release: CORNETO v1.0.0-rc.3

.github/workflows/build-and-publish.yml

@@ -89,6 +89,15 @@ jobs:
           poetry build
           poetry run twine check dist/*
 
+      # The tag is already covered by the merged PR's full test gate. Validate
+      # only the tag-specific artifact here, before it is published.
+      - name: Smoke-test the release wheel
+        if: steps.validate_tag.outputs.should_publish == 'true'
+        run: |
+          python -m venv /tmp/corneto-release-wheel-smoke
+          /tmp/corneto-release-wheel-smoke/bin/pip install dist/*.whl
+          /tmp/corneto-release-wheel-smoke/bin/python -c 'import corneto; print(corneto.__version__)'
+
       # 8. Create GitHub Release with automated notes
       - name: Create GitHub Release
         if: steps.validate_tag.outputs.should_publish == 'true'

.github/workflows/deploy-docs.yml

@@ -7,24 +7,8 @@ env:
 on:
   push:
     branches:
-      - dev
       - main
-    tags:
-      - '*'
   workflow_dispatch:
-    inputs:
-      target:
-        description: "What to build/deploy (dev=latest, main=stable, or tag)"
-        type: choice
-        required: true
-        options:
-          - dev
-          - main
-          - tag
-      tag:
-        description: "Tag to deploy when target=tag (e.g., v1.0.0-beta.3)"
-        type: string
-        required: false
   workflow_run:
     workflows: ["Publish Python Package"]
     types: [completed]
@@ -43,14 +27,7 @@ jobs:
         with:
           fetch-depth: 0
           fetch-tags: true
-          ref: >-
-            ${{
-              github.event_name == 'workflow_dispatch' &&
-              (github.event.inputs.target == 'tag' && format('refs/tags/{0}', github.event.inputs.tag) ||
-               format('refs/heads/{0}', github.event.inputs.target))
-              || github.event_name == 'workflow_run' && github.event.workflow_run.head_sha
-              || github.ref
-            }}
+          ref: ${{ github.event_name == 'workflow_run' && github.event.workflow_run.head_sha || github.ref }}
 
       - name: Set up Python & Graphviz
         uses: actions/setup-python@v5
@@ -89,22 +66,19 @@ jobs:
       - name: Determine version_folder
         id: set_version
         run: |
-          case "${GITHUB_REF}" in
-            refs/heads/dev)
-              echo "version_folder=latest" >> $GITHUB_OUTPUT
-              ;;
-            refs/heads/main)
-              echo "version_folder=stable" >> $GITHUB_OUTPUT
-              ;;
-            refs/tags/*)
-              v="${GITHUB_REF#refs/tags/}"
-              echo "version_folder=${v}" >> $GITHUB_OUTPUT
-              ;;
-            *)
-              echo "No docs to deploy for ${GITHUB_REF}" >&2
-              exit 0
-              ;;
-          esac
+          if [ "${{ github.event_name }}" = "workflow_run" ]; then
+            if [[ "${{ github.event.workflow_run.head_branch }}" == v* ]]; then
+              echo "version_folder=${{ github.event.workflow_run.head_branch }}" >> $GITHUB_OUTPUT
+            else
+              echo "Publish workflow did not run for a release tag" >&2
+              exit 1
+            fi
+          elif [ "${GITHUB_REF}" = "refs/heads/main" ]; then
+            echo "version_folder=stable" >> $GITHUB_OUTPUT
+          else
+            echo "No documentation target for ${GITHUB_REF}" >&2
+            exit 1
+          fi
 
       - name: Sync GitHub Releases to Docs
         env:
@@ -119,15 +93,6 @@ jobs:
           DOCS_BASE_URL: https://corneto.org
         run: poetry run sphinx-build -W --keep-going -b html docs docs/_build/html
 
-      - name: Deploy “latest” docs
-        if: ${{ steps.set_version.outputs.version_folder == 'latest' }}
-        uses: peaceiris/actions-gh-pages@v4
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/_build/html
-          destination_dir: latest
-          keep_files: true
-
       - name: Deploy “stable” docs
         if: ${{ steps.set_version.outputs.version_folder == 'stable' }}
         uses: peaceiris/actions-gh-pages@v4
@@ -137,8 +102,8 @@ jobs:
           destination_dir: stable
           keep_files: true
 
-      - name: Deploy versioned docs for tag
-        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+      - name: Deploy versioned docs for release tag
+        if: ${{ steps.set_version.outputs.version_folder != 'stable' }}
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/unit-tests.yml

@@ -4,8 +4,15 @@
 name: Unit tests
 
 on:
-  push:
   pull_request:
+    branches:
+      - main
+
+# A PR into the public trunk is the release gate.  Do not repeat this matrix
+# for every temporary branch push, merge to main, or release tag.
+concurrency:
+  group: unit-tests-${{ github.event.pull_request.number }}
+  cancel-in-progress: true
 
 env:
   POETRY_VERSION: "2.4.1"

CONTRIBUTING.md

@@ -13,7 +13,7 @@ For notebook execution in tutorials, we also support [Pixi](https://pixi.sh/) en
 Once installed, clone the repository and install it with poetry. This will create a virtual environment ready for development:
 
 ```bash
-git clone git+https://github.com/saezlab/corneto.git@dev
+git clone https://github.com/saezlab/corneto.git
 cd corneto
 poetry install --with dev
 ```
@@ -243,7 +243,7 @@ poetry run python docs/tutorials/run_notebooks.py
 - **Pixi integration**: Tutorial notebooks can use individual `pixi.toml` files for isolated execution environments with specific dependencies.
 - **Poetry and PEP 621**: The project uses both Poetry (legacy) and modern PEP 621 project configuration in `pyproject.toml`.
 
-Please see [contributing with tutorials](https://github.com/saezlab/corneto/blob/dev/docs/tutorials/README.md) for more information on how to contribute tutorials.
+Please see [contributing with tutorials](https://github.com/saezlab/corneto/blob/main/docs/tutorials/README.md) for more information on how to contribute tutorials.
 
 ## Releases
 

README.md

@@ -61,12 +61,14 @@ pip install corneto
 
 CORNETO provides several optional dependency groups:
 
+- **`plot`**: Graphviz, NetworkX, and Matplotlib visualization support
 - **`research`**: Full research stack with Gurobi, PICOS, visualization, and network tools
 - **`os`**: Open-source solvers (SCIP, HiGHS) with visualization and network tools
 - **`ml`**: Machine learning dependencies (JAX, Keras, scikit-learn)
 
 Install any combination with:
 ```bash
+pip install corneto[plot]         # Visualization without the full research stack
 pip install corneto[research,ml]  # Multiple extras
 ```