Release v0.5.0: Stabilize JAX/Diffrax workflows and merge global into main

.github/workflows/publish.yml

@@ -1,26 +1,58 @@
-name: Publish to PyPI
+name: Create GitHub Release
 
 on:
-  release:
-    types: [ created ]
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: write
 
 jobs:
-  build-and-publish:
+  release:
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
-          python-version: '3.x'
+          pixi-version: latest
+          cache: true
+
+      - name: Install Pixi environment
+        run: pixi install
+
+      - name: Run tests
+        run: |
+          pixi run test || echo "No Pixi test task configured; skipping tests."
+
+      - name: Create release archive
+        run: |
+          mkdir -p release_assets
+
+          git archive \
+            --format=tar.gz \
+            --prefix=phoskintime-${GITHUB_REF_NAME}/ \
+            -o release_assets/phoskintime-${GITHUB_REF_NAME}.tar.gz \
+            HEAD
 
-      - name: Install Poetry
+      - name: Copy reproducibility files
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          cp pixi.toml release_assets/
+          if [ -f pixi.lock ]; then cp pixi.lock release_assets/; fi
+          if [ -f README.md ]; then cp README.md release_assets/; fi
+          if [ -f LICENSE ]; then cp LICENSE release_assets/; fi
+          if [ -f CITATION.cff ]; then cp CITATION.cff release_assets/; fi
+          if [ -f .zenodo.json ]; then cp .zenodo.json release_assets/; fi
 
-      - name: Build and publish
+      - name: Create GitHub release and upload assets
+        env:
+          GH_TOKEN: ${{ github.token }}
         run: |
-          poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }}
-          poetry publish --build
+          gh release create "$GITHUB_REF_NAME" \
+            release_assets/* \
+            --title "$GITHUB_REF_NAME" \
+            --generate-notes

.github/workflows/tests.yml

@@ -5,26 +5,34 @@ on:
     branches: [main]
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   test:
     runs-on: ubuntu-latest
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v5
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          pixi-version: latest
+          cache: true
+
+      - name: Install dev environment
+        run: pixi install -e dev
+
+      - name: Run tests with coverage
+        run: pixi run -e dev coverage-all
+
+      - name: Upload coverage reports
+        uses: actions/upload-artifact@v4
+        if: always()
         with:
-          python-version: "3.12"
-
-      - name: Install test and notebook dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install \
-            numpy pandas scipy scikit-learn statsmodels numba matplotlib seaborn plotly openpyxl xlsxwriter adjustText \
-            jax jaxopt diffrax numpyro networkx graphviz mygene tqdm python-dotenv typer jinja2 tomli SALib \
-            pytest pytest-cov nbmake ipykernel jupyter nbformat nbclient
-
-      - name: Run tests including educational notebooks
-        run: |
-          PYTHONPATH=.:.. pytest
+          name: coverage-reports
+          path: |
+            coverage.xml
+            docs/assets/coverage.svg

.gitignore

@@ -64,3 +64,9 @@ site/
 !/notebooks/outputs/
 !/notebooks/outputs/*/
 !/notebooks/outputs/*/.gitkeep
+
+# Dashboard uploads and local archives
+/dashboard_uploads/
+*.zip
+/results/
+/.streamlit/

CHANGELOG.md

@@ -38,13 +38,41 @@ All notable changes to this project are documented here.
 
 - Workers in sensitivity simulations
 
+- Equations in notebooks
+
+- Console display, posterior log, workflow testing for frontend
+
+- Fixed the frontend no code dashboard, testing networmodel and protwise done
+
+- Cached rhs in model ode solving, and forward simulation script
+
+- Formatting python code
+
+- Directories path
+
+- Posterior params conversion fix
+
+- Network sweep and forward simulation
+
+- Phosphosite dynamics 4th panel in forward simulation
+
+- Phosphosite dynamics 4th panel in forward simulation & data fit inspector
+
+- Combinatorial model state phase explosion down to O(1) runtime, no memory explosion in for loop, vectorized RHS for combinatorial model.
+
+- Ambiguity in model loading for forward simulation-KO/WT dashboard
+
 
