Remove dependency on skbuild and switch to a src layout

doc/conf.py

@@ -5,35 +5,33 @@
 
 ROOT = os.path.abspath(os.path.dirname(__file__))
 sys.path.insert(1, ROOT)
-sys.path.insert(1, os.path.join(ROOT, ".."))
+sys.path.insert(1, os.path.join(ROOT, "..", "src"))
 
 # -- General configuration ------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'htmlhidden'
-]
-autoclass_content = 'both'
+extensions = ["sphinx.ext.autodoc", "htmlhidden"]
+autoclass_content = "both"
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'Python interface to chemfiles'
-copyright = u'2015-2017, Guillaume Fraux — BSD license'
+project = "Python interface to chemfiles"
+copyright = "2015-2017, Guillaume Fraux — BSD license"
 
 
 def version():
     import chemfiles
-    full_version = chemfiles.__version__.split('-')
+
+    full_version = chemfiles.__version__.split("-")
     release = full_version[0]
-    version = '.'.join(release.split('.')[0:2])
+    version = ".".join(release.split(".")[0:2])
     if len(full_version) > 1:
         # Developement release
         release += "-dev"
@@ -48,29 +46,27 @@ def version():
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'bootstrap'
+html_theme = "bootstrap"
 html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = [os.path.join(ROOT, "templates")]
 
 html_theme_options = {
-    'navbar_site_name': "Navigation",
-    'navbar_pagenav': False,
-    'source_link_position': None,
-    'bootswatch_theme': "flatly",
-    'bootstrap_version': "3",
+    "navbar_site_name": "Navigation",
+    "navbar_pagenav": False,
+    "source_link_position": None,
+    "bootswatch_theme": "flatly",
+    "bootstrap_version": "3",
 }
 
-html_sidebars = {
-    '**': ['sidebar-toc.html', 'searchbox.html']
-}
+html_sidebars = {"**": ["sidebar-toc.html", "searchbox.html"]}
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'chemfiles.py'
+htmlhelp_basename = "chemfiles.py"

pyproject.toml

@@ -2,7 +2,8 @@
 requires = [
     "setuptools >=44",
     "wheel >=0.36",
-    "scikit-build >=0.11"
+    "ninja",
+    "cmake",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -17,12 +18,15 @@ skipsdist = True
 passenv = LIB INCLUDE LIBPATH
 setenv =
     CHFL_PY_INTERNAL_CHEMFILES = 1
+
 commands =
-    pip install -e . --verbose
-    coverage run -m unittest discover -s tests -p "*.py"
-    coverage xml --include="chemfiles/*" -o .tox/coverage.xml
+    python setup.py install
+    coverage run --source=chemfiles -m unittest discover -s tests -p "*.py"
+    coverage xml -o .tox/coverage.xml
+
 deps =
-    discover
+    ninja
+    cmake
     coverage
     numpy
 """

scripts/check-used-functions.py

@@ -4,8 +4,8 @@
 effectively used in the chemfiles binding.
 """
 import os
-import sys
 import re
+import sys
 
 IGNORED = ["chfl_version", "chfl_trajectory_open"]
 ERROR = False
@@ -20,7 +20,7 @@ def error(message):
 
 def functions_list():
     functions = []
-    with open(os.path.join(ROOT, "chemfiles", "ffi.py")) as fd:
+    with open(os.path.join(ROOT, "src", "chemfiles", "_c_api.py")) as fd:
         for line in fd:
             line = line.strip()
             if line.startswith("# Function"):
@@ -31,9 +31,9 @@ def functions_list():
 
 def read_all_binding_functions():
     binding_functions = set()
-    for (dirpath, _, paths) in os.walk(os.path.join(ROOT, "chemfiles")):
+    for (dirpath, _, paths) in os.walk(os.path.join(ROOT, "src", "chemfiles")):
         for path in paths:
-            if path != "ffi.py" and path.endswith(".py"):
+            if path != "_c_api.py" and path.endswith(".py"):
                 with open(os.path.join(ROOT, dirpath, path)) as fd:
                     file_functions = re.findall(r"(chfl_[a-z A-Z 0-9 _]*)\(", fd.read())
                     binding_functions.update(file_functions)

setup.cfg

@@ -26,6 +26,12 @@ classifiers =
 
 [options]
 zip_safe = False
+packages=find:
+package_dir=
+    =src
+
+[options.packages.find]
+where = src
 
