Add AI-generated unit testing from SECQUOIA fork

.github/ci-config/ci-versions.yml

@@ -0,0 +1,3 @@
+# Centralized CI version configuration for LyoPRONTO
+# Update this file to change Python version across all workflows
+python-version: '3.13'

.github/workflows/docs.yml

@@ -27,19 +27,21 @@ jobs:
         # Could fetch it later on but this seems simpler and less finicky
         with:
           fetch-depth: 0
-      - run: pip install mkdocstrings-python mkdocs-material mike mkdocs-ipynb
+      - run: pip install .
+      - run: pip install .[docs]
       - run: echo ${{ github.event_name}} ${{ github.ref_name }}
       # Deploy docs according to type of event
-      - name: Deploy docs as latest
+      - name: Build docs as latest
         if: ${{ github.event_name == 'release' }}
         run: mike deploy ${{ github.ref_name }} latest
-      - name: Deploy docs for PR
+      - name: Build docs for PR
         if: ${{ github.event_name == 'pull_request' }}
         run: mike deploy pr-${{ github.event.number }}
-      - name: Deploy docs as dev
+      - name: Build docs as dev
         if: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
         run: mike deploy dev
-      - name: Get docs into GitHub Pages
+      - name: Deploy docs to GitHub Pages
+        if: ${{ github.event_name != 'pull_request' }}
         run: |
           git switch gh-pages
           git push origin gh-pages

.github/workflows/pr-tests.yml

@@ -0,0 +1,70 @@
+name: PR Tests
+
+# Smart CI workflow:
+# - Draft PRs: Fast tests only (no coverage) for rapid iteration
+# - Ready for Review: Full tests with coverage for quality assurance
+# - All subsequent commits: Continue with full coverage
+
+on:
+  pull_request:
+    branches: [ main ]
+    types: [ opened, synchronize, reopened, ready_for_review, converted_to_draft ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+
+    - name: Determine test mode
+      id: mode
+      run: |
+        if [ "${{ github.event.pull_request.draft }}" ]; then
+          echo "mode=fast" >> $GITHUB_OUTPUT
+        else
+          echo "mode=full" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install -e . --no-build-isolation
+
+    - name: Run tests
+    # Currently this conditional branching doesn't actually do anything,
+    # since pyproject.toml adds these coverage arguments to the testing anyway
+      run: |
+        if [ "${{ steps.mode.outputs.mode }}" == "fast" ]; then
+          echo "⚡ Skipping notebook tests (marked with @pytest.mark.notebook) - these run separately"
+          pytest tests/ -n auto -v -m "not notebook" --cov=lyopronto --cov-report=term-missing
+        else
+          echo "⚡ Skipping notebook tests (marked with @pytest.mark.slow), not running coverage"
+          pytest tests/ -n auto -v -m "not notebook"
+        fi
+
+    - name: Upload coverage (if run)
+      if: steps.mode.outputs.coverage == 'true'
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: pr-tests
+        name: pr-coverage
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/rundocs.yml

@@ -10,24 +10,54 @@ on:
 
 jobs:
   doctests:
-    # env:
-    #   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    #   GIT_COMMITTER_NAME: ${{ github.actor }}
-    #   GIT_COMMITTER_EMAIL: ${{ github.actor }}@users.noreply.github.com
-    name: Notebook
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: ./docs/examples
-    strategy:
-      matrix:
-        notebook: 
-         - knownRp_PD.ipynb
-         - unknownRp_PD.ipynb
+
     steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python
-        uses: actions/setup-python@v4
-      - run: pip install ruamel.yaml scipy numpy matplotlib papermill ipykernel
-      - name: Run notebooks
-        run: papermill ${{ matrix.notebook }} ${{ matrix.notebook }} -k python
+    - uses: actions/checkout@v4
+
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install -e . --no-build-isolation
+
+    - name: Run tests (draft = fast, ready = coverage)
+      run: pytest tests/ -n auto -v -m "notebook" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+# jobs:
+#   doctests:
+#     # env:
+#     #   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#     #   GIT_COMMITTER_NAME: ${{ github.actor }}
+#     #   GIT_COMMITTER_EMAIL: ${{ github.actor }}@users.noreply.github.com
+#     name: Notebook
+#     runs-on: ubuntu-latest
+#     defaults:
+#       run:
+#         working-directory: ./docs/examples
+#     strategy:
+#       matrix:
+#         notebook: 
+#          - knownRp_PD.ipynb
+#          - unknownRp_PD.ipynb
+#     steps:
+#       - uses: actions/checkout@v5
+#       - name: Set up Python
+#         uses: actions/setup-python@v4
+#       - run: pip install ruamel.yaml scipy numpy matplotlib papermill ipykernel
+#       - name: Run notebooks
+#         run: papermill ${{ matrix.notebook }} ${{ matrix.notebook }} -k python

