Incorporates pyproject.toml

.github/workflows/build_documentation.yml → .github/workflows/documentation.yml

@@ -1,28 +1,25 @@
-name: Build Documentation
+name: Publish Documentation
 
 on:
-  push:
-    branches:    
-      - main
+  workflow_call:
 
 jobs:
-  build:
-
+  publish-documentation:
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
     - name: Upgrade pip, install package, install requirements, build docs
       run: |
         pip install --upgrade pip
-        pip install -r ./docs/requirements.txt
+        pip install .
+        if [ -f ./docs/requirements.txt ]; then pip install -r ./docs/requirements.txt; fi
+        pip install sphinx
         sphinx-build docs ./docs/_build/html/
     # Create an artifact of the html output.
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: DocumentationHTML
         path: docs/_build/html/
@@ -35,9 +32,8 @@ jobs:
         git config --global user.name "${GITHUB_ACTOR}"
         git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
         git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" --branch gh-pages --single-branch gh-pages
-        cd gh-pages/
-        git rm -r .
-        cp -r ../docs/_build/html/* .
+        cp -r docs/_build/html/* gh-pages/
+        cd gh-pages
         touch .nojekyll
         git add .
         git commit -m "Update documentation." -a || true
@@ -49,4 +45,4 @@ jobs:
         branch: gh-pages
         directory: gh-pages
         github_token: ${{ secrets.GITHUB_TOKEN }}
-    # ===============================
+    # ===============================

.github/workflows/package_release.yml

@@ -0,0 +1,44 @@
+name: Package and Documentation Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release-version:
+    runs-on: ubuntu-latest
+    steps:
+      - id: parse-version
+        name: Parse release version
+        run: |
+          echo "version=${RELEASE_VERSION/v/}" >> "$GITHUB_OUTPUT"
+    env:
+      RELEASE_VERSION: ${{ github.event.release.tag_name }}
+    outputs:
+      version: ${{ steps.parse-version.outputs.version }}
+  publish-test-pypi:
+    uses: ./.github/workflows/pypi.yml
+    with:
+      repository_url: https://test.pypi.org/legacy/
+    secrets:
+      API_TOKEN: ${{ secrets.TEST_PYPI_API_TOKEN }}
+  test-test-pypi:
+    needs: [release-version, publish-test-pypi]
+    uses: ./.github/workflows/tests.yml
+    with:
+      install_command: "python3 -m pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple kegg-pull==${{ needs.release-version.outputs.version }}"
+  publish-pypi:
+    needs: test-test-pypi
+    uses: ./.github/workflows/pypi.yml
+    with:
+      repository_url: https://upload.pypi.org/legacy/
+    secrets:
+      API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+  test-pypi:
+    needs: [release-version, publish-pypi]
+    uses: ./.github/workflows/tests.yml
+    with:
+      install_command: "python3 -m pip install kegg-pull==${{ needs.release-version.outputs.version }}"
+  publish-documentation:
+    needs: test-pypi
+    uses: ./.github/workflows/documentation.yml

.github/workflows/pull_request.yml

@@ -0,0 +1,16 @@
+name: Pull request
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  pull-request:
+      uses: ./.github/workflows/tests.yml
+      with:
+        install_command: "python3 -m pip install -e ."

.github/workflows/pypi.yml

@@ -0,0 +1,32 @@
+name: Publish package
+
+on:
+  workflow_call:
+    inputs:
+      repository_url:
+        description: The URL of the PyPi distribution
+        required: true
+        type: string
+    secrets:
+      API_TOKEN:
+        required: true
+
+jobs:
+  publish-package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install build
+      - name: Build package
+        run: python3 -m build
+      - name: Publish package to a PyPi distribution
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.API_TOKEN }}
+          repository-url: ${{ inputs.repository_url }}

.github/workflows/tests.yml

@@ -0,0 +1,40 @@
+name: Run Tests
+
+on:
+  workflow_call:
+    inputs:
+      install_command:
+        description: The command for installing the package to test.
+        required: true
+        type: string
+
+jobs:
+  run-tests:
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        os: [ ubuntu-latest, windows-latest, macOS-latest ]
+    runs-on: ${{matrix.os}}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install testing environment
+      run: |
+        python3 -m pip install --upgrade pip
+        python3 -m pip install pytest pytest-mock pytest-cov deepdiff
+    - name: Install package
+      uses: Wandalen/wretry.action@master
+      with:
+        command: ${{ inputs.install_command }}
+        attempt_limit: 10
+        attempt_delay: 10000
+    - name: Run tests on package
+      run: python3 -m pytest dev --cov --cov-branch --cov-report=term-missing -x
+    - name: Debug with tmate on failure
+      if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3
+      with:
+        limit-access-to-actor: true

.gitignore

@@ -8,3 +8,4 @@ docs/_build
 docs/notebook/.ipynb_checkpoints/
 docs/notebook/tutorial.ipynb
 dist/
+src/kegg_pull/_version.py

pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools", "wheel", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "kegg-pull"
+description = "Pulls any and all entries from any and all KEGG databases, pulls KEGG entry IDs, and wraps all the KEGG REST API operations in both Python API and the command line."
+readme = "README.rst"
+requires-python = ">=3.10"
+keywords = ["kegg", "rest", "sdk", "api", "cli"]
+license = {file = "LICENSE"}
+classifiers = [
+     'Environment :: Console',
+     'Intended Audience :: Developers',
+     'License :: OSI Approved :: BSD License',
+     'Operating System :: OS Independent',
+     'Programming Language :: Python :: 3.10',
+     'Topic :: Software Development :: Libraries :: Python Modules',
+     'Topic :: Scientific/Engineering :: Medical Science Apps',
+     'Topic :: Scientific/Engineering :: Chemistry',
+     'Topic :: Scientific/Engineering :: Bio-Informatics',
+     'Typing :: Typed'
+
+]
+dynamic = ["version", "dependencies"]
+
+[project.urls]
+"Homepage" = "https://github.com/MoseleyBioinformaticsLab/kegg_pull"
+"Documentation" = "https://moseleybioinformaticslab.github.io/kegg_pull/"
+"GitHub" = "https://github.com/MoseleyBioinformaticsLab/kegg_pull"
+"Issues" = "https://github.com/MoseleyBioinformaticsLab/kegg_pull/issues"
+
+[tool.setuptools.dynamic]
+dependencies = {file = "requirements.txt"}
+
+[tool.setuptools_scm]
+write_to = "src/kegg_pull/_version.py"
+
+[project.scripts]
+kegg_pull = "kegg_pull.__main__:main"