Merge pull request #2497 from ohcnetwork/develop

Merge Develop to Staging v24.40.0

Author: sainak

.flake8

@@ -92,7 +92,7 @@ jobs:
             ${{ runner.os }}-buildx-build-
 
       - name: Build and push image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: docker/prod.Dockerfile
@@ -142,7 +142,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v1
+        uses: aws-actions/configure-aws-credentials@v4
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -154,22 +154,6 @@ jobs:
           IMAGE_TAG: latest-${{ github.run_number }}
         run: echo "IMAGE_VALUE=`echo ghcr.io/${{ github.repository }}:$IMAGE_TAG`" >> $GITHUB_ENV
 
-      - name: Fill Backend Api definition
-        id: task-def-api
-        uses: aws-actions/amazon-ecs-render-task-definition@v1
-        with:
-          task-definition: ${{ env.ECS_TASK_DEFINITION_BACKEND }}
-          container-name: ${{ env.CONTAINER_NAME_BACKEND }}
-          image: ${{env.IMAGE_VALUE}}
-
-      - name: Deploy Backend Api
-        uses: aws-actions/amazon-ecs-deploy-task-definition@v1
-        with:
-          task-definition: ${{ steps.task-def-api.outputs.task-definition }}
-          service: ${{ env.ECS_SERVICE_BACKEND }}
-          cluster: ${{ env.ECS_CLUSTER }}
-          wait-for-service-stability: true
-
       - name: Fill Celery Cron definition
         id: task-def-celery-cron
         uses: aws-actions/amazon-ecs-render-task-definition@v1
@@ -187,13 +171,29 @@ jobs:
           image: ${{env.IMAGE_VALUE}}
 
       - name: Deploy Backend Celery
-        uses: aws-actions/amazon-ecs-deploy-task-definition@v1
+        uses: aws-actions/amazon-ecs-deploy-task-definition@v2
         with:
           task-definition: ${{ steps.task-def-celery-worker.outputs.task-definition }}
           service: ${{ env.ECS_SERVICE_CELERY }}
           cluster: ${{ env.ECS_CLUSTER }}
           wait-for-service-stability: true
 
+      - name: Fill Backend Api definition
+        id: task-def-api
+        uses: aws-actions/amazon-ecs-render-task-definition@v1
+        with:
+          task-definition: ${{ env.ECS_TASK_DEFINITION_BACKEND }}
+          container-name: ${{ env.CONTAINER_NAME_BACKEND }}
+          image: ${{env.IMAGE_VALUE}}
+
+      - name: Deploy Backend Api
+        uses: aws-actions/amazon-ecs-deploy-task-definition@v2
+        with:
+          task-definition: ${{ steps.task-def-api.outputs.task-definition }}
+          service: ${{ env.ECS_SERVICE_BACKEND }}
+          cluster: ${{ env.ECS_CLUSTER }}
+          wait-for-service-stability: true
+
   deploy-staging-gcp:
     needs: build
     if: github.ref == 'refs/heads/staging'

.github/workflows/combine-dependencies.yml

@@ -23,11 +23,11 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: 'pipenv'
 
       - name: Install pipenv
-        run: curl https://raw.githubusercontent.com/pypa/pipenv/master/get-pipenv.py | python
+        run: pip install pipenv
 
       - name: Install dependencies
         run: pipenv sync --categories "docs"
@@ -54,7 +54,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Download sphinx documentation
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: sphinx-docs
           path: ./build

.github/workflows/deploy.yml

@@ -7,32 +7,14 @@ on:
       - staging
   merge_group:
 
