fix: strip chr prefix for grch38 (#10) (#11)

- Adapted docker build and github actions
- Performed isort
- Update to Django 3.2 and Python 3.10

.github/workflows/ci.yml

@@ -1,24 +1,16 @@
 name: CI
 
-on: [push]
+on:
+  - push
+  - pull_request
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version:
-          - 3.6
-          - 3.7
-          - 3.8
-          - 3.9
-
     steps:
       - name: Install Python via conda.
         uses: s-weigand/setup-conda@v1
         with:
-          python-version: ${{ matrix.python-version }}
           conda-channels: defaults,bioconda,conda-forge
       - name: Install mamba.
         run: conda install -y mamba
@@ -29,7 +21,6 @@ jobs:
         uses: actions/checkout@v2
       - name: Install project Python dependencies
         run: |
-          pip install -r requirements/local.txt
           pip install -r requirements/test.txt
       - name: Run tests
         run: |
@@ -43,4 +34,3 @@ jobs:
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: coverage.xml
-        if: ${{ matrix.python-version == '3.7' }}

.github/workflows/docker-build.yml

@@ -0,0 +1,52 @@
+# This workflow is run as part of CI to test that they run through.
+#
+# The images are pushed to `ghcr.io` for each PR and branch.  The ones for
+# the releases are pushed in `release-please.yml`.
+name: Docker Build
+
+on:
+  - push
+  - pull_request
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Write VERSION file for Python package
+        run: |
+          git describe --all | tee VERSION
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: utils/docker/Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docker-cleanup-pr.yml

@@ -0,0 +1,19 @@
+name: Cleanup PR Images
+
+on:
+  pull_request:
+    types:
+        - closed
+
+jobs:
+  purge-image:
+    name: Delete PR images
+    runs-on: ubuntu-latest
+    steps:
+      - uses: bots-house/ghcr-delete-image-action@v1.1.0
+        with:
+          owner: varfish-org
+          name: cadd-rest-api
+          token: ${{ secrets.GITHUB_TOKEN }}
+          tag: pr-${{github.event.pull_request.number}}
+        continue-on-error: true

.github/workflows/docker-cleanup-untagged.yml

@@ -0,0 +1,18 @@
+name: Cleanup Untagged Images
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * SUN"
+
+jobs:
+  delete-untagged-images:
+    name: Delete untagged images
+    runs-on: ubuntu-latest
+    steps:
+      - uses: bots-house/ghcr-delete-image-action@v1.1.0
+        with:
+          owner: varfish-org
+          name: cadd-rest-api
+          token: ${{ secrets.GITHUB_TOKEN }}
+          untagged-keep-latest: 3

.gitignore

@@ -1,3 +1,5 @@
+/VERSION
+
 # SQLite database.
 /*.db
 

Makefile

@@ -1,23 +1,35 @@
 SHELL = /bin/bash
 MANAGE = time python manage.py
 
-.PHONY: black serve _migrate migrate celery
-
+.PHONY: black
 black:
 	black -l 100 --exclude '/(\.eggs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.?v?env|_build|buck-out|build|dist|src)/' .
 
+.PHONY: isort
+isort:
+	isort --force-sort-within-sections --profile=black .
+
+.PHONY: flake8
+flake8:
+	flake8
+
+.PHONY: serve
 serve:
 	$(MANAGE) runserver
 
+.PHONY: _migrate
 _migrate:
 	$(MANAGE) makemigrations
 	$(MANAGE) migrate
 
+.PHONY: migrate
 migrate: _migrate black
 
+.PHONY: celery
 celery:
 	celery worker -A config.celery_app -l info --concurrency=4
 
+.PHONY: test
 test:
 	$(MANAGE) test --settings=config.settings.test -v2
 

README.rst

@@ -36,4 +36,4 @@ Or:
 
 .. code-block:: bash
 
-    $ docker build . --build-arg app_git_tag=v0.3.2 -t bihealth/cadd-rest-api:0.3.2-0
+    $ docker build . --build-arg app_git_tag=v0.3.2 -t varfish-org/cadd-rest-api:0.3.2-0

cadd_rest_api/contrib/sites/migrations/0003_set_site_domain_and_name.py

@@ -2,6 +2,7 @@
 
 http://cookiecutter-django.readthedocs.io/en/latest/faq.html#why-is-there-a-django-contrib-sites-directory-in-cookiecutter-django
 """
+
 from django.conf import settings
 from django.db import migrations
 

config/celery.py

@@ -1,4 +1,5 @@
 import os
+
 from celery import Celery
 
 # set the default Django settings module for the 'celery' program.

config/settings/base.py

@@ -162,7 +162,7 @@
 # Django Admin URL.
 ADMIN_URL = "admin/"
 # https://docs.djangoproject.com/en/dev/ref/settings/#admins
-ADMINS = [("""Oliver Stolpe""", "oliver.stolpe@bihealth.de")]
+ADMINS = [("""Oliver Stolpe""", "oliver.stolpe@bih-charite.de")]
 # https://docs.djangoproject.com/en/dev/ref/settings/#managers
 MANAGERS = ADMINS
 

