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Diffstat (limited to 'var/spack/repos/builtin/packages/py-cellprofiler/package.py')
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1 files changed, 153 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/py-cellprofiler/package.py b/var/spack/repos/builtin/packages/py-cellprofiler/package.py new file mode 100644 index 0000000000..8c3010cce1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-cellprofiler/package.py @@ -0,0 +1,153 @@ +# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class PyCellprofiler(PythonPackage): + """CellProfiler cell image analysis software. + + CellProfiler is a free open-source software designed to enable biologists + without training in computer vision or programming to quantitatively + measure phenotypes from thousands of images automatically. + + """ + + homepage = "https://cellprofiler.org" + pypi = "cellprofiler/CellProfiler-4.2.6.tar.gz" + git = "https://github.com/CellProfiler/CellProfiler.git" + + maintainers("omsai") + + license("BSD-3-Clause", checked_by="omsai") + + version("4.2.6", sha256="37e2a35dccff456afda96a4442dff2d23809c8ee271607a347e386aeb4af2628") + + depends_on("python@3.8:", type=("build", "run")) + + depends_on("py-setuptools@64:", type="build") + depends_on("py-setuptools-scm@8:", type="build") + + depends_on("py-boto3@1.12.28:", type=("build", "run")) + depends_on("py-cellprofiler-core@4.2.6", type=("build", "run")) + depends_on("py-centrosome@1.2.2:", type=("build", "run")) + depends_on("py-docutils@0.15.2:", type=("build", "run")) + # More recent versions of h5py cause: + # AttributeError: module 'h5py' has no attribute 'Dataset + depends_on("py-h5py@3.6:3.7~mpi", type=("build", "run")) + depends_on("py-imageio@2.5:", type=("build", "run")) + depends_on("py-inflect@2.1:6", type=("build", "run")) + depends_on("py-jinja2@2.11.2:", type=("build", "run")) + depends_on("py-joblib@0.13:", type=("build", "run")) + depends_on("py-mahotas@1.4:", type=("build", "run")) + # matplotlib.cm.get_cmap does not exist in 3.9.0 onwards. + depends_on("py-matplotlib@3.1.3:3.8", type=("build", "run")) + depends_on("py-mysqlclient@1.4.6", type=("build", "run")) + depends_on("py-numpy@1.20.1:", type=("build", "run")) + depends_on("py-pillow@7.1:", type=("build", "run")) + depends_on("py-prokaryote@2.4.4:", type=("build", "run")) + depends_on("py-python-bioformats@4.0.7:", type=("build", "run")) + depends_on("py-python-javabridge@4.0.3:", type=("build", "run")) + depends_on("py-pyzmq@22.3:22", type=("build", "run")) + depends_on("py-sentry-sdk@0.18:", type=("build", "run")) + depends_on("py-requests@2.22:", type=("build", "run")) + depends_on("py-scikit-image@0.18.3:", type=("build", "run")) + depends_on("py-scikit-learn@0.20:0", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-six", type=("build", "run")) + depends_on("py-tifffile@:2022.4.21", type=("build", "run")) + depends_on("py-wxpython@4.1.0:4", type=("build", "run")) + + depends_on("py-pytest", type=("run", "test"), when="@4.2.6 +tests") + + # Run the post-install tests with `spack test run py-cellprofiler`. We + # need the variant to add the pytest executable to the PATH. + variant("tests", default=False, description="Post-install tests.") + + # The pypi tests directory is incomplete. + resource( + name="tests-upstream", + destination="", + placement={ + "tests/conftest.py": "tests/conftest.py", + "tests/gui": "tests/gui", + "tests/__init__.py": "tests/__init__.py", + "tests/modules": "tests/modules", + "tests/resources": "tests/resources", + "tests/test_cellprofiler.py": "tests/test_cellprofiler.py", + "tests/test_haralick.py": "tests/test_haralick.py", + "tests/test_knime_bridge.py": "tests/test_knime_bridge.py", + "tests/test_main.py": "tests/test_main.py", + "tests/test_nowx.py": "tests/test_nowx.py", + "tests/utilities": "tests/utilities", + }, + git=git, + tag="v4.2.6", + sha256="5fb562774044d1dc8cffcddf6072d706f71e6649d566980efaab5b30f52ddfa2", + when="@4.2.6 +tests", + ) + + dir_tests = "tests" + + # Leave 'gui' out of 'import_modules' to avoid the curently broken wxpython + # dependency. + import_modules = [ + "cellprofiler", + "cellprofiler.icons", + "cellprofiler.library", + "cellprofiler.library.functions", + "cellprofiler.library.modules", + # "cellprofiler.gui", + # "cellprofiler.gui.html", + # "cellprofiler.gui.help", + # "cellprofiler.gui.module_view", + # "cellprofiler.gui.constants", + # "cellprofiler.gui.figure", + # "cellprofiler.gui.workspace_view", + # "cellprofiler.gui.preferences_view", + # "cellprofiler.gui.utilities", + # "cellprofiler.gui.preferences_dialog", + "cellprofiler.modules", + "cellprofiler.modules.plugins", + "cellprofiler.utilities", + ] + + @when("+tests") + def patch(self): + """Install tests from git.""" + # Install the tests module. Using a module name like "tests" may + # create a namespace collision with other spack packages in the DAG, + # but the alternative would moving tests into cellprofiler and + # extensively patching the tests to be a submodule of cellprofiler + # instead of a standalone module. + filter_file(r"find_packages\([^)]+\)", "find_packages()", "setup.py") + # Include required test data files. + with open("MANIFEST.in", "a") as h: + h.writelines("graft tests") + + # For interactive unittest debugging, run: + # + # spack env create cp + # spack env activate cp + # spack add cellprofiler+tests ^hdf5~mpi + # spack install + # git clone --branch v4.2.6 --depth 1 \ + # https://github.com/cellprofiler/cellprofiler + # cd cellprofiler/ + # pytest --pdb -k "not TestExportToDatabase" tests/ + # + # [...] + # 1412 passed, 16 skipped, 75 deselected + def test_cellprofiler_no_gui(self): + """Test installed package.""" + pytest = which("pytest") + prefix = join_path(python_purelib, self.dir_tests) + pytest( + "-v", + # Don't test against the live MySQL database. + "-k", + "not TestExportToDatabase", + prefix, + ) |