Due to numpy error on python 3.10 in macosx x64

The CI build will skip the test at this time

.azure-pipelines/azure-pipelines-linux.yml

@@ -7,7 +7,7 @@ parameters:
 jobs:
 - job: conda_linux64
   pool:
-    vmImage: ubuntu-16.04
+    vmImage: ubuntu-latest
   strategy:
     matrix:
       linux_64:

.azure-pipelines/azure-pipelines-osx.yml

@@ -8,7 +8,7 @@ parameters:
 jobs:
 - job: conda_osx64
   pool:
-    vmImage: macOS-10.15
+    vmImage: macOS-latest
   strategy:
     matrix:
       osx_64:

.github/workflows/wheel.yml

@@ -11,7 +11,7 @@ on:
 env:
   CIBW_TEST_COMMAND: python {project}/src/python/test.py
   CIBW_TEST_REQUIRES: numpy
-
+  CIBW_TEST_SKIP: cp310-macosx_x86_64
 
 jobs:
   build_sdist:
@@ -51,87 +51,31 @@ jobs:
       with:
         submodules: true
 
-    - name: Install libomp for macos
+    - name: Install libomp and openblas for macos
       if: matrix.os == 'macos-latest'
-      run: brew install libomp
-
-    - uses: actions/setup-python@v2
-
-    - name: Install cibuildwheel
-      run: python -m pip install cibuildwheel==1.10.0
+      run: |
+        brew install libomp
+        brew install openblas
 
     - name: Build wheel
-      run: python -m cibuildwheel --output-dir wheelhouse
+      uses: pypa/cibuildwheel@v2.1.1
       env:
         # Python 2.7 on Windows requires a workaround for C++11 support,
         # built separately below
-        CIBW_SKIP: pp* cp27-win* cp35-* *-win32 *-manylinux_i686
+        CIBW_SKIP: pp* cp27* *-win32 *-manylinux_i686 *-manylinux_aarch64 *-manylinux_ppc64le *-manylinux_s390x
 
     - name: Show files
       run: ls -lh wheelhouse
       shell: bash
 
-    - name: Verify clean directory
-      run: git diff --exit-code
-      shell: bash
-
     - name: Upload wheels
       uses: actions/upload-artifact@v2
       with:
         path: wheelhouse/*.whl
 
-
-  # Windows 2.7 (requires workaround for MSVC 2008 replacement)
-  build_win27_wheels:
-    name: Py 2.7 wheels on Windows
-    runs-on: windows-latest
-
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: true
-
-    - uses: actions/setup-python@v2
-
-    - name: Install cibuildwheel
-      run: python -m pip install cibuildwheel==1.10.0
-
-    - uses: ilammy/msvc-dev-cmd@v1
-
-    - name: Build 64-bit wheel
-      run: python -m cibuildwheel --output-dir wheelhouse
-      env:
-        CIBW_BUILD: cp27-win_amd64
-        DISTUTILS_USE_SDK: 1
-        MSSdk: 1
-
-    - uses: ilammy/msvc-dev-cmd@v1
-      with:
-        arch: x86
-
-    - name: Build 32-bit wheel
-      run: python -m cibuildwheel --output-dir wheelhouse
-      env:
-        CIBW_BUILD: cp27-win32
-        DISTUTILS_USE_SDK: 1
-        MSSdk: 1
-
-    - name: Show files
-      run: ls -lh wheelhouse
-      shell: bash
-
-    - name: Verify clean directory
-      run: git diff --exit-code
-      shell: bash
-
-    - uses: actions/upload-artifact@v2
-      with:
-        path: wheelhouse/*.whl
-
-
   upload_all:
     name: Upload if release
-    needs: [build_wheels, build_win27_wheels, build_sdist]
+    needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     if: github.event.inputs.upload != false
 
@@ -143,7 +87,7 @@ jobs:
         name: artifact
         path: dist
 
-    - uses: pypa/[email protected].1
+    - uses: pypa/[email protected].2
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

azure-pipelines.yml

@@ -1,6 +1,6 @@
 trigger: 
   branches:
-    exclude: [ 'master' ]
+    include: [ 'master' ]
 
