Merge pull request #2 from SciLifeLab/First_Draft

Merge First_Draft branch to main

.github/workflows/clippy.yml

@@ -0,0 +1,48 @@
+# Clippy is a tool that runs a bunch of tests on the Rust code to catch common mistakes and discouraged patterns.
+
+name: Analyze with Rust Clippy
+
+on:
+  push:
+    branches: 
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  rust-clippy-analyze:
+    name: Run rust-clippy analyzing
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      security-events: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@16499b5e05bf2e26879000db0c1d13f7e13fa3af #@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          components: clippy
+          override: true
+
+      - name: Install required cargo
+        run: cargo install clippy-sarif sarif-fmt
+
+      - name: Run rust-clippy
+        run:
+          cargo clippy
+          --all-features
+          --message-format=json | clippy-sarif | tee rust-clippy-results.sarif | sarif-fmt
+        continue-on-error: true
+
+      - name: Upload analysis results to GitHub
+        uses: github/codeql-action/upload-sarif@v1
+        with:
+          sarif_file: rust-clippy-results.sarif
+          wait-for-processing: true

.github/workflows/dockerhub.yml

@@ -0,0 +1,60 @@
+name: Publish to Dockerhub
+
+on:
+  push:
+    branches:
+      - main
+      - 'releases/**'
+      - AddCIpipelines
+    tags:
+      - 'v*' #if a push with a version tag like v0.0.2 is recorded
+
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    if: github.repository == 'SciLifeLab/umi-transfer'
+    name: Push Docker image to Docker Hub / GitHub Docker Registry
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Change repo name to lowercase
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >>${GITHUB_ENV}
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Push dev image
+        uses: docker/build-push-action@v2
+        if: github.event_name == 'push'
+        with:
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:dev
+            ghcr.io/${{ env.REPO_LOWERCASE }}:dev
+            
+      - name: Push release image
+        uses: docker/build-push-action@v2
+        if: github.event_name == 'release'
+        with:
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:${{ github.event.release.tag_name }}
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:latest
+            ghcr.io/${{ env.REPO_LOWERCASE }}:${{ github.event.release.tag_name }}
+            ghcr.io/${{ env.REPO_LOWERCASE }}:${{ github.sha }}
+            ghcr.io/${{ env.REPO_LOWERCASE }}:latest

.github/workflows/rust.yml

@@ -0,0 +1,21 @@
+name: Test successful compilation on Rust
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Rust
+      uses: actions-rs/toolchain@v1
+      with:
+          toolchain: stable
+          override: true
+          target: wasm32-unknown-unknown
+    - name: Build
+      uses: actions-rs/cargo@v1
+      with:
+        command: build