Merge pull request #419 from sanger/develop

Develop to master

.github/workflows/add_prs_to_tech_debt_project.yml

@@ -0,0 +1,19 @@
+# Calls a reusable workflow in the .github repo,
+# which adds the PR that triggered this to the Technical Debt project board, if it is a depfu one.
+# Passes the 'PSD-AddToProject' GitHub App key and App Id as secrets to the reusable workflow.
+
+name: Add dependencies to technical debt project
+
+on:
+  # Triggered on creation of pull requests with any label,
+  # or when a label is added to an existing pull request.
+  pull_request:
+    types:
+      - labeled
+
+jobs:
+  call-workflow-add_to_technical_debt_project:
+    uses: sanger/.github/.github/workflows/add_to_tech_debt_project_reusable.yml@master
+    secrets:
+      app_id: ${{ secrets.ADD_TO_PROJECT_APP_ID_PSD }}
+      app_key: ${{ secrets.ADD_TO_PROJECT_APP_KEY_PSD }}

.github/workflows/assign_issue_number.yml

@@ -0,0 +1,12 @@
+name: Assign Issue Number
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  call-add-to-project:
+    uses: sanger/.github/.github/workflows/generate_issue_number.yml@master
+    secrets:
+      app_id: ${{ secrets.ISSUE_GEN_APP_ID }}
+      app_key: ${{ secrets.ISSUE_GEN_APP_KEY }}

.github/workflows/automated_release.yml

@@ -13,7 +13,7 @@ jobs:
   build_test_release_push:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: nelonoel/[email protected]
 
@@ -75,6 +75,5 @@ jobs:
           account-type: org
           org-name: sanger
           keep-at-least: 5
-          skip-tags: latest
+          skip-tags: latest, *[!develop] # This will DELETE any images where the tag contains ANY characters in "develop", excluding '!'
           token: ${{ secrets.REMOVE_OLD_IMAGES }}
-

.github/workflows/check_release_version.yml

@@ -10,7 +10,7 @@ jobs:
   check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Get specific changed files
         id: changed-files-specific

.github/workflows/ci.yml

@@ -11,15 +11,25 @@ on:
       - master
 
 jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      python_version: ${{ steps.read_python_version.outputs.python_version }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Read Python version
+        id: read_python_version
+        run: echo "::set-output name=python_version::$(cat .python-version)"
   black:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
-      - uses: actions/cache@v1
+          python-version: ${{ needs.setup.outputs.python_version }}
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
@@ -37,13 +47,14 @@ jobs:
           python -m black --check .
   flake8:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
-      - uses: actions/cache@v1
+          python-version: ${{ needs.setup.outputs.python_version }}
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
@@ -61,13 +72,14 @@ jobs:
           flake8
   mypy:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-      - uses: actions/cache@v1
+          python-version: ${{ needs.setup.outputs.python_version }}
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
@@ -84,13 +96,14 @@ jobs:
           python -m mypy .
   test:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
-      - uses: actions/cache@v1
+          python-version: ${{ needs.setup.outputs.python_version }}
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
@@ -106,4 +119,6 @@ jobs:
         run: |
           python -m pytest -x
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docker_dispatch.yml

@@ -15,7 +15,7 @@ jobs:
   build_and_publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Build the Docker image
         run: >-

.python-version

@@ -0,0 +1 @@
+3.13.0

.release-version

@@ -1 +1 @@
-1.3.4
+1.4.0

Dockerfile

@@ -1,5 +1,5 @@
 # Use alpine for a smaller image size and install only the required packages
-FROM python:3.8-alpine
+FROM python:3.13-alpine
 
 # > Setting PYTHONUNBUFFERED to a non empty value ensures that the python output is sent straight to
 # > terminal (e.g. your container log) without being first buffered and that you can see the output

Pipfile

@@ -4,7 +4,7 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-black = "==24.3.0"
+black = "==25.1.0"
 coverage = {extras = ["toml"],version = "*"}
 flake8 = "*"
 flake8-bugbear = "*"
@@ -13,17 +13,18 @@ pytest = "*"
 pytest-cov = "*"
 
 [packages]
-colorlog = "~=6.8"
+colorlog = "~=6.9"
 flask = "~=3.0"
-gunicorn = "~=21.2"
+gunicorn = "~=23.0"
 python-dotenv = "~=1.0"
 slackclient = "~=2.6"
 markupsafe = "==2.1.5"
-click = "~=8.0"
+click = "~=8.1"
 types-flask = "*"
+typing_extensions = "*"
 
 [requires]
-python_version = "3.8"
+python_version = "3.13"
 
 [pipenv]
 allow_prereleases = true