 [bdist_wheel]
 universal = 1

setup.py

@@ -1,18 +1,25 @@
 # -*- coding=utf-8 -*-
-from wheel.bdist_wheel import bdist_wheel
-from skbuild import setup
-
-import site
-import sys
 import os
 import re
+import site
+import subprocess
+import sys
+
+import cmake
+import ninja
+from setuptools import Extension, setup
+from wheel.bdist_wheel import bdist_wheel
+
+from distutils.command.build_ext import build_ext  # type: ignore   isort: skip
+from distutils.command.install import install as distutils_install  # type: ignore   isort: skip
 
 # workaround https://github.com/pypa/pip/issues/7953
 site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
 
 # Read the version from chemfiles/__init__.py without importing chemfiles
+ROOT = os.path.realpath(os.path.dirname(__file__))
 __version__ = re.search(
-    r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]', open("chemfiles/__init__.py").read()
+    r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]', open("src/chemfiles/__init__.py").read()
 ).group(1)
 
 
@@ -23,18 +30,53 @@ def get_tag(self):
         return ("py2.py3", "none") + tag[2:]
 
 
-install_requires = ["numpy"]
-if sys.hexversion < 0x03040000:
-    install_requires.append("enum34")
+class cmake_ext(build_ext):
+    """
+    Build the native library using cmake
+    """
 
+    def run(self):
+        source_dir = ROOT
+        build_dir = os.path.join(ROOT, "build", "cmake-build")
+        install_dir = os.path.join(os.path.realpath(self.build_lib))
 
-# scikit-build options
-cmake_args = []
-if sys.platform.startswith("darwin"):
-    cmake_args.append("-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9")
+        try:
+            os.makedirs(build_dir)
+        except OSError:
+            pass
+
+        cmake_executable = os.path.join(cmake.CMAKE_BIN_DIR, "cmake")
+        ninja_executable = os.path.join(ninja.BIN_DIR, "ninja")
+        cmake_options = [
+            "-GNinja",
+            f"-DCMAKE_MAKE_PROGRAM={ninja_executable}",
+            f"-DCMAKE_INSTALL_PREFIX={install_dir}",
+            "-DCMAKE_BUILD_TYPE=Release",
+            "-DBUILD_SHARED_LIBS=ON",
+        ]
+
+        if sys.platform.startswith("darwin"):
+            cmake_options.append("-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9")
+
+        if os.getenv("CHFL_PY_INTERNAL_CHEMFILES"):
+            cmake_options.append("-DCHFL_PY_INTERNAL_CHEMFILES=ON")
+
+        ninja_args = []
+
+        subprocess.run(
+            [cmake_executable, source_dir, *cmake_options],
+            cwd=build_dir,
+            check=True,
+        )
+        subprocess.run(
+            [cmake_executable, "--build", build_dir, "--target", "install"],
+            check=True,
+        )
 
-if os.getenv("CHFL_PY_INTERNAL_CHEMFILES"):
-    cmake_args.append("-DCHFL_PY_INTERNAL_CHEMFILES=ON")
+
+install_requires = ["numpy"]
+if sys.hexversion < 0x03040000:
+    install_requires.append("enum34")
 
 
 def _get_lib_ext():
@@ -52,14 +94,18 @@ def _get_lib_ext():
 setup(
     version=__version__,
     install_requires=install_requires,
-    cmdclass={"bdist_wheel": universal_wheel},
-    cmake_args=cmake_args,
-    packages=["chemfiles"],
-    package_data={
-        "chemfiles": [
-            "*" + _get_lib_ext(),
-            "bin/*" + _get_lib_ext(),
-        ]
+    ext_modules=[
+        # only declare the extension, it is built & copied as required by cmake
+        # in the build_ext command
+        Extension(name="chemfiles", sources=[]),
+    ],
+    cmdclass={
+        "build_ext": cmake_ext,
+        "bdist_wheel": universal_wheel,
+        # HACK: do not use the new setuptools install implementation, it tries
+        # to install the package with `easy_install`, which fails to resolve the
+        # freshly installed package and tries to load it from pypi.
+        "install": distutils_install,
     },
     exclude_package_data={
         "chemfiles": [