Updates to Python.

.github/workflows/main.yml

@@ -1,5 +1,8 @@
 name: Notebook Testing
 
+env:
+  PYTHON_VERSION: "3.13"
+
 on:
   push:
     branches:
@@ -27,10 +30,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ env.PYTHON_VERSION }}
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{ env.PYTHON_VERSION }}
     - name: Install and run black for notebooks
       run: |
         python -m pip install --upgrade pip
@@ -40,8 +43,8 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        # not using macos-latest because pyenchant doesn't work with the new macos-14 arm64
-        os: [ubuntu-latest, macos-13, windows-latest]
+        # using macos-13, last available intel architecture. macos-latest is arm64 architecture.
+        os: [ubuntu-latest, windows-latest, macos-latest, macos-13]
         inputs: ["00_ or 01_ or 02_ or 03_ or 04_ or 05_", "06_ or 07_ or 08_ or 09_ or 10_"]
     runs-on: ${{ matrix.os }}
     steps:
@@ -54,10 +57,10 @@ jobs:
         key: notebook-data-${{ hashFiles('data/manifest.json') }}
         restore-keys: |
           notebook-data-${{ hashFiles('data/manifest.json') }}
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ env.PYTHON_VERSION }}
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{ env.PYTHON_VERSION }}
     - name: Install enchant on non windows systems
       shell: bash
       run: |
@@ -78,7 +81,11 @@ jobs:
       if: steps.cache.outputs.cache-hit != 'true'
       run: python downloaddata.py data/ data/manifest.json
     - name: run the test
+      shell: bash
       env: 
         SIMPLE_ITK_MEMORY_CONSTRAINED_ENVIRONMENT: 1
-      run: |
+      run: | # pyenchant has a problem locating libenchant on macOS-ARM64. setting this environment variable resolves the issue
+        if [ "$RUNNER_OS" == "macOS" ] && [ "${{ matrix.os }}" != "macos-13" ]; then
+           export PYENCHANT_LIBRARY_PATH=/opt/homebrew/lib/libenchant-2.dylib
+        fi
         pytest -v --tb=short -k "${{matrix.inputs}}" tests/test_notebooks.py::Test_notebooks::test_python_notebook

binder/runtime.txt

@@ -1 +1 @@
-python-3.9
+python-3.13

docs/index.html

@@ -129,10 +129,10 @@
 
 
 <p>
-In this tutorial we will use the Anaconda Python distribution. Please follow the
+In this tutorial we will use the Miniconda Python distribution. Please follow the
 instructions below to setup the environment. All
 commands below are issued on the <b>command line</b> (Linux/Mac - terminal,
-Windows - Anaconda Prompt).
+Windows - Miniconda Prompt).
 </p>
 
 <ol>
@@ -153,23 +153,22 @@
 </li>
 
 <li>
-<a href="https://www.anaconda.com/download/">Download and install</a> the most
-recent version of Anaconda for your operating system. We assume it is installed
-in a directory named anaconda3. Regardless of the installer, we will be working
-with Python 3.9
+<a href="https://www.anaconda.com/docs/getting-started/miniconda/main">Download and install</a> the most
+recent version of Miniconda for your operating system. We assume it is installed
+in a directory named miniconda3. Regardless of the installer, we will be working
+with Python 3.13
 </li>
 
 <li>
   <ul>
-   <li> On Windows: open the Anaconda Prompt (found under the Anaconda3 start menu).</li>
-   <li> On Linux/Mac: on the command line <code>source path_to_anaconda3/bin/activate base</code></li>
+   <li> On Windows: open the Miniconda Prompt (found under the Miniconda3 start menu).</li>
+   <li> On Linux/Mac: on the command line <code>source path_to_miniconda3/bin/activate base</code></li>
   </ul>
 </li>
 
 <li>
-Update the base anaconda environment and install the git version control system into it.
+Update the base environment and install the git version control system into it.
 <pre><code>conda update conda
-conda update anaconda
 conda install git
 </code></pre>
 </li>
@@ -189,9 +188,9 @@
 <li>
 Activate the virtual environment:
   <ul>
-   <li> On Windows: open the Anaconda Prompt (found under the Anaconda3 start menu)<br><code> 
+   <li> On Windows: open the Miniconda Prompt (found under the Miniconda3 start menu)<br><code> 
    conda activate sitkpy</code></li>
-   <li> On Linux/Mac: on the command line <br><code>source path_to_anaconda3/bin/activate 
+   <li> On Linux/Mac: on the command line <br><code>source path_to_miniconda3/bin/activate 
    sitkpy</code></li>
   </ul>
 </li>

environment.yml

@@ -1,11 +1,10 @@
 name: sitkpy
 
 channels:
-  - defaults
   - conda-forge
 
 dependencies:
-  - python=3.9
+  - python=3.13
   - jupyter
   - matplotlib
   - ipywidgets

environment_dev.yml

@@ -1,11 +1,10 @@
 name: sitkpy_dev
 
 channels:
-  - defaults
   - conda-forge
 
 dependencies:
-  - python=3.9
+  - python=3.13
   - jupyter
   - matplotlib
   - ipywidgets