Fix/localmodel

.github/workflows/codecov.yml

@@ -1,41 +1,29 @@
 name: Coverage (Codecov)
 
 on:
-  push:
-    branches: [ "main", "develop" ]
   pull_request:
-    branches: [ "main", "develop" ]
+    branches: ["main", "develop"]
 
 jobs:
-  test:
-    name: Run tests and upload coverage
+  coverage:
+    name: Compute coverage
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.10"
+          enable-cache: true
 
-      - name: Install pandoc
-        uses: pandoc/actions/setup@v1
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install coverage
-          python -m pip install sphinx myst_parser sphinx-rtd-theme nbsphinx pandoc jupyter jupyterlab
-          pip install -e .
+      - name: Install the project
+        run: uv sync --locked --all-extras --dev
 
       - name: Tests with coverage
-        run: |
-          coverage run --omit='./results/*','./docs/*','./examples/*' -m unittest discover tests
-          coverage xml -o coverage.xml
+        run: uv run pytest --cov=nnodely --cov-branch --cov-report=xml tests
 
       - name: Upload results to Codecov
-        uses: codecov/codecov-action@v5
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: coverage.xml
+        uses: codecov/codecov-action@v6
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/create-release.yml

@@ -1,130 +1,101 @@
-name: Publish New nnodely Release
+name: Publish
 
 on:
   push:
     tags:
-      - "v*"  # Push events to matching v*, i.e., v1.0, v20.15.10
+      - "v*"
 
 jobs:
-  check-tag-version:
-    name: Check tag version equal to file version
+  publish:
+    name: Build and publish to both TestPyPi and PyPi
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
-      - name: Extract tag version
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+
+      - name: Validate tag matches project version
         run: |
-          TAG_NAME="${{ github.ref_name }}"
-          TAG_VERSION=$(echo $TAG_NAME | sed 's/v//')
+          TAG_VERSION="${GITHUB_REF_NAME#v}"
+          PROJ_VERSION=$(uv version --short)
+
           echo "Tag version: $TAG_VERSION"
-          echo "TAG_VERSION=$TAG_VERSION" >> $GITHUB_ENV
-      - name: Extract file version
-        run: |
-          FILE_VERSION=$(awk -F"'" '/^__version__/ {print $2}' nnodely/__init__.py)
-          echo "File version: $FILE_VERSION"
-          echo "FILE_VERSION=$FILE_VERSION" >> $GITHUB_ENV
-      - name: Show tag and file versions
-        run: |
-          echo "The tag version: ${{ env.TAG_VERSION }}"
-          echo "The file version: ${{ env.FILE_VERSION }}"
-      - name: Check if tag and file versions match
-        if: ${{ env.TAG_VERSION != env.FILE_VERSION }}
-        run: |
-          echo "The tag version ${{ env.TAG_VERSION }} does not match file version ${{ env.FILE_VERSION }}"
-          exit 1
+          echo "Project version: $PROJ_VERSION"
 
-  build:
-    name: Build distribution of tagged version
-    needs:
-      - check-tag-version
-    runs-on: ubuntu-latest
+          if [ "$TAG_VERSION" != "$PROJ_VERSION" ]; then
+            echo "Mismatch: tag=$TAG_VERSION project=$PROJ_VERSION"
+            exit 1
+          fi
 
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        ref: ${{ github.ref_name }}
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.x"
-
-    - name: Install pypa/build
-      run: >-
-        python3 -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: python3 -m build
-    - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-
-  publish-to-pypi:
-    name: Publish to PyPI
-    needs:
-    - build
+      - name: Build
+        run: uv build
 
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/nnodely  # Replace <package-name> with your PyPI project name
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+      # Check that basic features work and we didn't miss to include crucial files
+      - name: Basic test (wheel)
+        run: uv run --isolated --no-project --with dist/*.whl python -c "import nnodely"
 
-    steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish nnodely to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Basic test (source distribution)
+        run: uv run --isolated --no-project --with dist/*.tar.gz python -c "import nnodely"
+
+      - name: TestPyPi publish
+        run: uv publish --index testpypi
+
+      - name: PyPI publish
+        run: uv publish
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v7
+        with:
+          name: python-package-distributions
+          path: dist/
 
   github-release:
-    name: >-
-      Sign the Python with Sigstore and upload them to GitHub Release
-    needs:
-    - publish-to-pypi
+    name: Sign the Python with Sigstore and upload them to GitHub Release
     runs-on: ubuntu-latest
+    needs:
+      - publish
 
     permissions:
-      contents: write  # IMPORTANT: mandatory for making GitHub Releases
-      id-token: write  # IMPORTANT: mandatory for sigstore
+      contents: write
+      id-token: write
 
     steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v3.0.0
-      with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
-    - name: Get the branch version
-      run: |
-          TAG_NAME="${{ github.ref_name }}"
-          TAG_MESSAGE=${{ github.event.workflow_run.head_commit.message }}
-          echo "Tag message: $TAG_MESSAGE"
-          echo "TAG_MESSAGE=$TAG_MESSAGE" >> $GITHUB_ENV
-    - name: Create GitHub release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-        tag: ${{ github.ref_name }}
-      run: |
-        echo "The branch version: $tag"
-        gh release create $tag --title "$tag" --repo ${{ github.repository }} --notes "${{ env.TAG_MESSAGE }}"
-    - name: Upload artifact signatures to GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-        tag: ${{ github.ref_name }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload $tag dist/** --repo ${{ github.repository }}
+      - uses: actions/download-artifact@v8
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Sign artifacts
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: |
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Detect prerelease
+        id: version
+        run: |
+          VERSION="${GITHUB_REF_NAME#v}"
+
+          if [[ "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+            echo "PRERELEASE=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "PRERELEASE=true" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Release
+        uses: softprops/action-gh-release@v3
+        if: github.ref_type == 'tag'
+        with:
+          files: |
+            dist/*.tar.gz
+            dist/*.whl
+          generate_release_notes: true
+          prerelease: ${{ steps.version.outputs.PRERELEASE }}

.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: ["main", "develop"]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+
+      - name: Install the project
+        run: uv sync --locked --all-extras --dev
+
+      - name: Lint
+        run: uv run ruff check

.github/workflows/run-tests.yml

@@ -1,51 +1,29 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: Run Tests
 
 on:
-  push:
-    branches: [ "main", "develop" ]
   pull_request:
-    branches: [ "main", "develop"]
+    branches: ["main", "develop"]
 
 jobs:
-  build:
-
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [ "3.10", "3.11", "3.12"]
-        architecture: ['x64', 'x86']
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install pandoc
-      uses: pandoc/actions/setup@v1
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest 
-        python -m pip install sphinx myst_parser sphinx-rtd-theme nbsphinx pandoc jupyter jupyterlab
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
-
-
-
+      - uses: actions/checkout@v6
 
+      - name: Install uv and set the Python version
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
 
+      - name: Install the project
+        run: uv sync --locked --all-extras --dev
 
+      - name: Run tests
+        run: uv run pytest tests