35.3',
# missing dependencies from aind-data-transfer[imaging]
# These supposed to be installed by post_install.sh
'hdf5plugin',
'kerchunk'
]
[tool.setuptools.packages.find]
where = ["src"]
[project.scripts]
imagej_wrapper = "aind_exaspim_pipeline_utils.imagej_wrapper:main"
imagej_wrapper_manifest = "aind_exaspim_pipeline_utils.imagej_wrapper:imagej_wrapper_main"
n5tozarr_da_converter = "aind_exaspim_pipeline_utils.n5tozarr.n5tozarr_da:n5tozarr_da_converter"
zarr_multiscale_converter = "aind_exaspim_pipeline_utils.n5tozarr.n5tozarr_da:zarr_multiscale_converter"
create_example_manifest = "aind_exaspim_pipeline_utils.exaspim_manifest:create_example_manifest"
bigstitcher_log_edge_analysis = "aind_exaspim_pipeline_utils.qc.bigstitcher_log_edge_analysis:main"
run_trigger_capsule = "aind_exaspim_pipeline_utils.trigger.capsule:capsule_main"
java_detreg_postprocess = "aind_exaspim_pipeline_utils.java_utils:java_detreg_postprocess_main"
run_tr_density_plot = "aind_exaspim_pipeline_utils.qc.ip_density:run_tr_density_plot"
run_aff_density_plot = "aind_exaspim_pipeline_utils.qc.ip_density:run_aff_density_plot"
run_aff_combined_plot = "aind_exaspim_pipeline_utils.qc.image_cutout:run_aff_combined_plot"
run_aff_yz_xz_combined_plot = "aind_exaspim_pipeline_utils.qc.image_cutout:run_aff_yz_xz_combined_plot"
[tool.setuptools.dynamic]
version = {attr = "aind_exaspim_pipeline_utils.__version__"}
[tool.black]
line-length = 110
target_version = ['py38']
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| build
| dist
)/
| .gitignore
)
'''
[tool.coverage.run]
omit = ["*__init__*", "*__main__*"]
source = ["aind_exaspim_pipeline_utils", "tests"]
[tool.coverage.report]
exclude_lines = [ "pragma: no cover", "if __name__ == .__main__.:"]
fail_under = 90
[tool.isort]
line_length = 110
profile = "black"
[tool.interrogate]
exclude = ["setup.py", "docs", "build"]
fail-under = 100