Update the project to use pyproject.toml

CMakeLists.txt

@@ -10,8 +10,8 @@ if(NOT ${CHFL_PY_INTERNAL_CHEMFILES})
     find_package(chemfiles CONFIG QUIET 0.9)
 endif()
 
-file(REMOVE ${CMAKE_BINARY_DIR}/external.py)
-file(REMOVE ${CMAKE_BINARY_DIR}/external.pyc)
+file(REMOVE ${PROJECT_SOURCE_DIR}/chemfiles/external.py)
+file(REMOVE ${PROJECT_SOURCE_DIR}/chemfiles/external.py)
 
 if(${chemfiles_FOUND})
     set(CHEMFILES_VERSION "${chemfiles_VERSION}")
@@ -25,10 +25,9 @@ if(${chemfiles_FOUND})
             "Define CHFL_PY_INTERNAL_CHEMFILES=ON to use use the internal chemfiles."
         )
     endif()
-    file(WRITE ${CMAKE_BINARY_DIR}/external.py
+    file(WRITE ${PROJECT_SOURCE_DIR}/chemfiles/external.py
         "EXTERNAL_CHEMFILES = \"${CHEMFILES_LOCATION}\"\n"
     )
-    install(FILES ${CMAKE_BINARY_DIR}/external.py DESTINATION ".")
 else()
     # Use the git submodule
     if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lib/CMakeLists.txt")
@@ -40,7 +39,12 @@ else()
 
     message(STATUS "Using internal chemfiles from ${CMAKE_CURRENT_SOURCE_DIR}/lib")
     set(BUILD_SHARED_LIBS ON CACHE BOOL "Build shared libraries instead of static ones" FORCE)
-    add_subdirectory(lib)
-    file(READ lib/VERSION CHEMFILES_VERSION)
-    string(STRIP ${CHEMFILES_VERSION} CHEMFILES_VERSION)
+    add_subdirectory(lib EXCLUDE_FROM_ALL)
+
+    add_custom_target(build_chemfiles ALL)
+    add_dependencies(build_chemfiles chemfiles)
+    install(TARGETS chemfiles
+        LIBRARY DESTINATION "chemfiles"
+        RUNTIME DESTINATION "chemfiles"
+    )
 endif()

MANIFEST.in

@@ -2,7 +2,6 @@ recursive-include chemfiles *
 recursive-include lib *
 prune lib/tests
 prune lib/doc
-include requirements.txt
 include CMakeLists.txt
 include README.md
 include LICENSE

chemfiles/.gitignore

@@ -1,3 +1,5 @@
-lib/
-include/
 external.py
+
+*.dylib
+*.so
+*.dll

chemfiles/clib.py

@@ -40,15 +40,15 @@ def __call__(self):
 def _lib_path():
     if EXTERNAL_CHEMFILES:
         return EXTERNAL_CHEMFILES
-    root = os.path.dirname(__file__)
+    root = os.path.abspath(os.path.dirname(__file__))
     if sys.platform.startswith("darwin"):
-        return os.path.join(root, "lib", "libchemfiles.dylib")
+        return os.path.join(root, "libchemfiles.dylib")
     elif sys.platform.startswith("linux"):
-        return os.path.join(root, "lib", "libchemfiles.so")
+        return os.path.join(root, "libchemfiles.so")
     elif sys.platform.startswith("win"):
         candidates = [
-            os.path.join(root, "bin", "libchemfiles.dll"),  # MinGW
-            os.path.join(root, "bin", "chemfiles.dll"),  # MSVC
+            os.path.join(root, "libchemfiles.dll"),  # MinGW
+            os.path.join(root, "chemfiles.dll"),  # MSVC
         ]
         for path in candidates:
             if os.path.isfile(path):

pyproject.toml

@@ -0,0 +1,22 @@
+[build-system]
+requires = ["setuptools", "wheel", "scikit-build"] #, "cmake", "ninja"]
+build-backend = "setuptools.build_meta"
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+skipsdist = True
+
+[testenv]
+; this is required on windows to ensure the compiler finds the standard lib
+; files (kernel32.lib, etc.) and headers
+passenv = LIB INCLUDE LIBPATH
+setenv =
+    CHFL_PY_INTERNAL_CHEMFILES = 1
+commands =
+    pip install -e .
+    discover -p "*.py" tests
+deps =
+    discover
+    numpy
+"""

