Merge pull request #92 from zest-derm/juliand/zst-1157

Implement patient programs

.github/workflows/pre-commit-autoupdate.yaml

@@ -0,0 +1,26 @@
+name: Pre-commit auto-update
+
+on:
+  # every day at midnight
+  schedule:
+    - cron: "0 0 * * *"
+  # on demand
+  workflow_dispatch:
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+
+      - uses: browniebroke/pre-commit-autoupdate-action@main
+
+      - uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update/pre-commit-hooks
+          title: Update pre-commit hooks
+          commit-message: "chore: update pre-commit hooks"
+          body: Update versions of pre-commit hooks to latest version.

.github/workflows/pre-commit.yaml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/[email protected]

.github/workflows/test.yaml

@@ -6,6 +6,10 @@ on:
       - main
       - develop
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   get-python-versions:
     runs-on: ubuntu-latest
@@ -15,12 +19,14 @@ jobs:
       - uses: snok/latest-python-versions@v1
         id: get-python-versions-action
         with:
-          min-version: 3.7
+          min-version: 3.8
 
   test:
+    permissions: write-all
     needs: [get-python-versions]
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         python-version: ${{ fromJson(needs.get-python-versions.outputs.python-matrix) }}
 
@@ -50,7 +56,16 @@ jobs:
         run: poetry install --with test --no-interaction
 
       - name: Run tests
-        run: poetry run pytest --cov
+        run: |
+          poetry run pytest \
+            --junitxml=pytest.xml \
+            --cov-report=term-missing:skip-covered \
+            --cov=welkin test/ | tee pytest-coverage.txt
 
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        continue-on-error: true
+        with:
+          pytest-coverage-path: ./pytest-coverage.txt
+          junitxml-path: ./pytest.xml
+          unique-id-for-comment: ${{ matrix.python-version }}

.gitignore

@@ -50,6 +50,8 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+pytest-coverage.txt
+pytest.xml
 
 # Translations
 *.mo

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        args: [--unsafe]
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  ## Python
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        types: [python]
+
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+        types: [python]

.vscode/settings.json

@@ -1,7 +1,7 @@
 {
   "[python]": {
     "editor.codeActionsOnSave": {
-      "source.organizeImports": true
+      "source.organizeImports": "explicit"
     }
   },
   "editor.formatOnSave": true,