.github/workflows/slow-tests.yml

@@ -0,0 +1,77 @@
+name: Slow Tests (Manual)
+
+# Manual workflow for running slow optimization tests
+# Useful for:
+# - Testing before merge if concerned about slow test failures
+# - Running comprehensive tests on feature branches
+# - Validating optimization behavior changes
+
+on:
+  workflow_dispatch:
+    inputs:
+      run_all:
+        description: 'Run all tests (true) or only slow tests (false)'
+        required: false
+        default: 'false'
+        type: choice
+        options:
+          - 'true'
+          - 'false'
+
+jobs:
+  slow-tests:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install -e . --no-build-isolation
+
+    - name: Run slow tests
+      run: |
+        if [ "${{ inputs.run_all }}" == "true" ]; then
+          echo "🔍 Running ALL tests (including slow optimization tests)"
+          echo "⏱️ This may take 30-40 minutes on CI"
+          pytest tests/ -n auto -v --cov=lyopronto --cov-report=xml --cov-report=term-missing
+        else
+          echo "🐌 Running ONLY slow tests (marked with @pytest.mark.slow)"
+          echo "⏱️ This focuses on optimization tests that take minutes"
+          pytest tests/ -n auto -v -m "slow" --cov=lyopronto --cov-report=xml --cov-report=term-missing
+        fi
+
+    - name: Upload coverage
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: slow-tests
+        name: slow-tests-coverage
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Test Summary
+      if: always()
+      run: |
+        if [ "${{ inputs.run_all }}" == "true" ]; then
+          echo "✅ Complete test suite finished"
+        else
+          echo "🐌 Slow tests completed"
+        fi
+        echo "📊 Coverage uploaded to Codecov"

.github/workflows/tests.yml

@@ -0,0 +1,55 @@
+name: Main Branch Tests
+
+# Full tests with coverage for main branch
+# (PRs are handled by pr-tests.yml)
+
+on:
+  push:
+    branches: [ main, dev-pyomo ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Read CI version config
+      id: versions
+      uses: mikefarah/yq@v4.44.1
+      with:
+        cmd: yq eval '.python-version' .github/ci-config/ci-versions.yml
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ steps.versions.outputs.result }}
+        cache: 'pip'
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install .
+        pip install .[dev]
+        pip install -e . --no-build-isolation
+
+    - name: Run ALL tests with pytest and coverage (including slow tests)
+      run: |
+        echo "🔍 Running complete test suite including slow tests"
+        echo "⏱️ This may take 30-40 minutes on CI (includes optimization tests)"
+        pytest tests/ -n auto -v --cov=lyopronto --cov-report=xml --cov-report=term-missing
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Coverage Summary
+      if: always()
+      run: |
+        echo "✅ Full coverage tests completed for main branch"
+        echo "📊 Coverage metrics updated in Codecov"

.gitignore

@@ -6,6 +6,11 @@
 *.csv
 
 docs/build
+
+# for conda environment install, converted from pyproject.toml
+environment.yml 
+# for local settings
+.vscode/
 ################################################################################
 #                               Jupyter Notebook                               #
 ################################################################################

README.md

@@ -33,15 +33,3 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY
 You should have received a copy of the GNU General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 By request, this software may also be distributed under the terms of the GNU Lesser General Public License (LGPL); for permission, contact the authors or maintainer.
-
-# Notes on contributing & maintenance
-
-There is a GitHub Action on this repo which will automatically build the documentation (which uses Material for MkDocs with `mike` for versioning). This action triggers on push to main (which creates a `dev` section of the docs), on publishing a release (which creates a numbered version of the docs), and on pull request edits (which makes a `pr-###` version of the docs). 
-After merging a pull request, it is a good idea to use [mike](https://github.com/jimporter/mike) to clear out the PR version of the docs. Locally, do something like the following
-```
-git fetch 
-mike delete pr-### # replace with correct PR number
-git switch gh-pages
-git push origin gh-pages
-```
-This could theoretically be automated but I decided against this for now. In the long run, it may be worth not generating PR versions of the docs if this is burdensome.

__init__.py

@@ -14,11 +14,4 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-
-import sys
-import scipy.optimize as sp
-import numpy as np
-import math
-import csv
-
 from .lyopronto import *