scripts/clean.sh

@@ -10,6 +10,8 @@ rm -rf _skbuild
 rm -rf dist
 rm -rf MANIFEST
 rm -rf chemfiles.egg-info
-rm -rf chemfiles/lib
-rm -rf chemfiles/include
+
+rm -rf chemfiles/*.dylib
+rm -rf chemfiles/*.so
+rm -rf chemfiles/*.dll
 rm -rf chemfiles/external.py

setup.cfg

@@ -0,0 +1,31 @@
+[metadata]
+name = chemfiles
+long_description = file: README.md
+long_description_content_type = text/markdown
+
+license_files = LICENSE
+author = Guillaume Fraux
+author_email = [email protected]
+description = Read and write computational chemistry files
+keywords = chemistry computational cheminformatics files formats
+url = http://github.com/chemfiles/chemfiles.py
+classifiers =
+    Development Status :: 4 - Beta
+    Environment :: Console
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: BSD License
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft :: Windows
+    Operating System :: Unix
+    Programming Language :: Python :: 2
+    Programming Language :: Python :: 3
+    Topic :: Scientific/Engineering :: Chemistry
+    Topic :: Software Development :: Libraries :: Python Modules
+    Topic :: Utilities
+
+[options]
+zip_safe = False
+
+[bdist_wheel]
+universal = 1

setup.py

@@ -1,9 +1,17 @@
 # -*- coding=utf-8 -*-
-import chemfiles
-import sys
 from wheel.bdist_wheel import bdist_wheel
 from skbuild import setup
 
+import sys
+import os
+import re
+
+
+# Read the version from chemfiles/__init__.py without importing chemfiles
+__version__ = re.search(
+    r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]', open("chemfiles/__init__.py").read()
+).group(1)
+
 
 class universal_wheel(bdist_wheel):
     # Workaround until https://github.com/pypa/wheel/issues/185 is resolved
@@ -12,49 +20,48 @@ def get_tag(self):
         return ("py2.py3", "none") + tag[2:]
 
 
-with open("requirements.txt", "r") as fd:
-    requirements = list(filter(bool, (line.strip() for line in fd)))
-    if sys.hexversion >= 0x03040000:
-        requirements = list(filter(lambda r: r != "enum34", requirements))
+install_requires = ["numpy"]
+if sys.hexversion < 0x03040000:
+    install_requires.append("enum34")
+
 
+# scikit-build options
+cmake_args = []
+if sys.platform.startswith("darwin"):
+    cmake_args.append("-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9")
+
+if os.getenv("CHFL_PY_INTERNAL_CHEMFILES"):
+    cmake_args.append("-DCHFL_PY_INTERNAL_CHEMFILES=ON")
+
+
+def _get_lib_ext():
+    if sys.platform.startswith("win32"):
+        ext = ".dll"
+    elif sys.platform.startswith("darwin"):
+        ext = ".dylib"
+    elif sys.platform.startswith("linux"):
+        ext = ".so"
+    else:
+        raise Exception("Unknown operating system: %s" % sys.platform)
+    return ext
 
-long_description = ""
-with open("README.md", "r") as fd:
-    for line in fd:
-        # remove github badges
-        if not line.startswith("[!["):
-            long_description += line
 
 setup(
-    name="chemfiles",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    version=chemfiles.__version__,
-    author="Guillaume Fraux",
-    author_email="[email protected]",
-    description="Read and write chemistry trajectory files",
-    keywords="chemistry computational cheminformatics files formats",
-    url="http://github.com/chemfiles/chemfiles.py",
-    packages=["chemfiles"],
-    zip_safe=False,
-    install_requires=requirements,
-    setup_requires=["scikit-build"],
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "Environment :: Console",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: Unix",
-        "Programming Language :: Python :: 2",
-        "Programming Language :: Python :: 3",
-        "Topic :: Scientific/Engineering :: Chemistry",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-        "Topic :: Utilities",
-    ],
-    cmake_install_dir="chemfiles",
-    cmake_args=['-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9'],
+    version=__version__,
+    install_requires=install_requires,
     cmdclass={"bdist_wheel": universal_wheel},
+    # cmake_install_dir="chemfiles",
+    cmake_args=cmake_args,
+    packages=["chemfiles"],
+    package_data={
+        "chemfiles": [
+            "*" + _get_lib_ext(),
+            "bin/*" + _get_lib_ext(),
+        ]
+    },
+    exclude_package_data={
+        "chemfiles": [
+            "include/*",
+        ]
+    },
 )