setup.py

#!/usr/bin/env python
# -*- coding: UTF-8 -*-
'''
=========================================================
Primer3-py: simple oligo analysis and primer design
=========================================================

**Primer3-py** is a collection of Python bindings for a derivative of the
popular Primer3 C library (version 2.6.1).

See README.md and http://libnano.github.io/primer3-py for more information
and primer3_test.py for usage examples.

Installation
------------

**Primer3-py** has no external runtime library dependencies and should compile
on easily most Linux and MacOS systems that are running Python 3.8 - 3.13.
Windows compilation is also generally easy.

To install from PyPI::

  $ pip install primer3-py

To install from local source::

  $ pip install .

For development installation (editable mode)::

  $ pip install -e .

To build distribution packages::

  $ python -m build

This will create both wheel and source distribution in the dist/ directory.
'''

import os
import shutil
import subprocess
import sys
from distutils import log as setup_log
from os.path import join as pjoin
from os.path import relpath as rpath

from setuptools import (
    Extension,
    setup,
)
from setuptools.command import (
    build_clib,
    install_lib,
    sdist,
)
from setuptools.command.build_ext import build_ext as _build_ext

# Read long description from README.md
with open('README.md', encoding='utf-8') as fd:
    LONG_DESCRIPTION = fd.read()

# Platform-dependent binary for `make` commands
WINDOWS_OS = sys.platform == 'win32'
MAKE_BIN = 'mingw32-make' if WINDOWS_OS else 'make'
# Indicates whether the Primer3 library has been built during install
P3_BUILT = False

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Package paths ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #

PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
MODULE_PATH = pjoin(PACKAGE_PATH, 'primer3')
SRC_PATH = pjoin(MODULE_PATH, 'src')
TESTS_PATH = pjoin(MODULE_PATH, 'tests')
LIBPRIMER3_PATH = pjoin(SRC_PATH, 'libprimer3')
THERMO_PARAMS_PATH = pjoin(LIBPRIMER3_PATH, 'primer3_config')
KLIB_PATH = pjoin(LIBPRIMER3_PATH, 'klib')

LIBPRIMER3_C_FPS = [
    rpath(pjoin(LIBPRIMER3_PATH, 'dpal.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'oligotm.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'p3_seq_lib.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'read_boulder.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal_parameters.c')),
]

LIBPRIMER3_C_FPS_FLEX = [
    rpath(pjoin(LIBPRIMER3_PATH, 'dpal.c')),
    # rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3flex.c')),  # primer3-py new
    rpath(pjoin(LIBPRIMER3_PATH, 'oligotm.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'p3_seq_lib.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'read_boulder.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thalflex.c')),        # primer3-py new
    rpath(pjoin(LIBPRIMER3_PATH, 'thal_parameters.c')),
]

LIBPRIMER3_H_FPS = [
    rpath(pjoin(LIBPRIMER3_PATH, 'amplicontm.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'dpal.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'format_output.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3flex.h')),   # primer3-py new
    rpath(pjoin(LIBPRIMER3_PATH, 'masker.h')),           # masker.h is required
    rpath(pjoin(LIBPRIMER3_PATH, 'oligotm.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'p3_seq_lib.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'print_boulder.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'read_boulder.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal.h')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thalflex.h')),            # primer3-py new
    rpath(pjoin(LIBPRIMER3_PATH, 'thalflexsignatures.h')),  # primer3-py new
    rpath(pjoin(LIBPRIMER3_PATH, 'thal_parameters.h')),
]

LIBPRIMER3_C_EXTRA_FPS = [
    rpath(pjoin(LIBPRIMER3_PATH, 'amplicontm.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'format_output.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'print_boulder.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal_parameters.c')),

    rpath(pjoin(LIBPRIMER3_PATH, 'amplicontm_main.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'masker_main.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'long_seq_tm_test_main.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'oligotm_main.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'primer3_boulder_main.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal.c')),
    rpath(pjoin(LIBPRIMER3_PATH, 'thal_main.c')),

    rpath(pjoin(LIBPRIMER3_PATH, 'MAKEFILE')),
]

