Poetry support,fix workflows, update python

.github/workflows/deploy_prod.yml

@@ -18,10 +18,10 @@ jobs:
             --fail \
             -X POST \
             -H "Accept: application/vnd.github.v3+json" \
-            -H "Authorization: token ${{ secrets.BUMPVERSION_TOKEN }}" \
-            https://api.github.com/repos/${{ github.repository }}/deployments \
+            -H "Authorization: token ${{secrets.BUMPVERSION_TOKEN}}" \
+            https://api.github.com/repos/${{github.repository}}/deployments \
             -d '{
-            "ref": "${{ github.event.inputs.tag_name }}",
+            "ref": "${{github.event.inputs.tag_name}}",
             "environment": "production",
             "auto_merge": false,
             "description": "${{secrets.DEPLOYMENT_INFO}}"}'

.github/workflows/deploy_stage.yml

@@ -1,5 +1,3 @@
----
-
 name: Deploy branch to staging environment
 
 on:
@@ -24,4 +22,4 @@ jobs:
             "ref": "${{ github.event.inputs.branch_name }}",
             "environment": "stage",
             "auto_merge": false,
-            "description": "${{secrets.DEPLOYMENT_INFO}}"}'
+            "description": "${{secrets.DEPLOYMENT_INFO}}"}'

.github/workflows/merge_master_ci.yml

@@ -23,31 +23,33 @@ jobs:
     name: Create staging image
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
-        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
+
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/arnold-stage:latest"
+          tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}},clinicalgenomics/arnold-stage:latest"
+
 
   tests-coverage:
     runs-on: ubuntu-latest
@@ -56,7 +58,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Check out cg_lims
         uses: actions/checkout@v2

.github/workflows/pull_request_ci.yml

@@ -5,41 +5,31 @@ name: Pull Request Actions
 on: [push]
 
 jobs:
-  black-lint:
-    runs-on: ubuntu-latest
-    name: Black
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
-        with:
-          black_args: ". --check --line-length 100"
-
   docker-image-push:
     runs-on: ubuntu-latest
     name: Create staging docker image
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v2
+       uses: actions/checkout@v3
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
        shell: bash
-       run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+       run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v1
+       uses: docker/login-action@v2
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v1
+       uses: docker/setup-buildx-action@v2
 
      - name: Build and push
        id: docker_build
-       uses: docker/build-push-action@v2
+       uses: docker/build-push-action@v3
        with:
          context: ./
          file: ./Dockerfile
@@ -53,7 +43,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Check out arnold
         uses: actions/checkout@v2

.github/workflows/release_ci.yml

@@ -16,8 +16,7 @@ jobs:
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
 
       - name: Login to Docker Hub
         uses: docker/login-action@v1
@@ -27,44 +26,13 @@ jobs:
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"
-
-  build-n-publish:
-    name: Build and publish Python distribution to PyPI
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out git repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install build tools
-        run: >-
-          python -m
-          pip install
-          wheel
-          twine
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python
-          setup.py
-          sdist
-          bdist_wheel
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.289
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        args: [ --line-length=100 ]

Dockerfile

@@ -1,6 +1,6 @@
-FROM python:3.10-slim
+FROM python:3.11-slim-bullseye
 
-LABEL base_image="python:3.10-slim"
+LABEL base_image="python:3.11-slim-bullseye"
 LABEL about.home="https://github.com/Clinical-Genomics/arnold"
 LABEL about.tags="CG Core database and API"