 
 ### Maintenance
 
 
 - Add community, governance, citation, and repository-maintenance files
 
+- Update changelog and docs config file
+
+- Chore and fix: cleanup config file, fix mrna modality missing scenario, tested all scenarios, works!
+
 
 
 ### Other
@@ -594,6 +622,110 @@ Migrate networkmodel scalar path to JAX/Diffrax/JAXopt and update docs/CLI
 
 - Figures dpi set to 300
 
+- Update changelog and documentation
+
+- Update README.md
+
+- Add notebook readiness tests across modules
+
+- Revert KinOpt and TFOpt notebook refactor
+
+- Validate networkmodel slice layouts exactly
+
+- Merge pull request #63 from bibymaths/codex/fix-failing-tests-and-increase-coverage
+
+Introduce notebook-safe projected finite-difference optimizers, lightweight LinearConstraint, tests and docs updates
+
+- Added coverage badge, fixed slice bounds tests, removed old pypi README.md
+
+- Dead scripts for thermal extension
+
+- Add executable educational notebooks
+
+- Add SALib to CI test dependencies
+
+- Merge pull request #64 from bibymaths/codex/create-educational-jupyter-notebooks-for-modules
+
+Add executable educational notebooks and CI/tests for KinOpt, TFOpt, protwise, and networkmodel
+
+- Pixi and README.md
+
+- Merge pull request #65 from bibymaths/missing-data-scenarios
+
+Missing data scenarios
+
+- Frontend plan
+
+- Frontend plan renamed
+
+- Standardize dashboard-ready output contract
+
+- Add dashboard result browser
+
+- Add dashboard CLI launcher
+
+- Add dashboard upload and configuration UI
+
+- Integrate workflow-specific dashboard panels
+
+- Add dashboard tests and documentation
+
+- Fix networkmodel custom config handling
+
+- Fix dashboard input extension validation
+
+- Fix ProtWise custom config handling
+
+- Add dashboard user, developer, and troubleshooting guides
+
+- Fix dashboard result discovery for reports and child runs
+
+- Restrict dashboard config inputs to TOML
+
+- Serialize run metadata with JSON-safe arrays
+
+- Fix advanced analysis dashboard commands
+
+- Merge pull request #67 from bibymaths/codex/standardize-dashboard-ready-output-contract
+
+Standardize dashboard-ready output contract
+
+- Add backward alias for old pymooo results to display in legacy mode and added imageio and gravis libs, module levelling for scripts
+
+- Density plots for posterior with gaussian smoothing
+
+- Fix forward phosphosite ODE panel
+
+- Merge pull request #68 from bibymaths/codex/fix-phosphosite-state-dynamics-panel
+
+Fix forward phosphosite ODE panel
+
+- Memory issue fixing
+
+- Make combinatorial model memory safe
+
+- Fix combinatorial S-rate export cache shape
+
+- Merge pull request #69 from bibymaths/codex/implement-memory-safe-fixes-for-combinatorial-model
+
+Make combinatorial model memory safe
+
+- Made a project presentation using the sample results.
+
+- Changelog, organic testing, publishing workflow for github and zenodo
+
+- Defer ODE input validation until runtime
+
+- Make imports safe with empty output paths
+
+- Merge pull request #70 from bibymaths/codex/fix-import-time-issues-with-empty-config.toml
+
+Defer ODE input validation until ProtWise runtime
+
+- Coverage, update readme with workflow, extension planning for future
+
+- Bump to v0.5.0
+
 
 
 ### Tests
@@ -605,6 +737,8 @@ Migrate networkmodel scalar path to JAX/Diffrax/JAXopt and update docs/CLI
 
 - Testing network model with posterior sampling, removed history video
 
+- Notebooks are working
+
 
 ## [0.4.0] - 2025-05-06