feat: exporting projects information (#142) (#143)

- Added celery
- Added hpc admin flag to user creation in django admin interface
- Added dotenv
- Transferred requirements to Pipfile
- Fixed bug with ag name creation when there is no full name available

.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/[email protected]
+        with:
+          owner: bihealth
+          name: hpc-access
+          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/[email protected]
+        with:
+          owner: bihealth
+          name: hpc-access
+          token: ${{ secrets.GITHUB_TOKEN }}
+          untagged-keep-latest: 3

.github/workflows/main.yml

@@ -0,0 +1,118 @@
+name: CI
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  Python-Test:
+    runs-on: ubuntu-latest
+    services:
+      redis:
+        image: redis:latest
+        ports:
+          - 6379:6379
+
+      postgres:
+        image: postgres:14
+        env:
+          POSTGRES_DB: hpcaccess
+          POSTGRES_USER: hpcaccess
+          POSTGRES_PASSWORD: hpcaccess
+          DATABASE_URL: postgres://hpcaccess:hpcaccess@postgres/hpcaccess
+          CELERY_BROKER_URL: redis://redis:6379/0
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+        ports:
+          - 5432:5432
+
+    env:
+      CELERY_BROKER_URL: redis://0.0.0.0:6379/0
+      DATABASE_URL: 'postgres://hpcaccess:[email protected]/hpcaccess'
+      POSTGRES_HOST: 0.0.0.0
+      POSTGRES_PORT: 5432
+
+    steps:
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential zlib1g-dev libtiff5-dev libjpeg8-dev \
+              libfreetype6-dev liblcms2-dev libwebp-dev libpq-dev graphviz-dev \
+              libldap2-dev libsasl2-dev
+
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          # We need to fix the patch version here otherwise, snapshot tests
+          # with randomness will / may fail.
+          python-version: "3.10.13"
+
+      - name: Install pip and Pipenv
+        run: |
+          pip install -U pip pipenv
+
+      - name: Install project dependencies with pipenv
+        run: |
+          pipenv install --verbose --categories=packages,dev-packages,ldap-packages
+
+      - name: Download icons
+        run: pipenv run python manage.py geticons
+
+      - name: Run collectstatic
+        run: pipenv run python manage.py collectstatic --noinput
+
+      - name: Run tests
+        run: |
+          pipenv run coverage run --rcfile=.coveragerc manage.py test -v 2 --settings=config.settings.test
+          pipenv run coverage xml
+          pipenv run coverage report
+        # Important: use shell that was initialized by micromamba.
+        # shell: bash -el {0}
+
+  Python-Lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install pip and Pipenv
+        run: |
+            pip install pip pipenv
+
+      - name: Install project dependencies with pipenv
+        run: |
+          pipenv install --categories=packages,dev-packages
+
+      - name: Check import order with isort
+        run: |
+          rm -rf src
+          pipenv run isort --force-sort-within-sections --profile=black --check .
+
+      - name: Check style with black
+        run: |
+          pipenv run black --check --line-length 100 .
+
+      - name: Run linting
+        run: |
+          pipenv run flake8
+

Makefile

@@ -8,6 +8,9 @@ arg =
 serve:
 	$(manage) runserver
 
+celery:
+	celery -A config.celery_app worker -l info --beat
+
 
 .PHONY: lack
 black:

Pipfile

@@ -0,0 +1,60 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+python-dotenv = "*"
+pytz = "~=2022.1"
+python-slugify = "~=6.1.1"
+Pillow = "~=9.1.0"
+argon2-cffi = "~=21.3.0"
+redis = "~=5.0"
+celery = "*"
+hiredis = "~=2.0.0"
+django = "~=4.2.0"
+django-environ = "~=0.8.1"
+django-model-utils = "~=4.2.0"
+django-allauth = "~=0.50.0"
+django-crispy-forms = "~=1.14.0"
+crispy-bootstrap5 = "~=0.6"
+django-redis = "~=5.2.0"
+django-celery-beat = "~=2.0"
+sentry-sdk = "~=1.5.11"
+rules = "~=3.3"
+ldap3 = "~=2.9.1"
+packages = "*"
+
+[dev-packages]
+Werkzeug = "*"
+ipdb = "*"
+psycopg2 = "*"
+mypy = "*"
+django-stubs = "*"
+pytest = "*"
+pytest-sugar = "*"
+django-test-plus = "*"
+sphinx = "*"
+sphinx-autobuild = "*"
+flake8 = "*"
+coverage = "*"
+black = "*"
+pylint-django = "*"
+pre-commit = "*"
+factory-boy = "*"
+django-debug-toolbar = "*"
+django-extensions = "*"
+django-coverage-plugin = "*"
+pytest-django = "*"
+
+[ldap-packages]
+django-auth-ldap = "~=4.0.0"
+python-ldap = "~=3.4.0"
+
+[prod-packages]
+gunicorn = "*"
+psycopg2 = "*"
+whitenoise = "*"
+
+[requires]
+python_version = "3.10"