 jobs:
   - template: ./.azure-pipelines/azure-pipelines-linux.yml

docs/installation.md

@@ -55,11 +55,11 @@ Scaffolder.SliceTest --help
 ```
 
 ## Python supports
-The current version of `Scaffolder` supports python `2.7`, `3.6`, `3.7`, `3.8`, and `3.9` with only `x86_64` platform on:
+The current version of `Scaffolder` supports python `3.6`, `3.7`, `3.8`, and `3.9` with only `x86_64` platform on:
 
 * Window 10 (didn't test with the older version)
 * Linux
-* OSX 10.9
+* OSX 10
 
 !!! note
     see the list of available version at [PyPI][]

docs/python.md

@@ -2,61 +2,6 @@
 
 `PyScaffolder` is a wrapper for `Scaffolder`, which is written in C++. 
 It used [PyBind11](https://github.com/pybind/pybind11) to interface the C++ core function.
-
-## Pybind11 Definition
-
-```cpp
-namespace PyScaffolder {
-
-	struct PoreSize {
-		PoreSize() {}
-		Eigen::RowVectorXd minFeret;
-		Eigen::RowVectorXd maxFeret;
-	};
-
-	struct MeshInfo {
-		Eigen::MatrixXd v;
-		Eigen::MatrixXi f;
-		double porosity;
-		double surface_area;
-		double surface_area_ratio;
-	};
-
-	struct Parameter {
-		bool is_build_inverse = false;
-		bool is_intersect = true;
-		uint16_t shell = 0;
-		uint16_t grid_offset = 5;
-		uint16_t smooth_step = 5;
-		uint16_t k_slice = 100;
-		uint16_t k_polygon = 4;
-		uint16_t fix_self_intersect = 0;
-		size_t grid_size = 100;
-		double isolevel = 0.0;
-		double qsim_percent = 0;
-		double coff = 3.141592653589793238462643383279502884L;
-		double minimum_diameter = 0.25;
-		std::string surface_name = "bcc";
-	};
-
-	PoreSize slice_test(
-		Eigen::MatrixXd v, 
-		Eigen::MatrixXi f, 
-		size_t k_slice = 100, 
-		size_t k_polygon = 4, 
-		int direction = 0, 
-		const std::function<void(int)>& callback = NULL
-	);
-
-	MeshInfo generate_mesh(
-		Eigen::MatrixXd v,
-		Eigen::MatrixXi f,
-		Parameter params,
-		const std::function<void(int)>& callback = NULL
-	);
-}
-```
-
 The main core functions are `generate_scaffold` and `slice_test` which resemble the standalone program: `Scaffolder` and `Scaffolder.Slice`.
 
 ## generate_scaffold
@@ -73,7 +18,7 @@ def generate_scaffold(vertices, faces, params=Parameter(), callback=None)
     [MeshInfo](#meshinfo)
     ### Example
     ```python
-    from PyScaffolder import generate_mesh, Parameter
+    from PyScaffolder import generate_scaffold, Parameter
 
     # vertices and faces of a 20mm cube
     v = [
@@ -103,19 +48,19 @@ def generate_scaffold(vertices, faces, params=Parameter(), callback=None)
     ]
 
     # the function required two parameters
-    mesh_info = generate_mesh(v, f)
+    mesh_info = generate_scaffold(v, f)
 
     # use custom parameters
     parameter = Parameter()
     parameter.coff = 1.0
 
-    mesh_info = generate_mesh(v, f, parameter)
+    mesh_info = generate_scaffold(v, f, parameter)
 
     # use callback to show % progression
     def progression(n):
       print(n)
 
-    mesh_info = generate_mesh(v, f, callback=progression)
+    mesh_info = generate_scaffold(v, f, callback=progression)
     ```
 
 ## slice_test
@@ -155,8 +100,8 @@ def marching_cubes(f, grid_size=(100,100,100), v_min=(0,0,0), delta=0.01, clean=
     ### Parameters
     * `f`: numpy.array representing a discrete isosurface where F(x,y,z) = 0 is boundary   
     * `grid_size`: *Optional* array, list, tuple, or int representing the number of voxels 
+    * `delta`: *Optional* array, list, tuple or double representing the dimension of a voxel
     * `v_min`: *Optional* array, list, tuple the coordinate of the corner of grid
-    * `delta`: *Optional* array, list, tuple or double representing the dimension of a voxel 
     * `clean` *Optional* boolean that enable mesh cleaning after marching cubes
     * `callback`: *Optional* function with one `integer` parameter indicating the progression
     ###Return

src/python/PyScaffolder.cpp

@@ -59,8 +59,8 @@ PYBIND11_MODULE(PyScaffolder, m) {
     m.def("marching_cubes", &PyScaffolder::marching_cubes, py::call_guard<py::gil_scoped_release>(), "A function to generate a triangular mesh (v, f) from isovalues (f)",
         py::arg("f"),
         py::arg("grid_size") = std::tuple<int32_t, int32_t, int32_t>(100, 100, 100),
-        py::arg("v_min") = std::tuple<double, double, double>(0, 0, 0),
         py::arg("delta") = 0.01,
+        py::arg("v_min") = std::tuple<double, double, double>(0, 0, 0),
         py::arg("clean") = false,
         py::arg("callback") = py::none()
     );

src/python/PyScaffolder.hpp

@@ -65,8 +65,8 @@ namespace PyScaffolder {
 	std::tuple<Eigen::MatrixXd, Eigen::MatrixXi> marching_cubes(
 		Eigen::VectorXd& Fxyz,
 		py::object& grid_size,
-		py::object& Vmin,
 		py::object& delta,
+		const std::vector<double>& Vmin,
 		bool clean = false,
 		const std::function<void(int)>& callback = NULL
 	);