Update to python 3.10-3.14

.github/dependabot.yml

@@ -0,0 +1,35 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+
+version: 2
+updates:
+  - package-ecosystem: "uv"
+    directories:
+      - "/"
+    schedule:
+      interval: "weekly"
+      day: "sunday"
+    open-pull-requests-limit: 10
+    groups:
+      patch-updates:
+        applies-to: version-updates
+        patterns:
+          - "*"
+        update-types:
+          - "patch"
+      minor-updates:
+        applies-to: version-updates
+        patterns:
+          - "*"
+        update-types:
+          - "minor"
+
+  - package-ecosystem: "github-actions"
+    directories:
+      - "/"
+    schedule:
+      interval: "monthly"
+    open-pull-requests-limit: 10

.github/workflows/main.yaml

@@ -1,62 +1,80 @@
-name: Build
-
+name: Test PyShEx
+env:
+  UV_VERSION: "0.7.13"
 on:
   push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 jobs:
-  update-requirements:
+  quality-checks:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - uses: dschep/install-pipenv-action@v1
-    - name: Update requirements
-      run: |
-          python -m pip install --upgrade pip
-          pip install pipenv-to-requirements
-          pipenv lock
-          pipenv_to_requirements
-          git add requirements*.txt
-          if [[ -n $(git status -s requirements*.txt) ]]
-          then
-            git config --local user.email "action@github.com"
-            git config --local user.name "GitHub Action"
-            git commit -m 'Automatically generated requirements' requirements*.txt
-            git push
-          fi
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.13
+      - name: Install tox
+        run: python -m pip install tox
+      - name: Run codespell
+        run: tox -e codespell
 
   test:
-    needs: update-requirements
-    name: Run TOX tests
-    runs-on: ubuntu-latest
+    needs:
+      - quality-checks
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [ 3.7, 3.8, 3.9, "3.10" ]
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        # Test on Windows with only the oldest and newest Python versions
+    # See https://github.com/snok/install-poetry#running-on-windows
+    defaults:
+      run:
+        shell: bash
+
+    runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: true
-    - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Run TOX
-      env:
-        # Prevents conflicts during concurrent runs. Further
-        # configuration takes place in the tox.ini file.
-        COVERAGE_FILE: .coverage.${{matrix.python-version}}
-      run: |
-        echo "Generated by build process" > tests/data/SKIP_EXTERNAL_URLS
-        pip install tox
-        tox -e py
-
-    - uses: codecov/codecov-action@v3
-      with:
-        # files: ./coverage1.xml,./coverage2.xml # optional
-        # flags: unittests # optional
-        # name: codecov-umbrella # optional
-        # fail_ci_if_error: true # optional (default = false)
-        verbose: true # optional (default = false)
+      - name: Check out repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          uv sync --group dev
+
+      - name: Verify uv.lock is up-to-date
+        run: uv lock --check
+
+      - name: Generate coverage results
+        # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
+        shell: bash
+        run: |
+          uv run coverage run -m pytest
+          uv run coverage xml
+          uv run coverage report -m
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v6.0.0
+        with:
+          name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: false

.github/workflows/pypi-publish.yaml

@@ -5,24 +5,76 @@ on:
     types: [created]
 
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+  build:
+    name: Build distributions 📦
     runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        fetch-tags: true
+
+    - name: Fetch full git tags
+      run: git fetch --tags
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+
+    - name: Install Python 3.13
+      run: uv python install 3.13
+
+    - name: Build
+      run: uv build
+
+    - name: Upload dist artifact
+      uses: actions/upload-artifact@v7
+      with:
+        name: dist
+        path: dist/
+
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event.release.prerelease == true
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+
+    environment: testpypi
+
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install wheel
-    - name: build a binary wheel dist
-      run: |
-        rm -fr dist
-        python setup.py bdist_wheel sdist
-
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.2.2
+    - name: Download dist
+      uses: actions/download-artifact@v7
+      with:
+        name: dist
+        path: dist/
+
+    - name: Publish to TestPyPI 📦
+      uses: pypa/gh-action-pypi-publish@v1.14.0
       with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+        repository-url: https://test.pypi.org/legacy/
+
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event.release.prerelease == false
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+
+    environment: pypi
+
+    steps:
+    - name: Download dist
+      uses: actions/download-artifact@v7
+      with:
+        name: dist
+        path: dist/
+
+    - name: Publish to PyPI 📦
+      uses: pypa/gh-action-pypi-publish@v1.14.0

README.md

@@ -1,3 +1,14 @@
+This repository was originally developed by [Harold Solbrig](https://github.com/hsolbrig) and was kindly contributed
+to the LinkML organization because of his retirement. All credit for the original development of this repository goes
+to him.
+
+# Special note
+Since development was taken over  after a long time of no development, there are tests that are not passing.
+The reasons are not always immediately clear, in some cases it is due to code not having been updated when dependencies
+updated their versions. In other cases, there are genuine bugs that have not been fixed. The current release was
+released in order to be able to support Python 3.14 in LinkML. Please get in touch by opening an issue if you
+encounter any bugs.
+
 # Python implementation of ShEx 2.0
 [![Pyversions](https://img.shields.io/pypi/pyversions/PyShEx.svg)](https://pypi.python.org/pypi/PyShEx)