Change the build system to use standard setup.py

This is way easier to do with scikit-build!

.gitignore

@@ -1 +1,7 @@
-build
+_skbuild/
+dist/
+chemfiles.egg-info/
+.tox/
+MANIFEST
+chemfiles/lib/
+chemfiles/include/

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "C++ library"]
-	path = chemfiles
+	path = lib
 	url = https://github.com/chemfiles/chemfiles

CMakeLists.txt

@@ -1,11 +1,6 @@
-cmake_minimum_required(VERSION 2.8.11)
-project(chemfiles.py)
+cmake_minimum_required(VERSION 2.8.12)
 
-set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake")
-cmake_policy(VERSION 2.8.11)
-
-option(CHFL_PY_CODE_COVERAGE "Enable python code coverage" OFF)
-option(CHFL_PY_BUILD_DOCUMENTATION "Build the python documentation" OFF)
+# set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake")
 option(CHFL_PY_INTERNAL_CHEMFILES "Use the internal version of chemfiles" OFF)
 
 if(NOT ${CHFL_PY_INTERNAL_CHEMFILES})
@@ -25,94 +20,16 @@ if(${chemfiles_FOUND})
     endif()
 else()
     # Use the git submodule
-    if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/chemfiles/CMakeLists.txt")
+    if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lib/CMakeLists.txt")
         message(FATAL_ERROR
             "The git submodule for chemfiles is not initalized.\n"
             "Please run `git submodule update --init."
         )
     endif()
 
-    message(STATUS "Using internal chemfiles from ${CMAKE_CURRENT_SOURCE_DIR}/chemfiles")
+    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(chemfiles)
-    file(READ chemfiles/VERSION CHEMFILES_VERSION)
+    add_subdirectory(lib)
+    file(READ lib/VERSION CHEMFILES_VERSION)
     string(STRIP ${CHEMFILES_VERSION} CHEMFILES_VERSION)
 endif()
-
-configure_file(
-  "${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in"
-  "${CMAKE_CURRENT_BINARY_DIR}/setup.py"
-)
-
-find_package(PythonInterp REQUIRED)
-set(SETUP_PY "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
-
-file(GLOB_RECURSE PYTHON_SRC src/chemfiles/**.py)
-set(SETUP_PY_BUILD_OUTPUT "")
-set(COPY_SRC_OUTPUT "")
-foreach(_file_ ${PYTHON_SRC})
-    file(RELATIVE_PATH _path_ ${CMAKE_CURRENT_SOURCE_DIR} ${_file_})
-    list(APPEND COPY_SRC_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${_path_})
-
-    file(RELATIVE_PATH _path_ ${CMAKE_CURRENT_SOURCE_DIR}/src/chemfiles ${_file_})
-    list(APPEND SETUP_PY_BUILD_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/build/lib/${_path_})
-endforeach()
-
-add_custom_command(
-    OUTPUT ${COPY_SRC_OUTPUT}
-    COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_CURRENT_BINARY_DIR}/src/
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src/ ${CMAKE_CURRENT_BINARY_DIR}/src/
-    DEPENDS ${PYTHON_SRC}
-    COMMENT "Copying python sources"
-)
-
-# We configure the same file twice: the one in `build/lib` will be the one
-# installed, and the one in `src/chemfiles` will be used for testing.
-add_custom_command(
-    OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/src/chemfiles/location.py"
-    COMMAND ${CMAKE_COMMAND}
-            -DLOCATION_PY_PATH=${CMAKE_CURRENT_BINARY_DIR}/src/
-            -DCHEMFILES_LOCATION=$<TARGET_FILE:chemfiles>
-            -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake/generate_location.cmake
-    COMMENT "Generating test location.py"
-)
-
-add_custom_command(
-    OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/build/lib/chemfiles/location.py"
-    COMMAND ${CMAKE_COMMAND}
-            -DLOCATION_PY_PATH=${CMAKE_CURRENT_BINARY_DIR}/build/lib
-            -DCHEMFILES_LOCATION=${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/$<TARGET_FILE_NAME:chemfiles>
-            -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake/generate_location.cmake
-    COMMENT "Generating install location.py"
-)
-
-add_custom_target(location.py ALL
-    DEPENDS ${COPY_SRC_OUTPUT}
-    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/src/chemfiles/location.py
-    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/build/lib/chemfiles/location.py
-)
-
-add_custom_command(
-    OUTPUT ${SETUP_PY_BUILD_OUTPUT}
-    COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} build
-    DEPENDS location.py
-    COMMENT "Running python setup.py build"
-)
-
-set(ADDITIONAL_CLEANUP "${CMAKE_CURRENT_BINARY_DIR}/build/")
-if(NOT "${CMAKE_CURRENT_BINARY_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
-    set(ADDITIONAL_CLEANUP "${ADDITIONAL_CLEANUP};${CMAKE_CURRENT_BINARY_DIR}/src/")
-endif()
-set_property(DIRECTORY PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${ADDITIONAL_CLEANUP})
-
-add_custom_target(chemfiles.py ALL DEPENDS ${SETUP_PY_BUILD_OUTPUT})
-add_dependencies(chemfiles.py chemfiles)
-
-install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} install --prefix=${CMAKE_INSTALL_PREFIX})")
-
-enable_testing()
-add_subdirectory(tests)
-
-if(${CHFL_PY_BUILD_DOCUMENTATION})
-    add_subdirectory(doc)
-endif()

