setup.py

"""Install file for RADIS.

Typical install procedure, plus:

- auto-convert README.rst to long_description, removing some sphinx-only syntax
so it can be rendered by PyPi
- read version number from __version__.txt
- some dependencies should be installed manually (typically: all packages with
compiled components such as numpy, pandas, etc.)


Examples
--------

Install (normal, use-only)::

    python setup.py install

Or (create an alias, so you can still edit)::

    python setup.py develop

Notes
-----

For developers:

when creating a new version, just update the __version__.txt file

to register it on Pypi see register.py::

    python register.py
"""
import io
import re
import sys
from os.path import abspath, dirname, exists, join

from numpy import get_include
from setuptools import Extension, find_packages, setup

# Build description from README (PyPi compatible)
# -----------------------------------------------

# Utils to format RST
def yield_sphinx_only_markup(lines):
    """Cleans-up Sphinx-only constructs (ie from README.rst), so that *PyPi*
    can format it properly.

    To check for remaining errors, install ``sphinx`` and run::

        python setup.py --long-description | sed -file 'this_file.sed' | rst2html.py  --halt=warning

    :param file_inp:     a `filename` or ``sys.stdin``?
    :param file_out:     a `filename` or ``sys.stdout`?`

    References
    ----------

    https://stackoverflow.com/questions/16367770/my-rst-readme-is-not-formatted-on-pypi-python-org

    Notes
    -----

    Check output with::

        python setup.py --long-description | rst2html.py > output.html
    """
    substs = [
        ## Selected Sphinx-only Roles.
        #
        (r":abbr:`([^`]+)`", r"\1"),
        (r":ref:`([^`]+)`", r"`\1`_"),
        (r":term:`([^`]+)`", r"**\1**"),
        (r":dfn:`([^`]+)`", r"**\1**"),
        (r":(samp|guilabel|menuselection):`([^`]+)`", r"``\2``"),
        ## Sphinx-only roles:
        #        :foo:`bar`   --> foo(``bar``)
        #        :a:foo:`bar` XXX afoo(``bar``)
        #
        # (r'(:(\w+))?:(\w+):`([^`]*)`', r'\2\3(``\4``)'),
        (r":(\w+):`([^`]*)`", r"\1(``\2``)"),
        ## Sphinx-only Directives.
        #
        (r"\.\. doctest", r"code-block"),
        (r"\.\. plot::", r".. "),
        (r"\.\. seealso", r"info"),
        (r"\.\. glossary", r"rubric"),
        (r"\.\. figure::", r".. "),
        ## Other
        #
        (r"\|version\|", r"x.x.x"),
        ## added to make RADIS docs Pypi compatible
        #        (r'\.\. image::',          r'.. '),
        #        (r'\.\. |CO2| replace:: CO\ :sub:`2`',          r'.. '),
    ]

    regex_subs = [(re.compile(regex, re.IGNORECASE), sub) for (regex, sub) in substs]

    def clean_line(line):
        try:
            for (regex, sub) in regex_subs:
                line = regex.sub(sub, line)
        except Exception as ex:
            print(("ERROR: %s, (line(%s)" % (regex, sub)))
            raise ex

        return line

    for line in lines:
        yield clean_line(line)


# (note: README.rst has been converted to README.md by register.py, and cleaned afterwards )
description = "A fast line-by-line code for high-resolution infrared molecular spectra"
readme_path = join(abspath(dirname(__file__)), "README.md")
if not exists(readme_path):
    long_description = description
else:
    with io.open(readme_path, encoding="utf-8") as f:
        long_description = f.read()

# Read version number from file
with open(join(dirname(__file__), "radis", "__version__.txt")) as version_file:
    __version__ = version_file.read().strip()


# %% Cython extensions:
# Ensures RADIS still builds if without Cython


class BuildFailed(Exception):
    pass


from distutils.errors import CCompilerError, DistutilsExecError, DistutilsPlatformError


def show_message(*lines):
    """Note : will only happen if user installs with `pip install -v`"""
    print("=" * 74, file=sys.stderr)
    for line in lines:
        print(line, file=sys.stderr)
    print("=" * 74, file=sys.stderr)


def get_ext_modules(with_binaries):
    """
    Parameters
    ----------
    with_binaries: bool
        if False, do not try to build Cython extensions
    """
    # Based on code from https://github.com/pallets/markupsafe/blob/main/setup.py

    print(sys.version)
    ext_modules = []
    cmdclass = {}

    if not with_binaries:
        # skip building extensions
        return {"cmdclass": cmdclass, "ext_modules": ext_modules}

