Fix many issues in deployment process

* Fix conflicting folder name between python package and fcl dependency
* Move to `src/module` tree schema
* Fix `setup.cfg` options
* Merge clone and build bash scripts for clarity (future mac/win builds)

Author: CyrilWaechter

.gitignore

@@ -25,6 +25,7 @@ wheels/
 .installed.cfg
 *.egg
 MANIFEST
+deps/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

MANIFEST.in

@@ -0,0 +1,41 @@
+mkdir -p deps
+cd deps
+get eigen
+curl -OL https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz
+tar -zxf eigen-3.3.9.tar.gz
+
+rm -rf libccd
+git clone --depth 1 --branch v2.1 https://github.com/danfis/libccd.git
+
+rm -rf octomap 
+git clone --depth 1 --branch v1.8.0 https://github.com/OctoMap/octomap.git
+
+rm -rf fcl
+git clone --depth 1 --branch v0.6.1 https://github.com/flexible-collision-library/fcl.git
+
+echo "Install eigen"
+cmake -B build -S eigen-3.3.9
+cmake --install build
+
+echo "Build and install libccd"
+cd libccd
+cmake .
+make -j4
+make install
+cd ..
+
+echo "Build and install octomap"
+cd octomap 
+cmake .
+make -j4
+make install
+cd ..
+
+echo "Build and install fcl"
+cd fcl
+cmake .
+make -j4
+make install
+cd ..
+
+cd ..

requirements/Dockerfile build_dependencies/Dockerfilerequirements/Dockerfile renamed to build_dependencies/Dockerfile

@@ -3,7 +3,7 @@ requires = ["setuptools", "wheel", "numpy", "Cython"]
 build-backend = "setuptools.build_meta"
 
 [tool.cibuildwheel]
-before-all = "bash requirements/clone.bash && bash requirements/build.bash"
+before-all = "bash build_dependencies/install_linux.sh"
 before-build = "pip install numpy cython"
 manylinux-x86_64-image = "manylinux_2_24"
 test-requires = "pytest"

build_dependencies/install_linux.sh

@@ -24,10 +24,21 @@ classifiers =
     Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
 keywords = fcl collision distance
-packages = fcl
+
+[options]
+include_package_data = True
+package_dir =
+    = src
+packages = find:
 setup_requires =
     numpy
     Cython
 install_requires =
     numpy
     Cython
+
+[options.package_data]
+* = *.pyx, *.pxd
+
+[options.packages.find]
+where = src

fcl/__init__.py

@@ -2,20 +2,23 @@
 import sys
 
 from setuptools import Extension, setup
+from Cython.Build import cythonize
 
 
 def get_include_dirs():
     platform_supported = False
-    for prefix in ['darwin', 'linux', 'bsd']:
+    for prefix in ["darwin", "linux", "bsd"]:
         if prefix in sys.platform:
             platform_supported = True
-            include_dirs = ['/usr/include',
-                            '/usr/local/include',
-                            '/usr/include/eigen3',
-                            '/usr/local/include/eigen3']
-            
-            if 'CPATH' in os.environ:
-                include_dirs += os.environ['CPATH'].split(':')
+            include_dirs = [
+                "/usr/include",
+                "/usr/local/include",
+                "/usr/include/eigen3",
+                "/usr/local/include/eigen3",
+            ]
+
+            if "CPATH" in os.environ:
+                include_dirs += os.environ["CPATH"].split(":")
 
             break
     if sys.platform == "win32":
@@ -25,32 +28,35 @@ def get_include_dirs():
 
     # get the numpy include path from numpy
     import numpy
+
     include_dirs.append(numpy.get_include())
     return include_dirs
 
+
 def get_libraries_dir():
-    for prefix in ['darwin', 'linux', 'bsd']:
+    for prefix in ["darwin", "linux", "bsd"]:
         if prefix in sys.platform:
             platform_supported = True
-            lib_dirs = ['/usr/lib',
-                        '/usr/local/lib']
-            
-            if 'LD_LIBRARY_PATH' in os.environ:
-                lib_dirs += os.environ['LD_LIBRARY_PATH'].split(':')
+            lib_dirs = ["/usr/lib", "/usr/local/lib"]
+
+            if "LD_LIBRARY_PATH" in os.environ:
+                lib_dirs += os.environ["LD_LIBRARY_PATH"].split(":")
             return lib_dirs
     raise NotImplementedError(sys.platform)
 
 
 setup(
-    ext_modules=[Extension(
-        "fcl.fcl",
-        ["fcl/fcl.pyx"],
-        include_dirs = get_include_dirs(),
-        library_dirs = get_libraries_dir(),
-        libraries=[
-                "fcl","octomap"
-                ],
-        language="c++",
-        extra_compile_args = ["-std=c++11"]
-    )]
+    ext_modules=cythonize(
+        [
+            Extension(
+                "fcl.fcl",
+                ["src/fcl/fcl.pyx"],
+                include_dirs=get_include_dirs(),
+                library_dirs=get_libraries_dir(),
+                libraries=["fcl", "octomap"],
+                language="c++",
+                extra_compile_args=["-std=c++11"],
+            )
+        ],
+    )
 )