KLIB_H_FPS = [
    rpath(pjoin(KLIB_PATH, 'khash.h')),
]

LIBPRIMER3_BINARIES = [
    'amplicon3_core',
    'oligotm',
    'ntdpal',
    'ntthal',
    'primer3_core',
]

if WINDOWS_OS:
    LIBPRIMER3_BINARIES = [bin_fn + '.exe' for bin_fn in LIBPRIMER3_BINARIES]
else:
    LIBPRIMER3_C_FPS.append(rpath(pjoin(LIBPRIMER3_PATH, 'masker.c')))
    LIBPRIMER3_C_FPS_FLEX.append(rpath(pjoin(LIBPRIMER3_PATH, 'masker.c')))
    LIBPRIMER3_BINARIES.append('primer3_masker')

LIBPRIMER3_BINARY_FPS = [
    pjoin(LIBPRIMER3_PATH, fn) for fn in LIBPRIMER3_BINARIES
]

LIBPRIMER3_THERMO_PARAMS_FPS = [
    rpath(pjoin(root, fp), MODULE_PATH) for root, _, fps in
    os.walk(THERMO_PARAMS_PATH) for fp in fps
]

LIBPRIMER3_TEST_FPS = [
    rpath(pjoin(root, fp), MODULE_PATH) for root, _, fps in
    os.walk(TESTS_PATH) for fp in fps
]

PACKAGE_FPS = (
    LIBPRIMER3_THERMO_PARAMS_FPS +
    LIBPRIMER3_TEST_FPS +
    LIBPRIMER3_C_FPS_FLEX +
    LIBPRIMER3_C_EXTRA_FPS +
    LIBPRIMER3_H_FPS +
    KLIB_H_FPS +
    ['p3helpers.pyx', 'p3helpers.h'] +
    ['thermoanalysis.pxd', 'thermoanalysis.pxi', 'thermoanalysis.pyx']
)

# ~~~~~~~~~~~~~~~~~~~~~ Primer3 C library build helpers ~~~~~~~~~~~~~~~~~~~~~ #


def p3Clean():
    '''
    Run `make clean` for libprimer3 in a platform-dependent manner
    '''
    proc = subprocess.Popen(
        f'{MAKE_BIN} clean',
        shell=True,
        cwd=LIBPRIMER3_PATH,
    )
    proc.wait()


def p3Build():
    '''
    Run `make clean && make` for libprimer3 in a platform-dependent manner
    '''
    proc = subprocess.Popen(
        f'{MAKE_BIN} all TESTOPTS=--windows' if WINDOWS_OS else f'{MAKE_BIN}',
        shell=True,
        cwd=LIBPRIMER3_PATH,
    )
    proc.wait()


# Insure that the copied binaries are executable
def makeExecutable(fp):
    '''
    Adds the executable bit to the file at filepath `fp`
    '''
    mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
    setup_log.info('Adding executable bit to %s (mode is now %o)', fp, mode)
    os.chmod(fp, mode)


class CustomInstallLib(install_lib.install_lib):
    '''
    Custom library installer to ensure that libprimer3 binaries are installed
    and made executable.

    Installed and invoked internally by `setuptools`/`distutils`
    '''

    def run(self):
        global P3_BUILT
        super().run()
        if not P3_BUILT:
            p3Clean()
            p3Build()
            P3_BUILT = True
        binary_dest_fps = [
            pjoin(
                self.install_dir,
                'primer3',
                'src',
                'libprimer3',
                fn,
            ) for fn in LIBPRIMER3_BINARIES
        ]
        for src_fp, dest_fp in zip(LIBPRIMER3_BINARY_FPS, binary_dest_fps):
            shutil.copyfile(src_fp, dest_fp)
            makeExecutable(dest_fp)


class CustomSdist(sdist.sdist):
    '''
    Custom sdist packager, ensures that libprimer3 build artifacts are removed
    prior to packaging.

