Merge pull request #352 from sanger/develop

Develop into master

.github/dependabot.yml

@@ -7,3 +7,8 @@ updates:
       time: "07:00"
       timezone: Europe/London
     open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+      - "Technical Debt"
+      - "python"
+

.github/workflows/automated_release.yml

@@ -32,17 +32,20 @@ jobs:
           docker.pkg.github.com/${IMAGE_NAME}:${BRANCH_NAME}
           python -m pytest --no-cov -vx
 
-      - name: Set release tag
+      - name: Set release name
         # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
-        # On the develop branch this might create RELEASE_VERSION=2.4.6-987654321-develop
-        # On the master branch this would then only create RELEASE_VERSION=2.4.6
-        run: echo "RELEASE_VERSION=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV
+        # On the develop branch this might create RELEASE_NAME=2.4.6-987654321-develop
+        # On the master branch this would then only create RELEASE_NAME=2.4.6
+        run: echo "RELEASE_NAME=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV
+
+      - name: Set release tag
+        run: echo "RELEASE_TAG=v$RELEASE_NAME" >> $GITHUB_ENV
 
       - name: Create release
         uses: ncipollo/release-action@v1.8.8
         with:
-          name: ${{ env.RELEASE_VERSION }}
-          tag: v${{ env.RELEASE_VERSION }}
+          name: ${{ env.RELEASE_NAME }}
+          tag: ${{ env.RELEASE_TAG }}
           prerelease: ${{ !(github.ref == 'refs/heads/master') }}
           commit: ${{ github.sha }}
 
@@ -57,14 +60,21 @@ jobs:
         run: >-
           docker tag
           docker.pkg.github.com/${IMAGE_NAME}:${BRANCH_NAME}
-          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }}
+          docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
 
       - name: Push release tag image to registry
         run: >-
-          docker push docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }}
+          docker push docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }}
 
-      - name: Remove the oldest package
-        uses: actions/delete-package-versions@v1
-        if: false
+      - name: Remove old releases
+        uses: snok/container-retention-policy@v2
         with:
-          package-name: "${{ github.event.repository.name }}"
+          image-names: ${{ github.event.repository.name }}/*
+          cut-off: Four months ago UTC
+          timestamp-to-use: updated_at
+          account-type: org
+          org-name: sanger
+          keep-at-least: 5
+          skip-tags: latest
+          token: ${{ secrets.REMOVE_OLD_IMAGES }}
+

.github/workflows/check_release_version.yml

@@ -14,7 +14,7 @@ jobs:
 
       - name: Get specific changed files
         id: changed-files-specific
-        uses: tj-actions/changed-files@v23
+        uses: tj-actions/changed-files@v41
         with:
           files: |
             .release-version

.release-version

@@ -1 +1 @@
-1.3.3
+1.3.4

.vscode/settings.json

@@ -7,7 +7,7 @@
   "python.analysis.typeCheckingMode": "basic",
   "[python]": {
     "editor.codeActionsOnSave": {
-      "source.organizeImports": true
+      "source.organizeImports": "explicit"
     }
   }
 }

Pipfile

@@ -4,7 +4,7 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-black = "==22.10.0"
+black = "==24.3.0"
 coverage = {extras = ["toml"],version = "*"}
 flake8 = "*"
 flake8-bugbear = "*"
@@ -13,12 +13,12 @@ pytest = "*"
 pytest-cov = "*"
 
 [packages]
-colorlog = "~=6.7"
-flask = "~=2.0"
-gunicorn = "~=20.0"
-python-dotenv = "~=0.21"
+colorlog = "~=6.8"
+flask = "~=3.0"
+gunicorn = "~=21.2"
+python-dotenv = "~=1.0"
 slackclient = "~=2.6"
-markupsafe = "==2.1.1"
+markupsafe = "==2.1.5"
 click = "~=8.0"
 types-flask = "*"
 

tests/helpers/test_rack_helpers.py

@@ -66,7 +66,6 @@ def test_parse_tube_rack_csv(app):
 
 def test_parse_tube_rack_csv_ignores_no_read(app, client, tmpdir):
     with app.app_context():
-
         expected_output = {
             "rack_barcode": "DN_48_no_read",
             "layout": {"FR05653780": "A1", "FR05653808": "A2", "FR05653801": "F8"},

wrangler/__init__.py

@@ -1,13 +1,14 @@
 import logging
 import logging.config
 from http import HTTPStatus
+from typing import Optional
 
 from flask import Flask
 
 logger = logging.getLogger(__name__)
 
 
-def create_app(test_config_path: str = None) -> Flask:
+def create_app(test_config_path: Optional[str] = None) -> Flask:
     app = Flask(__name__, instance_relative_config=False)
 
     if test_config_path is None:

wrangler/exceptions.py

@@ -1,11 +1,14 @@
+from typing import Optional
+
+
 class Error(Exception):
     """Base class for exceptions in this module."""
 
     pass
 
 
 class CsvNotFoundError(Error):
-    def __init__(self, tube_rack_barcode: str, message: str = None):
+    def __init__(self, tube_rack_barcode: str, message: Optional[str] = None):
         """Raised when a CSV file named after a tube rack barcode is not found in the NFS.
 
         Arguments: