Merge branch 'release/5.1.0'

Author: dermatologist

.coveragerc

@@ -1,47 +1,29 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
-    "name": "Python 3",
-    "build": {
-        "dockerfile": "Dockerfile",
-        "context": "..",
-        "args": {
-            // Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
-            "VARIANT": "3.11",
-            // Options
-            "INSTALL_NODE": "false",
-            "NODE_VERSION": "lts/*"
-        }
-    },
-    "containerEnv": {
-        "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
-        "GITHUB_USER": "${localEnv:GITHUB_USER}"
-    },
-    "workspaceFolder": "/fhiry",
-    "workspaceMount": "src=fhiry,dst=/fhiry,type=volume,volume-driver=local",
-    // Set *default* container specific settings.json values on container create.
-    "settings": {
-        "python.pythonPath": "/usr/local/bin/python",
-        "python.languageServer": "Pylance",
-        "python.linting.enabled": true,
-        "python.linting.pylintEnabled": true,
-        "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
-        "python.formatting.blackPath": "/usr/local/py-utils/bin/black",
-        "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
-        "python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
-        "python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
-        "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
-        "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
-        "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
-        "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
-    },
-    // Add the IDs of extensions you want installed when the container is created.
-    "extensions": [
-        "ms-python.python",
-        "ms-python.vscode-pylance"
-    ],
-    // Use 'forwardPorts' to make a list of ports inside the container available locally.
-    // "forwardPorts": [],
+    "name": "fhiry",
+    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+    "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+    "runArgs": [
+        // avoid UID/GID remapping under rootless Podman
+        "--userns=keep-id"
+      ],
+    "features": {},
+
     // Use 'postCreateCommand' to run commands after the container is created.
-    "postCreateCommand": "pip3 install --user -e .",
-    // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
-    // "remoteUser": "vscode"
-}
+    "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": ["ms-python.python", "editorconfig.editorconfig"],
+            "settings": {
+                "python.testing.pytestArgs": ["tests"],
+                "python.testing.unittestEnabled": false,
+                "python.testing.pytestEnabled": true,
+                "python.defaultInterpreterPath": "/workspaces/fhiry/.venv/bin/python",
+                "python.testing.pytestPath": "/workspaces/fhiry/.venv/bin/pytest"
+            }
+        }
+    }
+}

.devcontainer/Dockerfile

@@ -0,0 +1,10 @@
+#! /usr/bin/env bash
+
+# Install uv
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Install Dependencies
+uv sync
+
+# Install pre-commit hooks
+uv run pre-commit install --install-hooks

.devcontainer/devcontainer.json

@@ -0,0 +1,30 @@
+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.11"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.8.8"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: 'true'
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: uv sync --frozen
+      shell: bash

.devcontainer/postCreateCommand.sh

@@ -6,29 +6,15 @@ on:
     types: [published]
 
 jobs:
-  deploy:
+  deploy-docs:
     runs-on: ubuntu-latest
-    timeout-minutes: 15
+    timeout-minutes: 20
     steps:
-    - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-      with:
-        enable-cache: true
-    - name: "Set up Python"
-      uses: actions/setup-python@v5
-      with:
-          python-version-file: "pyproject.toml"
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
-        uv pip install -r docs/requirements.txt
-    - name: Create docs
-      run: |
-        uv run python -m sphinx -b html docs/ docs/_build/html
-        cp docs/_config.yml docs/_build/html/_config.yml
-    - name: Deploy Docs 🚀
-      uses: JamesIves/github-pages-deploy-action@v4
-      with:
-        branch: gh-pages # The branch the action should deploy to.
-        folder: docs/_build/html # The folder the action should deploy.
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Deploy documentation
+        run: uv run mkdocs gh-deploy --force

.github/actions/setup-python-env/action.yml

@@ -11,20 +11,13 @@ jobs:
     timeout-minutes: 20
     steps:
     - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-      with:
-        enable-cache: true
-    - name: "Set up Python"
-      uses: actions/setup-python@v5
-      with:
-          python-version-file: "pyproject.toml"
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
+
     - name: Build and publish
       run: |
-        uv run python setup.py bdist_wheel
+        uv build
     - name: Publish distribution 📦 to PyPI
       if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/docs.yml

@@ -1,13 +1,16 @@
 name: Python Test
 
 on:
+  schedule:
+    - cron: '1 1 2,16 * *'  # every 2nd and 16th at 01:01. To flag any dependency issues.
   push:
     branches:
       - develop
   pull_request:
     branches:
       - master
       - develop
+      - main
 
 jobs:
   build:
@@ -21,17 +24,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-      with:
-        enable-cache: true
-    - name: "Set up Python"
-      uses: actions/setup-python@v5
-      with:
-          python-version-file: "pyproject.toml"
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
 
     - name: Run tests
-      run: uv run pytest tests
+      run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Check if documentation can be built
+        run: uv run mkdocs build

.github/workflows/publish.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - main
 
 jobs:
   build:
@@ -17,17 +18,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-      with:
-        enable-cache: true
-    - name: "Set up Python"
-      uses: actions/setup-python@v5
-      with:
-          python-version-file: "pyproject.toml"
-    - name: Install dependencies
-      run: |
-        uv sync --all-extras --dev
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
+
     - name: Test with tox
       run: |
         uv run tox

.github/workflows/pytest.yml

@@ -0,0 +1,27 @@
+name: Dependencies upgrade
+
+on: workflow_dispatch
+
+jobs:
+  flake-update:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: astral-sh/setup-uv@v6
+
+    # https://docs.astral.sh/uv/concepts/projects/#upgrading-locked-package-versions
+    - run: uv lock --upgrade
+
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v7
+      with:
+        title: "[Automated] Dependencies upgrade"
+        commit-message: "[Automated] Dependencies upgrade"
+        branch: "auto/uv-sync-upgrade"
+        add-paths: uv.lock
+        delete-branch: true
+        labels: |
+            automated pr
+        body-path: result
+        draft: true