    Installed and invoked internally by `setuptools`/`distutils`
    '''

    def run(self):
        global P3_BUILT
        # Clean up the primer3 build prior to sdist command to remove
        # binaries and object/library files
        p3Clean()
        P3_BUILT = False

        # Remove the build Cython artifact
        try:
            os.remove(os.path.join(MODULE_PATH, 'thermoanalysis.c'))
        except FileNotFoundError:
            # support possibly not existing in CI
            pass
        super().run()


class CustomBuildClib(build_clib.build_clib):
    '''
    Custom C library builder, ensures that libprimer3 is built prior to C
    library builds.

    Installed and invoked internally by `setuptools`/`distutils`
    '''

    def run(self):
        global P3_BUILT
        # Build primer3 prior to building the extension, if not already built
        if not P3_BUILT:
            p3Clean()
            p3Build()
            P3_BUILT = True
        super().run()


class CustomBuildExt(_build_ext):
    """Custom build_ext command that ensures primer3 binaries are built."""

    def run(self):
        global P3_BUILT
        if not P3_BUILT:
            p3Clean()
            p3Build()
            P3_BUILT = True
        super().run()


# ~~~~~~~~~~~~~~~~~~~~~~ Cython / C API extension setup ~~~~~~~~~~~~~~~~~~~~~ #

if WINDOWS_OS:
    EXTRA_COMPILE_ARGS = ['']
else:
    EXTRA_COMPILE_ARGS = [
        '-Wno-error=declaration-after-statement',
        '-Wno-unused-function',
    ]

cython_extensions = [
    Extension(
        'primer3.p3helpers',
        sources=[pjoin('primer3', 'p3helpers.pyx')],
        include_dirs=[MODULE_PATH],
        extra_compile_args=EXTRA_COMPILE_ARGS,
    ),
    Extension(
        'primer3.thermoanalysis',
        sources=(
            [pjoin('primer3', 'thermoanalysis.pyx')] + LIBPRIMER3_C_FPS_FLEX
        ),
        include_dirs=[SRC_PATH, LIBPRIMER3_PATH, KLIB_PATH],
        extra_compile_args=EXTRA_COMPILE_ARGS,
    ),
]

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #

# Ensure that libprimer3 is built prior to the `build_ext` or `install` cmds
if ('build_ext' in sys.argv or 'install' in sys.argv):
    if not P3_BUILT:
        p3Clean()
        p3Build()
        P3_BUILT = True


def try_cythonize(extension_list, *args, **kwargs):
    '''
    Light cythonize wrapper
    '''
    try:
        from Cython.Build import cythonize
    except (ImportError, ModuleNotFoundError):
        def cythonize(x, **kwargs):
            return x

    cython_compiler_directives = dict(
        # always_allow_keywords=False,
        # boundscheck=False,
        # embedsignature=False,
        # initializedcheck=False,
        # wraparound=False,
        language_level='3',
        c_string_encoding='utf-8',
    )

    return cythonize(
        extension_list,
        compiler_directives=cython_compiler_directives,
    )


setup(
    # Note: We intentionally ignore setuptools warnings about undeclared
    # packages in primer3/src/libprimer3/ and its subdirectories. These
    # directories contain C source code, headers, and configuration files -
    # they are not meant to be Python packages despite being potentially
    # importable by Python's rules. They are correctly handled as package
    # data via package_data.
    packages=['primer3'],
    ext_modules=try_cythonize(cython_extensions),
    package_data={'primer3': PACKAGE_FPS},
    cmdclass={
        'install_lib': CustomInstallLib,
        'sdist': CustomSdist,
        'build_clib': CustomBuildClib,
        'build_ext': CustomBuildExt,
    },
    install_requires=[],
    zip_safe=False,
    # Build configuration
    options={
        'build': {
            'build_base': 'build',
        },
    },
)