Clean actions

.github/workflows/build_dockerfile_on_push.yml

@@ -0,0 +1,37 @@
+---
+
+name: Build and publish docker image on push
+
+on: [push]
+
+jobs:
+  docker-image-push:
+    runs-on: ubuntu-latest
+    name: Create staging docker image
+    steps:
+     - name: Check out git repository
+       uses: actions/[email protected]
+
+     - 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/})")"
+
+     - name: Login to Docker Hub
+       uses: docker/[email protected]
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/[email protected]
+
+     - name: Build and push
+       id: docker_build
+       uses: docker/[email protected]
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/genotype-api-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/genotype-api-stage:latest"

.github/workflows/bumpversion.yml

@@ -0,0 +1,18 @@
+name: "Bump2version-CI"
+on:
+  push:
+    branches:
+      - "master"
+      - "main"
+jobs:
+  bump-version:
+    runs-on: ubuntu-latest
+    name: Bump version and push tags to master
+    steps:
+      - name: Bump version
+        uses: Clinical-Genomics/bump2version-ci@v3
+        env:
+          BUMPVERSION_TOKEN: ${{ secrets.BUMPVERSION_TOKEN }}
+          BUMPVERSION_AUTHOR: ${{ secrets.BUMPVERSION_AUTHOR }}
+          BUMPVERSION_EMAIL: ${{ secrets.BUMPVERSION_EMAIL }}
+          GITHUB_REPOSITORY: ${{ github.repository }}

.github/workflows/merge_master_ci.yml

@@ -1,79 +0,0 @@
-name: 'Merge-master-CI'
-on:
-  push:
-    branches:
-      - 'master'
-      - 'main'
-
-jobs:
-  bump-version:
-    runs-on: ubuntu-latest
-    name: Bump version and push tags to master
-    steps:
-      - name: Bump version
-        uses: Clinical-Genomics/bump2version-ci@v3
-        env:
-          BUMPVERSION_TOKEN: ${{ secrets.BUMPVERSION_TOKEN }}
-          BUMPVERSION_AUTHOR: ${{ secrets.BUMPVERSION_AUTHOR }}
-          BUMPVERSION_EMAIL: ${{ secrets.BUMPVERSION_EMAIL }}
-          GITHUB_REPOSITORY: ${{ github.repository }}
-
-  docker-image-push:
-    runs-on: ubuntu-latest
-    name: Create staging image
-    steps:
-      - name: Check out git repository
-        uses: actions/[email protected]
-
-      - name: Extract branch name and remove illegal chars
-        id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
-
-      - name: Login to Docker Hub
-        uses: docker/[email protected]
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-
-      - name: Set up Docker Buildx
-        id: buildx
-        uses: docker/[email protected]
-
-      - name: Build and push
-        id: docker_build
-        uses: docker/[email protected]
-        with:
-          context: ./
-          file: ./Dockerfile
-          push: true
-          tags: "clinicalgenomics/genotype-api-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/genotype-api-stage:latest"
-
-  tests-coverage:
-    runs-on: ubuntu-latest
-    name: Test and coveralls
-    steps:
-      - name: Set up Python
-        uses: actions/[email protected]
-        with:
-          python-version: "3.10"
-
-      - name: Check out genotype-api
-        uses: actions/[email protected]
-        with:
-          repository: "Clinical-Genomics/genotype-api"
-
-      - name: Install genotype-api dependencies
-        run: |
-          pip install -r requirements.txt -r requirements-dev.txt .
-      - name: Install coveralls dependencies
-        run: |
-          pip install pytest-cov coveralls
-      - name: Test with pytest & Coveralls
-        run: |
-          pytest --cov=genotype-api/
-          coveralls
-        env:
-          GITHUB: 1
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

.github/workflows/pull_request_ci.yml

@@ -1,78 +0,0 @@
----
-
-name: Pull Request Actions
-
-on: [push]
-
-jobs:
-  black-lint:
-    runs-on: ubuntu-latest
-    name: Black
-    steps:
-      - uses: actions/[email protected]
-      - uses: actions/[email protected]
-      - 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/[email protected]
-
-     - 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/})")"
-
-     - name: Login to Docker Hub
-       uses: docker/[email protected]
-       with:
-         username: ${{ secrets.DOCKER_USERNAME }}
-         password: ${{ secrets.DOCKER_PASSWORD }}
-
-     - name: Set up Docker Buildx
-       id: buildx
-       uses: docker/[email protected]
-
-     - name: Build and push
-       id: docker_build
-       uses: docker/[email protected]
-       with:
-         context: ./
-         file: ./Dockerfile
-         push: true
-         tags: "clinicalgenomics/genotype-api-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/genotype-api-stage:latest"
-
-  tests-coverage:
-    runs-on: ubuntu-latest
-    name: Test and coveralls
-    steps:
-      - name: Set up Python
-        uses: actions/[email protected]
-        with:
-          python-version: "3.10"
-
-      - name: Check out genotype-api
-        uses: actions/[email protected]
-        with:
-          repository: "Clinical-Genomics/genotype-api"
-
-      - name: Install genotype-api dependencies
-        run: |
-          pip install -r requirements.txt -r requirements-dev.txt .
-
-      - name: Install coveralls dependencies
-        run: |
-          pip install pytest-cov coveralls
-
-      - name: Test with pytest & Coveralls
-        run: |
-          pytest --cov=genotype_api/
-          coveralls
-        env:
-          GITHUB: 1
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}