Merge pull request #31 from MSDLLCpapers/main

Update app branch with main

.coveragerc

@@ -3,4 +3,5 @@ omit =
     obsidian/dash/*
     obsidian/tests/*
     obsidian/experiment/benchmark/*
-    obsidian/plotting/branding.py
+    obsidian/plotting/branding.py
+    app.py

.flake8

@@ -1,21 +1,24 @@
 [flake8]
+
 # VScode adds blank whitespaces
 extend-ignore = W293
+# More manageable for desktop editing
 max-line-length = 140
-per-file-ignores =
 
+per-file-ignores =
     # Imported but unused / Unable to detect names
     __init__.py: F401, F403
     obsidian/dash/*: F401, F403
 
-    # Often creating variables but not accessing them in testing
-    obsidian/tests/*: F841
+    # Often importing and creating unaccessed objects during testing
+    obsidian/tests/*: F401, F841
+
+    # No good way around comparing types for recursive state-dict comparison
+    obsidian/tests/utils.py: E721
 
 exclude =
     projects/
     demo/
     logs/
     dev/
-    source/
-    docs/
-    build/
+    docs/

.github/workflows/codecov.yml

@@ -0,0 +1,21 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Pytest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'
+    - name: Install requirements
+      run: pip install obsidian-apo[dev]
+    - name: Run tests and collect coverage
+      run: pytest --cov=.
+    - name: Upload coverage reports to Codecov with GitHub Action
+      uses: codecov/[email protected]
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/documentation.yml

@@ -0,0 +1,27 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install obsidian-apo[docs]
+      - name: Sphinx build
+        run: |
+          sphinx-build docs _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.gitignore

@@ -85,9 +85,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 .pybuilder/
 target/

CHANGELOG.md

@@ -1,5 +1,52 @@
 # Changelog
 
+## [0.8.0]
+### Added
+- Major improvements to testing and numerous small bug fixes to improve code robustness
+- Code coverage > 90%
+- New method for asserting equivalence of state_dicts during serialization
+
+### Modified
+- Objective PyTests separated
+- Constraint PyTests separated
+
+## [0.7.13]
+### Added
+- Campaign.Explainer now added to PyTests
+- Docstrings and typing to Explainer methods
+- Campaign.out property to dynamically capture measured responses "y" or objectives as appropriate
+- Campaign.evaluate method to map optimizer.evaluate method
+- DNN to PyTests
+
+### Modified
+- Fixed SHAP explainer analysis and visualization functions
+- Changed SHAP visualization colors to use obsidian branding
+- Moved sensitivity method from campaign.analysis to campaign.explainer
+- Moved Explainer testing from optimizer pytests to campaign pytests
+- Generalized plotting function MOO_results and renamed optim_progress
+- Campaign analysis and plotting methods fixed for 
+- Greatly increased the number of samples used for DNNPosterior, increasing the stability of posterior predictions
+
+### Removed
+- Removed code chunks regarding unused optional inputs to PDP ICE function imported from SHAP GitHub
+
+## [0.7.12]
+### Added
+- More informative docstrings for optimizer.bayesian, optimizer.predict, to explain choices of surrogate models and aq_funcs
+
+### Modified
+- Renamed aq_func hyperparmeter "Xi_f" to "inflate"
+- Moved default aq_func choices for single/multi into aq_defaults of acquisition.config
+- Fixed and improved campaign analysis methods
+
+## [0.7.11]
+### Added
+- Documentation improvements
+
+### Modified
+- Naming conventions for modules (config, utils, base)
+- Import order convention for modules
+
 ## [0.7.10]
 ### Added
 - First (working) release on PyPI