CI Pipeline Fixes (#107)

.github/workflows/documentation.yaml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@main
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: '3.10'
     - name: Setup Linux Environment
@@ -59,7 +59,7 @@ jobs:
         cd -
         
     - name: Upload artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@main
       with:
         name: microstructpy_${{ matrix.doc-type }}_documentation
         path: ${{ env.art_path }} 

.github/workflows/ossar-analysis.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       # Checkout your code repository to scan
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@main
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
@@ -29,17 +29,17 @@ jobs:
 
       # Install dotnet, used by OSSAR
     - name: Install .NET
-      uses: actions/setup-dotnet@v1
+      uses: actions/setup-dotnet@main
       with:
         dotnet-version: '6.0.x'
 
       # Run open source static analysis tools
     - name: Run OSSAR
-      uses: github/ossar-action@v1
+      uses: github/ossar-action@main
       id: ossar
 
       # Upload results to the Security tab
     - name: Upload OSSAR results
-      uses: github/codeql-action/upload-sarif@v1
+      uses: github/codeql-action/upload-sarif@main
       with:
         sarif_file: ${{ steps.ossar.outputs.sarifFile }}

.github/workflows/python_package.yaml

@@ -9,13 +9,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
+        python-version: [3.9, '3.10', '3.11', '3.12']
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel
-        pip install flake8 pytest pytest-cov coveralls
+        pip install flake8 pytest==6.2.5 pytest-cov coveralls
     - name: Install package requirements
       run: pip install -r requirements.txt
     - name: Install package
@@ -56,13 +56,13 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: '3.x'
     - name: Cache pip
-      uses: actions/cache@v3
+      uses: actions/cache@main
       with:
         # This path is specific to Ubuntu
         path: ~/.cache/pip

docs/requirements.txt

@@ -2,6 +2,9 @@ gmsh==4.11.1
 matplotlib>=3.7.3
 numpy>=1.24.4
 pybind11==2.4.3
-setuptools>=65.5.1 
-sphinx==4.2.0
+requests>=2.32.0 # not directly required, pinned by Snyk to avoid a vulnerability
+setuptools>=70.0.0
+sphinx==5.3.0
 sphinx-gallery==0.8.1
+urllib3>=2.2.2 # not directly required, pinned by Snyk to avoid a vulnerability
+zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

docs/source/api/index.rst

@@ -4,6 +4,7 @@ API
 ===
 
 .. toctree::
+    :maxdepth: 2
 
     cli
     geometry/index

requirements.txt

@@ -3,11 +3,12 @@ matplotlib>=3.7.3
 pybind11==2.4.3
 pygmsh==7.1.17
 MeshPy==2022.1.3
-numpy>=1.24.4
+numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.4
 scipy>=1.10.1
-setuptools>=65.5.1 
+setuptools>=70.0.0 
 xmltodict==0.12.0
 tox==3.14.0
 lsq-ellipse==2.0.1
+zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability

setup.py

@@ -57,7 +57,6 @@ def find_version(*fname):
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX :: Linux',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',

src/microstructpy/examples/grain_neighborhoods.py

@@ -44,7 +44,7 @@
 dx = np.insert(np.diff(x_perim), 0, 0)
 dy = np.insert(np.diff(y_perim), 0, 0)
 ds = np.sqrt(dx * dx + dy * dy)
-arc_len = scipy.integrate.cumtrapz(ds, x=t_perim, initial=0)
+arc_len = scipy.integrate.cumulative_trapezoid(ds, x=t_perim, initial=0)
 eq_spaced = arc_len[-1] * np.arange(n) / n
 x_pts = np.interp(eq_spaced, arc_len, x_perim)
 y_pts = np.interp(eq_spaced, arc_len, y_perim)

src/microstructpy/geometry/ellipse.py

@@ -182,7 +182,7 @@ def best_fit(self, points):
             points (list or numpy.ndarray): An Nx2 list of points to fit.
 
         Returns:
-            .Ellipse: An instance of the class that best fits the points.
+            Ellipse: An instance of the class that best fits the points.
 
         .. _`least-squares-ellipse-fitting`: https://github.com/bdhammel/least-squares-ellipse-fitting