-permissions: { }
-
 jobs:
-  build:
-    name: Lint Code Base
+  lint:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: read
-      statuses: write
-
     steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
-      - name: Lint Code Base
-        uses: super-linter/super-linter/slim@v6
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          VALIDATE_ALL_CODEBASE: false
-          VALIDATE_PYTHON_BLACK: true
-          VALIDATE_PYTHON_FLAKE8: true
-          VALIDATE_PYTHON_ISORT: true
-          LINTER_RULES_PATH: /
-          PYTHON_BLACK_CONFIG_FILE: "pyproject.toml"
-          PYTHON_FLAKE8_CONFIG_FILE: ".flake8"
-          PYTHON_ISORT_CONFIG_FILE: "pyproject.toml"
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}

.github/workflows/docs.yml

@@ -30,13 +30,15 @@ jobs:
             ${{ runner.os }}-buildx-
 
       - name: Bake docker images
-        uses: docker/bake-action@v4
+        uses: docker/bake-action@v5
         with:
           load: true
           set: |
             *.cache-from=type=local,src=/tmp/.buildx-cache
             *.cache-to=type=local,dest=/tmp/.buildx-cache-new
           files: docker-compose.yaml,docker-compose.local.yaml
+        env:
+          DOCKER_BUILD_NO_SUMMARY: true
 
       - name: Start services
         run: |

.github/workflows/linter.yml

@@ -352,3 +352,5 @@ secrets.sh
 
 # Redis
 *.rdb
+
+jwks.b64.txt

.github/workflows/reusable-test.yml

@@ -16,21 +16,9 @@ repos:
       - id: check-yaml
       - id: check-toml
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.7
     hooks:
-      - id: isort
-        additional_dependencies: ["isort[pyproject]"]
-
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        args: ["--config=pyproject.toml"]
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.0
-    hooks:
-      - id: flake8
-        args: ["--config=.flake8"]
-        additional_dependencies: [flake8-isort]
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

.gitignore

@@ -3,6 +3,6 @@
     "boto3typed.boto3-ide",
     "ms-python.python",
     "ms-python.vscode-pylance",
-    "ms-python.isort"
+    "charliermarsh.ruff"
   ]
 }

.pre-commit-config.yaml

@@ -3,10 +3,12 @@
     "editor.formatOnSave": false
   },
   "[python]": {
+    "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
+      "source.fixAll": "explicit",
       "source.organizeImports": "explicit"
     },
-    "editor.formatOnSave": true
+    "editor.defaultFormatter": "charliermarsh.ruff"
   },
   "files.associations": {
     "*.envrc": "shellscript",
@@ -19,10 +21,5 @@
   "files.trimFinalNewlines": true,
   "files.trimTrailingWhitespace": true,
   "githubPullRequests.ignoredPullRequestBranches": ["develop", "staging"],
-  "python.formatting.blackPath": "${workspaceFolder}/.venv/bin/black",
-  "python.formatting.provider": "black",
-  "python.languageServer": "Pylance",
-  "python.linting.flake8Args": ["--config=.flake8"],
-  "python.linting.flake8Path": "${workspaceFolder}/.venv/bin/flake8",
-  "isort.args": ["--profile", "black"]
+  "python.languageServer": "Pylance"
 }

.vscode/extensions.json

@@ -52,5 +52,20 @@ reset_db:
 	docker compose exec backend bash -c "python manage.py reset_db --noinput"
 	docker compose exec backend bash -c "python manage.py migrate"
 
+ruff-all:
+	ruff check .
+
+ruff-fix-all:
+	ruff check --fix .
+
+ruff:
+	ruff check --fix $(shell git diff --name-only --staged | grep -E '\.py$$|\/pyproject.toml$$')
+
+ruff-all-docker:
+	docker exec care bash -c "ruff check ."
+
+ruff-docker:
+	docker exec care bash -c "ruff check --fix $(shell git diff --name-only --staged | grep -E '\.py$$|\/pyproject.toml$$')"
+
 %:
 	docker compose exec backend bash -c "python manage.py $*"

.vscode/settings.json

@@ -5,15 +5,14 @@ name = "pypi"
 
