Use CMake as primary build system via scikit-build (#215)

* general except clause in module_available
* switched to scikit-build as build system
* update versioneer
* remove legacy dependency specifiers from setup.py
* use pytest xdist with 2 jobs

.gitignore

@@ -1,5 +1,6 @@
 .idea
 build
+_skbuild
 *.so
 *.egg-info
 cmake-build-*

CMakeLists.txt

@@ -1,13 +1,29 @@
-cmake_minimum_required(VERSION 3.9)
+cmake_minimum_required(VERSION 3.15...3.19)
 
 set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+set(DEEPTIME_VERSION "0.0.0" CACHE STRING "The version without commit offset. Defaults to 0.0.0")
+set(DEEPTIME_VERSION_INFO "0.0.0" CACHE STRING "The full version. Defaults to 0.0.0")
 set(DEEPTIME_BUILD_CPP_TESTS OFF CACHE BOOL "Whether to build the c++ unit tests")
 
 if(DEFINED PROJECT_NAME)
     set(DEEPTIME_IS_SUBPROJECT ON)
 endif()
-project(deeptime LANGUAGES C CXX VERSION 0.0.0)
+project(deeptime LANGUAGES C CXX VERSION ${DEEPTIME_VERSION})
+set(DEEPTIME_ROOT_DIRECTORY "${CMAKE_CURRENT_LIST_DIR}")
+
+if(SKBUILD)
+    # Scikit-Build does not add your site-packages to the search path
+    # automatically, so we need to add it _or_ the pybind11 specific directory
+    # here.
+    execute_process(
+            COMMAND "${PYTHON_EXECUTABLE}" -c
+            "import pybind11; print(pybind11.get_cmake_dir())"
+            OUTPUT_VARIABLE _tmp_dir
+            OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND_ECHO STDOUT)
+    list(APPEND CMAKE_PREFIX_PATH "${_tmp_dir}")
+endif()
 
 find_package(OpenMP 4)
 if(OpenMP_FOUND)
@@ -18,19 +34,32 @@ if(MSVC)
     add_compile_options(/W3 /EHsc /bigobj /permissive- /std:c++17)
 endif()
 
-find_package(pybind11 REQUIRED)
+# use cmake 3.12+ FindPython
+# find_package(Python COMPONENTS Interpreter Development)  # this doesn't work with conda, picks up the wrong python interpreter on OSX
+# now find pybind
+find_package(pybind11 REQUIRED CONFIG)
+
+function(register_pybind_module name)
+    cmake_parse_arguments(PARSE_ARGV 1 ARG "" "" "")
+    pybind11_add_module(${name} ${ARG_UNPARSED_ARGUMENTS})
+    target_link_libraries(${name} PUBLIC deeptime::deeptime)
+    if (OpenMP_FOUND)
+        target_link_libraries(${name} PUBLIC OpenMP::OpenMP_CXX)
+    endif()
+    file(RELATIVE_PATH REL_PATH "${DEEPTIME_ROOT_DIRECTORY}/deeptime" "${CMAKE_CURRENT_LIST_DIR}")
+    install(TARGETS ${name} DESTINATION ${REL_PATH})
+    if(NOT SKBUILD)
+        set_target_properties(${name} PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_LIST_DIR})
+    endif()
+endfunction()
 
 add_subdirectory(deeptime/src)
-add_subdirectory(deeptime/numeric/_bindings)
+add_subdirectory(deeptime/numeric)
 add_subdirectory(deeptime/data)
 add_subdirectory(deeptime/covariance/util/covar_c)
 add_subdirectory(deeptime/clustering)
 add_subdirectory(deeptime/basis)
-add_subdirectory(deeptime/markov/_bindings)
-add_subdirectory(deeptime/markov/hmm/_bindings)
-add_subdirectory(deeptime/markov/msm/tram/_bindings)
-add_subdirectory(deeptime/markov/tools/estimation/dense/_bindings)
-add_subdirectory(deeptime/markov/tools/estimation/sparse/_bindings)
+add_subdirectory(deeptime/markov)
 
 add_subdirectory(examples/clustering_custom_metric)
 

deeptime/__init__.py

@@ -1,5 +1,4 @@
 from ._version import get_versions
-
 __version__ = get_versions()['version']
 del get_versions