config/settings/production.py

@@ -73,7 +73,7 @@
 # ------------------------------------------------------------------------------
 # https://docs.djangoproject.com/en/dev/ref/settings/#default-from-email
 DEFAULT_FROM_EMAIL = env(
-    "DJANGO_DEFAULT_FROM_EMAIL", default="CADD REST API <noreply@bihealth.org>"
+    "DJANGO_DEFAULT_FROM_EMAIL", default="CADD REST API <noreply@bih-charite.org>"
 )
 # https://docs.djangoproject.com/en/dev/ref/settings/#server-email
 SERVER_EMAIL = env("DJANGO_SERVER_EMAIL", default=DEFAULT_FROM_EMAIL)

config/urls.py

@@ -1,6 +1,5 @@
 from django.conf import settings
-from django.conf.urls import url
-from django.conf.urls import include
+from django.conf.urls import include, url
 from django.conf.urls.static import static
 
 urlpatterns = [url(r"", include("restapi.urls"))] + static(

config/wsgi.py

@@ -12,6 +12,7 @@
 framework.
 
 """
+
 import os
 import sys
 

requirements/base.txt

@@ -1,26 +1,27 @@
-pytz==2019.2  # https://github.com/stub42/pytz
-python-slugify==3.0.3  # https://github.com/un33k/python-slugify
-Pillow==6.1.0  # https://github.com/python-pillow/Pillow
-argon2-cffi==19.1.0  # https://github.com/hynek/argon2_cffi
-redis==3.3.8  # https://github.com/antirez/redis
-celery==4.3.1  # pyup: < 5.0  # https://github.com/celery/celery
-django-celery-beat==1.5.0  # https://github.com/celery/django-celery-beat
+pytz
+python-slugify
+Pillow
+argon2-cffi
+redis
+celery
 
-Werkzeug==0.14.1  # pyup: < 0.15 # https://github.com/pallets/werkzeug
-Sphinx==2.2.0  # https://github.com/sphinx-doc/sphinx
+Werkzeug
+Sphinx
 
 # Django
 # ------------------------------------------------------------------------------
-django<2.0  # pyup: < 3.0  # https://www.djangoproject.com/
-django-environ==0.4.5  # https://github.com/joke2k/django-environ
-django-model-utils==3.2.0  # https://github.com/jazzband/django-model-utils
-django-allauth==0.40.0  # https://github.com/pennersr/django-allauth
-django-crispy-forms==1.7.2  # https://github.com/django-crispy-forms/django-crispy-forms
-django-redis==4.10.0  # https://github.com/niwinz/django-redis
-django-debug-toolbar==2.0  # https://github.com/jazzband/django-debug-toolbar
+#django==3.2
+django<4
+django-environ
+django-model-utils
+django-allauth
+django-crispy-forms
+django-redis
+django-debug-toolbar
 
 # Django REST Framework
-djangorestframework==3.10.3  # https://github.com/encode/django-rest-framework
-coreapi==2.3.3  # https://github.com/core-api/python-client
+djangorestframework
+coreapi
 
-jsonfield==2.1.1
+jsonfield
+ipdb

requirements/production.txt

@@ -2,9 +2,9 @@
 
 -r ./base.txt
 
-gunicorn==19.9.0  # https://github.com/benoitc/gunicorn
-Collectfast==1.0.0  # https://github.com/antonagestam/collectfast
+gunicorn
+Collectfast
 
 # Django
 # ------------------------------------------------------------------------------
-django-anymail[mailgun]==6.1.0  # https://github.com/anymail/django-anymail
+django-anymail[mailgun]

requirements/test.txt

@@ -2,22 +2,23 @@
 
 # Testing
 # ------------------------------------------------------------------------------
-mypy==0.720  # https://github.com/python/mypy
-pytest==5.1.2  # https://github.com/pytest-dev/pytest
-pytest-sugar==0.9.2  # https://github.com/Frozenball/pytest-sugar
+mypy
+pytest
+pytest-sugar
 
 # Code quality
 # ------------------------------------------------------------------------------
-flake8==3.7.8  # https://github.com/PyCQA/flake8
-coverage==4.5.4  # https://github.com/nedbat/coveragepy
-black==19.3b0  # https://github.com/ambv/black
-pylint-django==2.0.11  # https://github.com/PyCQA/pylint-django
-pylint-celery==0.3  # https://github.com/PyCQA/pylint-celery
+flake8
+coverage
+black
+pylint-django
+pylint-celery
 
 # Django
 # ------------------------------------------------------------------------------
-factory-boy==2.12.0  # https://github.com/FactoryBoy/factory_boy
+factory-boy
 
-django-extensions==2.2.1  # https://github.com/django-extensions/django-extensions
-django-coverage-plugin==1.6.0  # https://github.com/nedbat/django_coverage_plugin
-pytest-django==3.5.1  # https://github.com/pytest-dev/pytest-django
+django-extensions
+django-coverage-plugin
+django-test-plus
+pytest-django