    # TO-DO: set language level

    try:
        import cython
    except (ModuleNotFoundError) as err:
        raise BuildFailed(
            "Cython not found : Skipping all Cython extensions...!"
        ) from err

    print("Cython " + cython.__version__)

    from Cython.Distutils import build_ext

    class build_ext_subclass(build_ext):
        def build_extensions(self):
            c = self.compiler.compiler_type
            copt = {
                "msvc": ["/openmp", "/Ox", "/fp:fast", "/favor:INTEL64"],
                "mingw32": ["-fopenmp", "-O3", "-ffast-math", "-march=native"],
            }

            lopt = {"mingw32": ["-fopenmp"]}

            print("Compiling with " + c + "...")
            try:
                for e in self.extensions:
                    e.extra_compile_args = copt[c]
            except (KeyError):
                pass
            try:
                for e in self.extensions:
                    e.extra_link_args = lopt[c]
            except (KeyError):
                pass
            try:
                build_ext.build_extensions(self)
            except (CCompilerError, DistutilsExecError, DistutilsPlatformError) as err:
                raise BuildFailed() from err

    ext_modules.append(
        Extension(
            "radis_cython_extensions",
            sources=[
                "./radis/cython/radis_cython_extensions.pyx",
                "./radis/lbl/gpu.cpp",
            ],
            include_dirs=[get_include()],
            language="c++",
            extra_link_args=[],
            define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],
        )
    )

    cmdclass["build_ext"] = build_ext_subclass

    return {"cmdclass": cmdclass, "ext_modules": ext_modules}


#%% Main install routine
def run_setup(with_binary):
    setup(
        name="radis",
        version=__version__,
        description=description,
        long_description=long_description,
        long_description_content_type="text/markdown",
        url="https://github.com/radis/radis",
        author="Erwan Pannier",
        author_email="erwan.pannier@gmail.com",
        license="GNU Lesser General Public License v3 (LGPLv3)",
        keywords=[
            "spectrum",
            "infrared",
            "spectra",
            "radiation",
            "nonequilibrium",
            "spectroscopy",
            "molecules",
            "HITRAN",
            "hitemp",
            "exomol",
            "line-by-line",
        ],
        packages=find_packages(),
        install_requires=[
            "astropy",  # Unit aware calculations
            "astroquery>=0.3.9",  # to fetch HITRAN databases
            "beautifulsoup4",  # parse ExoMol website
            "configparser",
            "cython",
            "hitran-api",
            "lxml",  # parser used for ExoMol website
            "numpy<=1.22.3 ",
            "matplotlib",  # ">=3.4.0" to suppress the Ruler warning, but only available for Python >= 3.7
            "habanero",  # CrossRef API to retrieve data from doi
            "h5py",  # HDF5
            "hjson",
            "ipython>=7.0.0",
            "joblib",  # for parallel loading of SpecDatabase
            "json-tricks>=3.15.0",  # to deal with non jsonable formats
            "pandas>=1.0.5",
            "plotly>=2.5.1",
            "progressbar2",  # used in vaex
            "numba",
            "mpldatacursor",
            "publib>=0.3.2",  # Plotting styles for Matplotlib
            "plotly>=2.5.1",  # for line survey HTML output
            "peakutils",
            "termcolor",
            "tables",  # for pandas to HDF5 export
            "pytest",  # to run test suite
            "numba",  # just-in-time compiler
            "psutil",  # for getting user RAM
            "seaborn",  # other matplotlib themes
            "scipy>=1.4.0",
            # "tuna",  # to generate visual/interactive performance profiles
            "vaex>=4.9.2",  # load HDF5 files  (version needed to fix https://github.com/radis/radis/issues/486). #TODO : install only required sub-packages
        ],
        extras_require={
            "dev": [
                "numpydoc",  # for Jedi (autocompletion) to recognize
                "black>=20.8b1",  # for code-linting in accordance to PEP8
                "isort",  # for sorting imports
                "pre-commit",  # to enforce Black before each commit
            ]
        },
        classifiers=[
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
            "Topic :: Scientific/Engineering",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9",
            "Operating System :: OS Independent",
        ],
        **get_ext_modules(with_binary),
        include_package_data=True,  # add non .py data files in MANIFEST.in
        # package_data={'radis': ['radis/phys/units.txt']},
        zip_safe=False,  # impossible as long as we have external files read with __file__ syntax
        platforms="any",
    )


# %% Run Main install routine
try:
    run_setup(with_binary=True)
except BuildFailed:
    import traceback

    traceback.print_exc()
    show_message(
        "WARNING: RADIS C-extension could not be compiled, speedups",
        " are not enabled.",
        "Failure information, if any, is above.",
        "Retrying the build without the C extension now.",
    )
    run_setup(with_binary=False)
    show_message(
        "WARNING: RADIS C-extension could not be compiled, speedups"
        " are not enabled.",
        "Plain-Python build succeeded.",
    )