Pyproject.toml Update to python standard/UV Update For Oak (#849)

Standardized pyproject.toml to PEP 621. Allowing UV to build/run oak. Currently maintaining previous poetry functionality (which all tested to work). Added job to github workflows to have some also run test using UV (make minor changes to get all workflows functional).

Version restricted any pyproject.toml files which led to errors in executing tests.

Author: DnlRKorn

.github/workflows/doc_pages.yaml

@@ -1,5 +1,6 @@
 name: Sphinx Documentation
 on:
+  workflow_dispatch:
   push:
     branches: [ main ]
 
@@ -13,12 +14,17 @@ jobs:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
 
     - name: Set up Python 3.
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v6.2.0
       with:
-        python-version: 3.9
+        python-version: 3.12
+
+        #    - name: Install Poetry.
+#      uses: snok/install-poetry@v1.3
+    - name: Install Poetry
+      run: |
+        pip install --upgrade pip
+        pip install poetry
 
-    - name: Install Poetry.
-      uses: snok/install-poetry@v1.3
 
     - name: install
       run: poetry install -E docs

.github/workflows/main.yaml

@@ -5,6 +5,7 @@
 name: Build and test
 
 on:
+  workflow_dispatch:
   push:
     branches: [ main ]
   pull_request:
@@ -15,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.12' ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -33,7 +34,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.9", "3.10", "3.11" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
         exclude:
           - os: windows-latest
             python-version: "3.9"
@@ -46,10 +47,10 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6.0.2
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -80,8 +81,8 @@ jobs:
       #----------------------------------------------
       - name: Install dependencies
         # if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: |
-          poetry add setuptools@latest
+        run:
+#          poetry add setuptools@latest
           poetry install --no-interaction --no-root
 
       #----------------------------------------------
@@ -119,3 +120,41 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           fail_ci_if_error: false
+
+  test_with_uv:
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        exclude:
+          - os: windows-latest
+            python-version: "3.9"
+
+    runs-on: ${{ matrix.os }}
+
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.3.0
+
+      - name: setup python environment
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          uv sync --extra "semsimian" --extra "gilda"
+          uv run python -c 'import nltk; nltk.download("stopwords"); nltk.download("punkt_tab")' #TODO; directly put this into our GildaImplementation class/in function _gilda_annotate
+
+      - name: Run tests
+        run: |
+         uv run pytest tests/*
+        shell: bash
+        env:
+          BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }}
+

.github/workflows/pypi-publish-dry-run.yaml

@@ -0,0 +1,42 @@
+name: Publish Python Package (Dry Run)
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-n-publish-dry-run:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI (DRY RUN)
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.12
+
+    - name: Install Poetry
+      run: |
+        pip install --upgrade pip
+        pip install poetry
+
+    - name: Install dependencies
+      run: poetry install --no-interaction
+
+    - name: Build source and wheel archives
+      run: |
+        poetry version $(git describe --tags --abbrev=0)
+        poetry build
+
+
+#    - name: Publish package to TestPyPI
+#      uses: pypa/gh-action-pypi-publish@release/v1
+#      with:
+#        password: "TEST_PASSWORD"
+#        repository-url: https://test.pypi.org/legacy/
+    

.github/workflows/pypi-publish.yaml

@@ -15,13 +15,18 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: 3.9
+        python-version: 3.12
+
+#    - name: Install Poetry
+#      uses: snok/install-poetry@v1.3.1
+#      with:
+#        virtualenvs-create: true
+#        virtualenvs-in-project: true
 
     - name: Install Poetry
-      uses: snok/install-poetry@v1.3.1
-      with:
-        virtualenvs-create: true
-        virtualenvs-in-project: true
+      run: |
+        pip install --upgrade pip
+        pip install poetry
 
     - name: Install dependencies
       run: poetry install --no-interaction

.gitignore

@@ -32,3 +32,6 @@ oak_semsimian_hp.profile
 notebooks/demo.tsv
 tests/input/obo_conf.yaml
 tests/input/obojson_conf.yaml
+uv.lock
+poetry.lock
+.panther_requests_cache.sqlite