# 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 PyDeeptools(PythonPackage):
    """deepTools addresses the challenge of handling the large amounts of data
    that are now routinely generated from DNA sequencing centers."""

    # The test suite and associated test data is missing in the pypi tarball.
    homepage = "https://pypi.python.org/pypi/deepTools/"
    url = "https://github.com/deeptools/deepTools/archive/3.3.0.tar.gz"

    version("3.5.2", sha256="4d8be1bafa1e8f54a26f5eaac54da6c6e50709f3a3a72a57cd96ac0f22c30383")
    version("3.3.0", sha256="a7aaf79fe939ca307fe6ec5e156750389fdfa4324bf0dd6bf5f53d5fda109358")
    version("3.2.1", sha256="dbee7676951a9fdb1b88956fe4a3294c99950ef193ea1e9edfba1ca500bd6a75")
    version("2.5.2", sha256="16d0cfed29af37eb3c4cedd9da89b4952591dc1a7cd8ec71fcba87c89c62bf79")

    depends_on("py-setuptools", type="build")
    depends_on("py-numpy@1.9.0:", type=("build", "run"))
    depends_on("py-scipy@0.17.0:", type=("build", "run"))
    depends_on("py-matplotlib@3.3.0:", when="@3.5.1:", type=("build", "run"))
    depends_on("py-matplotlib@2.1.2:", when="@:3.3.0", type=("build", "run"))
    depends_on("py-pysam@0.14.0:", type=("build", "run"))
    depends_on("py-numpydoc@0.5:", type=("build", "run"))
    depends_on("py-pybigwig@0.2.1:", type=("build", "run"))
    depends_on("py-py2bit@0.2.0:", type=("build", "run"))
    depends_on("py-plotly@4.9:", when="@3.5.1:", type=("build", "run"))
    depends_on("py-plotly@2.0.0:", when="@:3.5.0", type=("build", "run"))
    depends_on("py-deeptoolsintervals@0.1.8:", type=("build", "run"))

    def patch(self):
        # Add nosetest hook for "python setup.py test" argument.
        filter_file(
            r"^setup\(",
            r"""setup(
    tests_require='nose',
    test_suite='nose.collector',""",
            "setup.py",
        )