e66e572656
* py-cellprofiler: add 4.2.6 new package * py-mysqlclient: Limit pkg-config patch to @1.4: Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
154 lines
6.0 KiB
Python
154 lines
6.0 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class PyCellprofiler(PythonPackage):
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"""CellProfiler cell image analysis software.
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CellProfiler is a free open-source software designed to enable biologists
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without training in computer vision or programming to quantitatively
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measure phenotypes from thousands of images automatically.
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"""
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homepage = "https://cellprofiler.org"
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pypi = "cellprofiler/CellProfiler-4.2.6.tar.gz"
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git = "https://github.com/CellProfiler/CellProfiler.git"
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maintainers("omsai")
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license("BSD-3-Clause", checked_by="omsai")
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version("4.2.6", sha256="37e2a35dccff456afda96a4442dff2d23809c8ee271607a347e386aeb4af2628")
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depends_on("python@3.8:", type=("build", "run"))
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depends_on("py-setuptools@64:", type="build")
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depends_on("py-setuptools-scm@8:", type="build")
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depends_on("py-boto3@1.12.28:", type=("build", "run"))
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depends_on("py-cellprofiler-core@4.2.6", type=("build", "run"))
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depends_on("py-centrosome@1.2.2:", type=("build", "run"))
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depends_on("py-docutils@0.15.2:", type=("build", "run"))
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# More recent versions of h5py cause:
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# AttributeError: module 'h5py' has no attribute 'Dataset
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depends_on("py-h5py@3.6:3.7~mpi", type=("build", "run"))
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depends_on("py-imageio@2.5:", type=("build", "run"))
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depends_on("py-inflect@2.1:6", type=("build", "run"))
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depends_on("py-jinja2@2.11.2:", type=("build", "run"))
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depends_on("py-joblib@0.13:", type=("build", "run"))
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depends_on("py-mahotas@1.4:", type=("build", "run"))
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# matplotlib.cm.get_cmap does not exist in 3.9.0 onwards.
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depends_on("py-matplotlib@3.1.3:3.8", type=("build", "run"))
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depends_on("py-mysqlclient@1.4.6", type=("build", "run"))
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depends_on("py-numpy@1.20.1:", type=("build", "run"))
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depends_on("py-pillow@7.1:", type=("build", "run"))
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depends_on("py-prokaryote@2.4.4:", type=("build", "run"))
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depends_on("py-python-bioformats@4.0.7:", type=("build", "run"))
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depends_on("py-python-javabridge@4.0.3:", type=("build", "run"))
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depends_on("py-pyzmq@22.3:22", type=("build", "run"))
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depends_on("py-sentry-sdk@0.18:", type=("build", "run"))
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depends_on("py-requests@2.22:", type=("build", "run"))
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depends_on("py-scikit-image@0.18.3:", type=("build", "run"))
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depends_on("py-scikit-learn@0.20:0", type=("build", "run"))
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depends_on("py-scipy", type=("build", "run"))
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depends_on("py-six", type=("build", "run"))
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depends_on("py-tifffile@:2022.4.21", type=("build", "run"))
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depends_on("py-wxpython@4.1.0:4", type=("build", "run"))
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depends_on("py-pytest", type=("run", "test"), when="@4.2.6 +tests")
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# Run the post-install tests with `spack test run py-cellprofiler`. We
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# need the variant to add the pytest executable to the PATH.
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variant("tests", default=False, description="Post-install tests.")
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# The pypi tests directory is incomplete.
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resource(
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name="tests-upstream",
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destination="",
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placement={
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"tests/conftest.py": "tests/conftest.py",
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"tests/gui": "tests/gui",
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"tests/__init__.py": "tests/__init__.py",
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"tests/modules": "tests/modules",
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"tests/resources": "tests/resources",
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"tests/test_cellprofiler.py": "tests/test_cellprofiler.py",
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"tests/test_haralick.py": "tests/test_haralick.py",
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"tests/test_knime_bridge.py": "tests/test_knime_bridge.py",
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"tests/test_main.py": "tests/test_main.py",
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"tests/test_nowx.py": "tests/test_nowx.py",
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"tests/utilities": "tests/utilities",
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},
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git=git,
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tag="v4.2.6",
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sha256="5fb562774044d1dc8cffcddf6072d706f71e6649d566980efaab5b30f52ddfa2",
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when="@4.2.6 +tests",
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)
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dir_tests = "tests"
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# Leave 'gui' out of 'import_modules' to avoid the curently broken wxpython
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# dependency.
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import_modules = [
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"cellprofiler",
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"cellprofiler.icons",
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"cellprofiler.library",
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"cellprofiler.library.functions",
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"cellprofiler.library.modules",
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# "cellprofiler.gui",
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# "cellprofiler.gui.html",
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# "cellprofiler.gui.help",
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# "cellprofiler.gui.module_view",
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# "cellprofiler.gui.constants",
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# "cellprofiler.gui.figure",
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# "cellprofiler.gui.workspace_view",
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# "cellprofiler.gui.preferences_view",
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# "cellprofiler.gui.utilities",
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# "cellprofiler.gui.preferences_dialog",
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"cellprofiler.modules",
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"cellprofiler.modules.plugins",
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"cellprofiler.utilities",
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]
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@when("+tests")
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def patch(self):
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"""Install tests from git."""
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# Install the tests module. Using a module name like "tests" may
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# create a namespace collision with other spack packages in the DAG,
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# but the alternative would moving tests into cellprofiler and
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# extensively patching the tests to be a submodule of cellprofiler
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# instead of a standalone module.
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filter_file(r"find_packages\([^)]+\)", "find_packages()", "setup.py")
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# Include required test data files.
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with open("MANIFEST.in", "a") as h:
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h.writelines("graft tests")
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# For interactive unittest debugging, run:
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#
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# spack env create cp
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# spack env activate cp
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# spack add cellprofiler+tests ^hdf5~mpi
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# spack install
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# git clone --branch v4.2.6 --depth 1 \
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# https://github.com/cellprofiler/cellprofiler
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# cd cellprofiler/
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# pytest --pdb -k "not TestExportToDatabase" tests/
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#
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# [...]
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# 1412 passed, 16 skipped, 75 deselected
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def test_cellprofiler_no_gui(self):
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"""Test installed package."""
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pytest = which("pytest")
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prefix = join_path(python_purelib, self.dir_tests)
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pytest(
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"-v",
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# Don't test against the live MySQL database.
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"-k",
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"not TestExportToDatabase",
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prefix,
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)
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