gentroutils 0.2.0__tar.gz → 1.6.0.dev1__tar.gz

gentroutils-1.6.0.dev1/.github/workflows/labeler.yaml

@@ -0,0 +1,14 @@
+name: label-pr
+
+"on":
+  - pull_request
+  - issues
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: srvaroa/labeler@master
+        env:
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

gentroutils-1.6.0.dev1/.github/workflows/pr.yaml

@@ -0,0 +1,42 @@
+name: checks
+
+on:
+  pull_request:
+    branches:
+      - dev
+      - main
+
+
+jobs:
+  check:
+    name: ${{ matrix.command }}-${{ matrix.python-version }}
+    strategy:
+      max-parallel: 2
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        command: ["test", "type-check", "dep-check", "lint"]
+        # Skip redundant checks.
+        exclude:
+          - command: "lint"
+            python-version: "3.11"
+          - command: "lint"
+            python-version: "3.12"
+          - command: "dep-check"
+            python-version: "3.11"
+          - command: "dep-check"
+            python-version: "3.12"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+          python-version:  ${{ matrix.python-version }}
+      - name: Install project
+        run: uv sync --all-extras
+      - name: Run test
+        run: make ${{ matrix.command }}

gentroutils-1.6.0.dev1/.github/workflows/release.yaml

@@ -0,0 +1,73 @@
+name: release
+on:
+  push:
+    tags: ['v[0-9]+.[0-9]+.[0-9]']
+  workflow_dispatch:
+
+concurrency:
+  group: prod
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: pyproject.toml
+      - uses: astral-sh/setup-uv@v5
+      - name: Install project
+        run: uv sync --all-extras
+      - name: Build package
+        run: make build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  release:
+    name: test-pypi-release
+    needs: build
+    environment:
+      name: DEV
+      url:  https://test.pypi.org/p/gentroutils
+    permissions:
+      id-token: write
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to  ${{ vars.PYPI_NAME }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: ${{ vars.PYPI_URL }}
+          packages-dir: dist/
+          verbose: true
+
+
+  dev-release:
+    needs:
+      - build
+    permissions:
+      id-token: write
+      contents: write
+    runs-on: ubuntu-latest
+    environment:
+      name: PyPI
+      url: https://pypi.org/p/gentroutils
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to  ${{ vars.PYPI_NAME }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: ${{ vars.PYPI_URL }}
+          packages-dir: dist/
+          verbose: true

{gentroutils-0.2.0 → gentroutils-1.6.0.dev1}/.github/workflows/release_pr.yaml

@@ -1,19 +1,19 @@
-name: Trigger Release
+name: trigger-release
 
-"on":
+on:
   schedule:
     - cron: "0 11 * * 2"
   workflow_dispatch:
 
 jobs:
-  pull-request:
+  prepare-release-pr:
     runs-on: ubuntu-latest
     environment: DEV
     steps:
       - uses: actions/create-github-app-token@v1
         id: trigger-token
         with:
-          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}}
+          app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID }}
           private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }}
       - uses: actions/checkout@v4
         with:

{gentroutils-0.2.0 → gentroutils-1.6.0.dev1}/.github/workflows/tag.yaml

@@ -1,27 +1,20 @@
-name: Tag
-
-"on":
+name: tag-release
+on:
   push:
-    branches: ["main"]
-
-concurrency:
-  group: deploy
-  # NOTE: prevent hickups with semantic-release
-  cancel-in-progress: false
+    branches:
+      - dev
+      - main
 
-env:
-  PYTHON_VERSION_DEFAULT: "3.10.8"
 
 jobs:
-  tag:
+  create-tag:
     # NOTE: only trigger the workflow when the commit is not from the GitHubActions bot (prevent self-triggering)
-    if: github.event.commits[0].author.name != 'github-actions'
+    if: github.event.commits[0].author.name != 'github-actions[botg]'
     runs-on: ubuntu-latest
     concurrency: release
     environment: DEV
     permissions:
       contents: write
-
     steps:
       # NOTE: commits using GITHUB_TOKEN does not trigger workflows and we want to trigger PiPY from tag
       - uses: actions/create-github-app-token@v1
@@ -35,22 +28,31 @@ jobs:
           repository: opentargets/gentroutils
           token: ${{ secrets.GITHUB_TOKEN }}
           persist-credentials: false
-          ref: main
-      - name: Python Semantic Release
+          ref: ${{ github.ref_name }}
+      - name: Create package release
         id: semrelease
         # v9.6.0 is required due to the python v3.12 in the newer version of semantic release action which
         # breaks the poetry build command.
-        uses: python-semantic-release/python-semantic-release@v9.6.0
+        uses: python-semantic-release/python-semantic-release@v9.19.1
         with:
           github_token: ${{ steps.trigger-token.outputs.token }}
-
       - name: Publish package to GitHub Release
-        uses: python-semantic-release/upload-to-gh-release@main
+        uses: python-semantic-release/publish-action@v9.19.1
         if: ${{ steps.semrelease.outputs.released }} == 'true'
         with:
-          # NOTE: allow to start the workflow when push action on tag gets executed
-          # requires using GH_APP to authenitcate, otherwise push authorised with
-          # the GITHUB_TOKEN does not trigger the tag artifact workflow.
-          # see https://github.com/actions/create-github-app-token
           github_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ steps.semrelease.outputs.tag }}
+      - name: Sync dev and main branch
+        if: ${{ github.ref_name == 'main' }}
+        shell: bash
+        run: |
+          git config user.name 'github-actions[bot]'
+          git config user.email 'github-actions[bot]@users.noreply.github.com'
+          git checkout dev
+          git merge main
+      - name: Push changes
+        if: ${{ github.ref_name == 'main' }}
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ steps.trigger-token.outputs.token }}
+          branch: dev

{gentroutils-0.2.0 → gentroutils-1.6.0.dev1}/.gitignore

@@ -12,6 +12,22 @@ wheels/
 # covarage
 .coverage
 coverage.xml
-
+.coverage*
 # interrogate
 interrogate_badge.svg
+
+.idea
+.cloudstorage
+.mypy_cache
+.pytest_cache
+.ruff_cache
+
+
+# R
+.RData
+.Rhistory
+data
+
+
+# otter
+work/

gentroutils-1.6.0.dev1/.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+    "recommendations": [
+      "charliermarsh.ruff",
+      "ms-python.python",
+      "ms-python.vscode-pylance",
+    ],
+  }

gentroutils-1.6.0.dev1/.vscode/settings.json

@@ -0,0 +1,19 @@
+{
+  "python.analysis.typeCheckingMode": "standard",
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit"
+    }
+  },
+  "python.testing.pytestArgs": ["tests", "src"],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true,
+  "cSpell.words": [
+    "aioftp",
+    "gentroutils",
+    "harmonised",
+    "sumstat"
+  ]
+}