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include chemfiles *
+recursive-include lib *
+include requirements.txt

README.md

@@ -25,31 +25,21 @@ conda install -c conda-forge chemfiles
 ### Source compilation
 
 You can install this python module from sources if you have all the
-[dependencies][installation] of the C++ chemfiles library installed on your
-computer.
+[dependencies] of the C++ chemfiles library installed on your computer.
 
 ```bash
 # To get the latest developement version:
 git clone https://github.com/chemfiles/chemfiles.py
 cd chemfiles.py
 git submodule update --init
-mkdir build
-cd build
-cmake .. <options>  # see below for configuration options.
-make
-# Optionally
-make test
-make install
+# Install developement dependencies
+pip install -r dev-requirements.txt
+pip install .
+# Optionally run the test suite
+tox
 ```
 
-You can use the same [configuration options][installation] as the C++ chemfiles
-library. Additionally, you may also want to specify which python interpreter and
-installation to use with `-DPYTHON_EXECUTABLE=/full/path/to/python`, and where
-to install the code with `-DCMAKE_INSTALL_PREFIX=<PREFIX>`. The C++ library will
-be installed to `PREFIX/lib/`; and the python code will be installed in
-`PREFIX/lib/python<x.y>/site-packages/`.
-
-[installation]: http://chemfiles.readthedocs.org/en/latest/installation.html
+[dependencies]: http://chemfiles.readthedocs.org/en/latest/installation.html
 
 ## Usage example
 

src/chemfiles/__init__.py → chemfiles/__init__.py

@@ -11,10 +11,4 @@
 from .selection import Selection
 from .property import Property
 
-# Setup work
-from .utils import _set_default_warning_callback
-from .clib import _get_c_library
-_set_default_warning_callback()
-
-__version__ = _get_c_library().chfl_version().decode("utf8")
-assert(__version__.startswith("0.8"))
+__version__ = "0.8.0"

src/chemfiles/clib.py → chemfiles/clib.py

@@ -1,31 +1,18 @@
 # -* coding: utf-8 -*
 import os
 import sys
-import struct
 from ctypes import cdll, c_double, POINTER
 from ctypes import sizeof, c_voidp
 
-from .location import CHEMFILES_LOCATION, __file__ as location_file_path
-
 
 class FindChemfilesLibrary(object):
     def __init__(self):
         self._cache = None
 
     def __call__(self):
         if self._cache is None:
-            check_dll(CHEMFILES_LOCATION)
-            try:
-                self._cache = cdll.LoadLibrary(CHEMFILES_LOCATION)
-            except OSError:
-                if location_file_path.endswith(".pyc"):
-                    path = location_file_path[:-1]
-                else:
-                    path = location_file_path
-                raise ImportError(
-                    "Could not find chemfiles c++ library. " +
-                    "Please check the path defined in " + path
-                )
+            path = _lib_path()
+            self._cache = cdll.LoadLibrary(path)
 
             from .ffi import set_interface
             from .ffi import CHFL_FRAME, CHFL_ATOM, chfl_vector3d
@@ -36,15 +23,33 @@ def __call__(self):
                 POINTER(CHFL_FRAME), POINTER(CHFL_ATOM),
                 chfl_vector3d, POINTER(c_double)
             ]
+
+            from .utils import _set_default_warning_callback
+            _set_default_warning_callback()
         return self._cache
 
 
-def check_dll(path):
-    if not sys.platform.startswith("win"):
-        return
-    if not os.path.isfile(path):
-        return
+def _lib_path():
+    root = os.path.dirname(__file__)
+    if sys.platform.startswith("darwin"):
+        return os.path.join(root, "lib", "libchemfiles.dylib")
+    elif sys.platform.startswith("linux"):
+        return os.path.join(root, "lib", "libchemfiles.so")
+    elif sys.platform.startswith("win"):
+        candidates = [
+            os.path.join(root, "bin", "libchemfiles.dll"),  # MinGW
+            os.path.join(root, "bin", "chemfiles.dll"),     # MSVC
+        ]
+        for path in candidates:
+            if os.path.isfile(path):
+                _check_dll(path)
+                return path
+        raise ImportError("Could not find chemfiles DLL")
+    else:
+        raise ImportError("Unknown platform. Please edit this file")
+
 
+def _check_dll(path):
     import struct
 
     IMAGE_FILE_MACHINE_I386 = 332