Merge pull request #4 from jeremymanning/main

Major refactoring: CLI system, comprehensive testing, and Windows compatibility

Author: jeremymanning

.github/workflows/tests.yml

@@ -0,0 +1,83 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache dependencies
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pip
+          ~/miniconda3/envs
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt', '**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov
+        pip install "numpy<2" scipy transformers matplotlib seaborn pandas tqdm
+        pip install cleantext plotly scikit-learn
+        pip install torch --index-url https://download.pytorch.org/whl/cpu
+        pip install -e .
+
+    - name: Create test data
+      run: |
+        cd tests
+        python create_test_data.py
+        cd ..
+
+    - name: Run visualization tests
+      run: |
+        pytest tests/test_visualization.py -v --tb=short
+
+    - name: Run CLI tests
+      run: |
+        pytest tests/test_cli.py -v --tb=short
+
+    - name: Run model training tests
+      run: |
+        pytest tests/test_model_training.py -v --tb=short
+
+    - name: Test figure generation (single)
+      run: |
+        python generate_figures.py --figure 1a --data tests/data/test_model_results.pkl --output tests/output_single
+
+    - name: Test figure generation (all)
+      run: |
+        python generate_figures.py --data tests/data/test_model_results.pkl --output tests/output_all
+      timeout-minutes: 5
+
+    - name: Upload test artifacts
+      if: failure()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test-results-${{ matrix.os }}-${{ matrix.python-version }}
+        path: |
+          tests/output_*
+          tests/data/*.csv
+
+    - name: Check generated files
+      run: python tests/check_outputs.py

.gitignore

@@ -8,4 +8,19 @@
 *.out
 *.synctex.gz
 __pycache__/
-CLAUDE.md
+CLAUDE.md
+
+# Python
+*.pyc
+*.pyo
+*.egg-info/
+.pytest_cache/
+htmlcov/
+.coverage
+*.cover
+
+# Test outputs
+tests/output_*/
+tests/data/*.csv
+tests/data/*.pkl
+!tests/data/test_model_results.pkl

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Contextual Dynamics Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.