 [packages]
 argon2-cffi = "==23.1.0"
-authlib = "==1.3.1"
-boto3 = "==1.35.0"
+authlib = "==1.3.2"
+boto3 = "==1.35.25"
 celery = "==5.4.0"
-django = "==4.2.15"
+django = "==5.1.1"
 django-environ = "==0.11.2"
-django-cors-headers = "==4.3.1"
-django-filter = "==24.2"
+django-cors-headers = "==4.4.0"
+django-filter = "==24.3"
 django-maintenance-mode = "==0.21.1"
-django-model-utils = "==4.5.1"
 django-queryset-csv = "==1.1.0"
 django-ratelimit = "==4.1.0"
 django-redis = "==5.4.0"
@@ -26,51 +25,47 @@ dry-rest-permissions = "==0.1.10"
 drf-nested-routers = "==0.94.1"
 drf-spectacular = "==0.27.2"
 "fhir.resources" = "==6.5.0"
-gunicorn = "==22.0.0"
+gunicorn = "==23.0.0"
 healthy-django = "==0.1.0"
-jsonschema = "==4.22.0"
+jsonschema = "==4.23.0"
 jwcrypto = "==1.5.6"
 newrelic = "==9.13.0"
-pillow = "==10.3.0"
-psycopg = { extras = ["c"], version = "==3.1.19" }
+pillow = "==10.4.0"
+psycopg = { extras = ["c"], version = "==3.2.2" }
 pycryptodome = "==3.20.0"
-pydantic = "==1.10.15" # fix for fhir.resources < 7.0.2
-pyjwt = "==2.8.0"
+pydantic = "==1.10.18" # fix for fhir.resources < 7.0.2
+pyjwt = "==2.9.0"
 python-slugify = "==8.0.4"
 pywebpush = "==2.0.0"
-redis = { extras = ["hiredis"], version = "==5.0.5" } # constraint for redis-om
-redis-om = "==0.3.1"
+redis = { extras = ["hiredis"], version = "==5.0.8" } # constraint for redis-om
+redis-om = "==0.3.1" # > 0.3.1 broken with pydantic < 2
 requests = "==2.32.3"
-sentry-sdk = "==2.13.0"
-whitenoise = "==6.6.0"
+sentry-sdk = "==2.14.0"
+whitenoise = "==6.7.0"
 
 [dev-packages]
-black = "==24.4.2"
-boto3-stubs = { extras = ["s3", "boto3"], version = "==1.35.0" }
-coverage = "==7.5.3"
-debugpy = "==1.8.1"
+boto3-stubs = { extras = ["s3", "boto3"], version = "==1.35.25" }
+coverage = "==7.6.1"
+debugpy = "==1.8.5"
 django-coverage-plugin = "==3.1.0"
-django-debug-toolbar = "==4.4.2"
 django-extensions = "==3.2.3"
-django-silk = "==5.1.0"
-django-stubs = "==5.0.2"
-djangorestframework-stubs = "==3.15.0"
-factory-boy = "==3.3.0"
-flake8 = "==7.1.1"
+django-silk = "==5.2.0"
+djangorestframework-stubs = "==3.15.1"
+factory-boy = "==3.3.1"
 freezegun = "==1.5.1"
-ipython = "==8.25.0"
-isort = "==5.13.2"
-mypy = "==1.10.0"
-pre-commit = "==3.7.1"
+ipython = "==8.27.0"
+mypy = "==1.11.2"
+pre-commit = "==3.8.0"
 requests-mock = "==1.12.1"
 tblib = "==3.0.0"
-watchdog = "==4.0.1"
-werkzeug = "==3.0.3"
+watchdog = "==5.0.2"
+werkzeug = "==3.0.4"
+ruff = "==0.6.7"
 
 [docs]
-furo = "==2024.5.6"
-sphinx = "==7.3.7"
-myst-parser = "==3.0.1"
+furo = "==2024.8.6"
+sphinx = "==8.0.2"
+myst-parser = "==4.0.0"
 
 [requires]
-python_version = "3.11"
+python_version = "3.12"