CI: update workflows to Python 3.13 and align deps with setup.py

Author: Marcraven

.github/workflows/python-package-conda-linux-py38.yml

@@ -10,19 +10,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10.10
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.10.10
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
         python --version
-        conda install python=3.10.10
-        conda install -c conda-forge netcdf4=1.6.1
+        conda install python=3.13
+        conda install -c conda-forge netcdf4
         conda install -c conda-forge xrd_simulator
     - name: Lint with flake8
       run: |

.github/workflows/python-package-conda-macos-py38.yml

@@ -11,19 +11,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10.0
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.10.0
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
         python --version
-        sudo conda install python=3.10.0
-        sudo conda install -c conda-forge xrd_simulator
+        conda install python=3.13
+        conda install -c conda-forge xrd_simulator
     - name: Lint with flake8
       run: |
         sudo conda install flake8

.github/workflows/python-package-run-tests-linux-py38.yml

@@ -14,19 +14,20 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10.10
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.10.10
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
         python --version
-        conda install python=3.10.10
-        conda install -c conda-forge matplotlib numpy meshio pygalmesh scipy numba pycifrw dill xfab netcdf4=1.6.1 h5py
+        # Use conda to install core scientific packages from conda-forge
+        conda install python=3.13
+        conda install -c conda-forge matplotlib numpy meshio pygalmesh scipy numba pycifrw dill xfab netcdf4 h5py meshpy pillow scikit-image pandas tifffile typing-extensions
         python -m pip install .
     - name: Lint with flake8
       run: |

.github/workflows/python-package-run-tests-macos-py38.yml

@@ -14,19 +14,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10.0
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.10.0
+        python-version: 3.13
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
         python --version
-        sudo conda install python=3.10.0
-        sudo conda install -c conda-forge matplotlib numpy meshio pygalmesh scipy numba pycifrw dill xfab
+        conda install python=3.13
+        conda install -c conda-forge matplotlib numpy meshio pygalmesh scipy numba pycifrw dill xfab meshpy pillow scikit-image pandas tifffile typing-extensions
         python -m pip install .
     - name: Lint with flake8
       run: |