Release version:

 - Added a workflow to package and publish on PyPi.
 - Changed ':' to '.' in structure snapshot save names to fix compatability with windows.
 - Added requirements.txt

.github/workflows/build.yml

@@ -0,0 +1,58 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Build febid for win and mac
+
+on:
+  push:
+    branches: [ $default-branch ]
+  pull_request:
+    branches: [ $default-branch ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        include:
+          - arch: arm64
+            os: macos-latest
+            pypthon-version: "3.7-3.11"
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install build twine
+#    - name: Build package for linux
+#      if: ${{ matrix.os == 'ubuntu-latest' }}
+#      uses: RalfG/python-wheels-manylinux-build@v0.7.1-manylinux2014_x86_64
+#      with:
+#        python-versions: ${{ matrix.python-version }}
+#        build-requirements: 'setuptools cython numpy'
+#        pre-build-command: python -m pip install --upgrade pip setuptools wheel
+    - name: Build package for mac and windows
+      if: ${{ matrix.os == 'windows-latest' }} || ${{ matrix.os == 'macos-latest' }}
+      run: |
+        python -m build --outdir dist
+
+    - name: Save wheels as artifacts
+      uses: actions/upload-artifact@v3
+      with:
+        path: dist/*
+    - name: Publish wheels to PyPI
+      env:
+        TWINE_USERNAME: ${{ secrets.TEST_PYPI_USER }}
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
+      run: |
+        twine upload dist/*

febid/libraries/__init__.py

@@ -0,0 +1,3 @@
+"""
+Extension modules. Contains electron ray-tracing, stencil and visualisation modules
+"""

febid/libraries/ray_traversal/__init__.py

@@ -0,0 +1,3 @@
+"""
+Ray-tracing utilities
+"""

febid/libraries/rolling/__init__.py

@@ -0,0 +1,3 @@
+"""
+Stencil-based utilities
+"""

febid/libraries/vtk_rendering/VTK_Rendering.py

@@ -423,7 +423,7 @@ def save_deposited_structure(structure, sim_t=None, t=None, beam_position=None,
     vtk_obj.field_data['beam_position'] = [beam_position]
     if filename == None:
         filename = "Structure"
-    vtk_obj.save(f'{filename}_{time.strftime("%H:%M:%S", time.localtime())}.vtk')
+    vtk_obj.save(f'{filename}_{time.strftime("%H.%M.%S", time.localtime())}.vtk')
 
 
 def export_obj(structure, filename=None):

requirements.txt

@@ -0,0 +1,12 @@
+matplotlib
+numpy
+numpy<1.23.0
+pyvista
+pandas
+ruamel.yaml
+cython
+openpyxl
+tqdm
+pyqt5
+pyaml
+numexpr_mod

setup.py

@@ -12,8 +12,8 @@
 platform = sys.platform
 libraries = []
 if 'darwin' in platform:  # darwin == OSX
-    os.environ["CC"] = "/usr/local/opt/llvm/bin/clang"
-    os.environ["CXX"] = "/usr/local/opt/llvm/bin/clang++"
+    # os.environ["CC"] = "/usr/local/opt/llvm/bin/clang"
+    # os.environ["CXX"] = "/usr/local/opt/llvm/bin/clang++"
     openMP_arg = '-lomp'
 if 'linux' in platform:
     openMP_arg = '-fopenmp'
@@ -44,16 +44,16 @@
                Extension("febid.libraries.rolling.roll", ['febid/libraries/rolling/roll.pyx'],
                          include_dirs=["/usr/local/opt/llvm/include"],
                          library_dirs=["/usr/local/opt/llvm/lib"],
-                         extra_compile_args=["-w", '-fopenmp'],
-                         libraries=libraries,
-                         extra_link_args=[openMP_arg]
+                         # extra_compile_args=["-w", '-fopenmp'],
+                         # libraries=libraries,
+                         # extra_link_args=[openMP_arg]
                          ),
               Extension("febid.libraries.pde.tridiag", ['febid/libraries/pde/tridiag.pyx'],
                          include_dirs=["/usr/local/opt/llvm/include"],
                          library_dirs=["/usr/local/opt/llvm/lib"],
-                         extra_compile_args=["-w", "-fopenmp"],
-                         libraries=libraries,
-                         extra_link_args=[openMP_arg]
+                         # extra_compile_args=["-w", "-fopenmp"],
+                         # libraries=libraries,
+                         # extra_link_args=[openMP_arg]
                          ),
                ]