Update this branch for testing all recent pull requests & fixing minor issues

.github/workflows/CD.yml

@@ -0,0 +1,28 @@
+# Publishes to PyPi on release tag
+name: Continuous Deployment
+
+on:
+  push:
+    tags:
+      - "*.*.*"
+
+jobs:
+  dev-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build and publish to test pypi
+        uses: JRubics/poetry-publish@v2.0
+        with:
+          pypi_token: ${{ secrets.TEST_PYPI_TOKEN }}
+          repository_name: "testpypi"
+          repository_url: "https://test.pypi.org/legacy/"
+
+  prod-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build and publish to pypi
+        uses: JRubics/poetry-publish@v2.0
+        with:
+          pypi_token: ${{ secrets.PYPI_TOKEN }}

.github/workflows/CI.yml

@@ -0,0 +1,56 @@
+name: Continuous Integration
+
+on: [push, pull_request]
+
+permissions:
+  contents: write
+
+jobs:
+  test:
+    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/codecov-action@v4.2.0
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - 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
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: flake8 Lint
+        uses: py-actions/flake8@v2

.gitignore

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

CHANGELOG.md

@@ -1,5 +1,78 @@
 # Changelog
 
+## [Untracked Changes]
+
+### Added
+- Factor plots can take objectives
+
+### Modified
+- Bugfix for correlation plot respecting minimized targets
+- Improvements to objective visualization
+
+## [0.8.6]
+### Added
+- Improved methods for fitting PyTorch surrogates, including auto-stopping by parameter value norm
+
+### Modified
+- Greatly reduced the number of samples for DNN posterior, speeding up optimization
+- Stabilized the mean estimate of ensemble surrogates by avoiding resampling
+- Disabled root caching for ensemble surrogates during optimization
+- Increased the maximum length of a category name to 32 characters
+- Bug fix for incorrect symmetry in correlation calculation of calc_ofat_ranges
+- OFAT range calcs and plots now respect minimum targets and not just maximum
+
+## [0.8.5]
+### Added
+- More optional outputs for verbose settings
+- Parameters in ParamSpace can also be indexed by name
+- Parameters now have search_space property, to modify the optimizer search space from the full space
+- Continuous parameters have search_min/search_max; Discete parameteres have search_categories
+- Constraints are now defined by Constraint class
+- Input constraints can now be included in ParamSpace, and serialized from there
+- Output constraints can now be included in Campaign, and serialized from there
+- New interface class IParamSpace to address circular import issues between ParamSpace and Constraint
+
+### Modified
+- Optimizer and Campaign X_space attributes are now assigned using setter
+- Optimizer.maximize() appropriately recognizes fixed_var argument
+
+### Removed
+- Torch device references and options (GPU compatibility may be re-added)
+
+## [0.8.4]
+### Added
+- Campaign X_best method
+- Optimizer X_best_f attribute(s)
+- Sequence of colors "color_list" to branding
+- Informative hoverdata for MDS plot
+- Created Product_Objective and Divide_Objective
+
+### Modified
+- Switched all usages of X_ref = X_space.mean() to optimizer.X_best_f
+- Refactored mpl "visualize_inputs" as plotly "visualize_inputs" for better interactivity
+- Text formatting for some plotly hoverdata
+
+## [0.8.3]
+### Added
+- Default values for NParEGO scalarization_weights
+- SHAP PDP ICE plots now work with categorical values
+- Added scikit-learn to dependencies, for MDS
+- Added MDS plot
+
+### Modified
+- SHAP PDP ICE plots must now have color and x-axis indices that are distinct
+
+## [0.8.2]
+### Added
+- Project metadata properly captured on PyPI based on changes in pyproject.toml
+
+## [0.8.1]
+### Modified
+- Fixed infobar on dash app
+- Better handling of X_space on dash app
+- Bug fixes for optim_progress
+- Improved color and axes of parity_plot
+
 ## [0.8.0]
 ### Added
 - Major improvements to testing and numerous small bug fixes to improve code robustness

app.py

@@ -1,6 +1,6 @@
 from dash import html, Dash
 import dash_bootstrap_components as dbc
-from obsidian.dash import setup_data, setup_config, setup_optimize, setup_plots, setup_predict, setup_help
+from obsidian.dash import setup_data, setup_config, setup_optimize, setup_plots, setup_predict, setup_infobar
 import pandas as pd
 from PIL import Image
 
@@ -15,7 +15,7 @@
 dbc_css = "https://cdn.jsdelivr.net/gh/AnnMarieW/dash-bootstrap-templates/dbc.min.css"  # For data tables
 app.config.external_stylesheets = [dbc.themes.SANDSTONE, dbc_css, dbc.icons.BOOTSTRAP]
 
-logo = Image.open('docs/figures/obsidian_logo.png')
+logo = Image.open('docs/_static/obsidian_logo.png')
 
 app_image = html.Div(html.Img(src=logo, style={'width': '5%', 'height': '5%'}), style={'textAlign': 'center'})
 app_title = html.Div([html.H1(children='obsidian'),
@@ -35,7 +35,7 @@
     Param_Continuous('Concentration', 10, 150),
     Param_Continuous('Enzyme', 0.01, 0.30),
     Param_Categorical('Variant', ['MRK001', 'MRK002', 'MRK003']),
-    Param_Ordinal('Stir Rate', ['Low', 'Medium', 'High']),
+    Param_Ordinal('Stir Rate', ['0 - Low', '1 - Medium', '2 - High']),
 ]
 X_space = ParamSpace(params)
 designer = ExpDesigner(X_space, seed=0)
@@ -45,8 +45,8 @@
 default_data = pd.concat([X0, y0], axis=1)
 
 # Set up each tab
-setup_help(app, app_infobar)
-setup_data(app, app_tabs, default_data)
+setup_infobar(app, app_infobar)
+setup_data(app, app_tabs, default_data, X_space)
 setup_config(app, app_tabs)
 setup_optimize(app, app_tabs)
 setup_plots(app, app_tabs)