Merge pull request #105 from RNAcentral/separate-base-image

Separate base image build
RNAcentral · Sep 22, 2023 · d122951 · d122951
2 parents 0e84632 + 32358ac
commit d122951
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diff --git a/.dockerignore b/.dockerignore
@@ -8,3 +8,4 @@ docs/_*
 .github
 .vscode
 .git
+1.4/
diff --git a/.github/workflows/base-image.yml b/.github/workflows/base-image.yml
@@ -0,0 +1,76 @@
+name: Publish Base Docker image to DockerHub
+
+on:
+  push:
+    paths:
+      - 'base_image/**'
+      - '.github/workflows/base-image.yml'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Docker Meta
+        id: docker_meta
+        uses: docker/metadata-action@v4
+        with:
+          images: rnacentral/r2dt-base
+          flavor: latest=false
+          tags: |
+            type=raw,value=latest
+            type=ref,event=pr
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+
+      - name: Build and push Docker image
+        id: build
+        uses: docker/build-push-action@v4
+        with:
+          push: true
+          labels: ${{ steps.docker_meta.outputs.labels }}
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          file: base_image/Dockerfile
+          context: base_image/
+
+
+      - name: Find comment for image tags
+        uses: peter-evans/find-comment@v2
+        if: github.event_name == 'pull_request'
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: Docker base image tag(s) pushed
+
+      - name: Create or update comment for image tags
+        uses: peter-evans/create-or-update-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            Docker base image tag(s) pushed:
+            ```text
+            ${{ steps.docker_meta.outputs.tags }}
+            ```
+            Labels added to images:
+            ```text
+            ${{ steps.docker_meta.outputs.labels }}
+            ```
+          edit-mode: replace
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,15 +1,19 @@
-# Workflow to create/update images in Docker Hub.
+name: Building Docker image
 
-name: Building Docker containers
-
-# Triggers the workflow on push or pull request events
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+      - develop
 
 jobs:
   initial-notification:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Initial notification
         uses: rtCamp/action-slack-notify@v2
@@ -21,45 +25,71 @@ jobs:
   create-docker-tag:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-
-      - name: docker login
-        env:
-          DOCKER_USER: ${{ secrets.DOCKER_USER }}
-          DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
-        run: docker login -u $DOCKER_USER -p $DOCKER_PASSWORD
+      - uses: actions/checkout@v3
 
-      - name: Get branch name
-        if: github.event_name != 'pull_request'
-        shell: bash
-        run: echo "BRANCH_NAME=$(echo ${GITHUB_REF#refs/heads/} | tr / -)" >> $GITHUB_ENV
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
 
-      - name: Get branch name (pull request)
-        if: github.event_name == 'pull_request'
-        shell: bash
-        run: echo "BRANCH_NAME=$(echo ${GITHUB_HEAD_REF} | tr / -)" >> $GITHUB_ENV
+      - name: Log in to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
 
-      - name: docker build (latest)
-        if: env.BRANCH_NAME == 'master'
-        run: docker build -f Dockerfile -t rnacentral/r2dt:latest .
+      - name: Docker Meta
+        id: docker_meta
+        uses: docker/metadata-action@v4
+        with:
+          images: rnacentral/r2dt
+          flavor: latest=false
+          tags: |
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=ref,event=pr
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
 
-      - name: docker build (branch name)
-        if: env.BRANCH_NAME != '' && env.BRANCH_NAME != 'master'
-        run: docker build -f Dockerfile -t rnacentral/r2dt:${{ env.BRANCH_NAME }} .
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          push: true
+          labels: ${{ steps.docker_meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          platforms: linux/amd64
 
-      - name: docker push (latest)
-        if: env.BRANCH_NAME == 'master'
-        run: docker push rnacentral/r2dt:latest
+      - name: Find comment for image tags
+        uses: peter-evans/find-comment@v2
+        if: github.event_name == 'pull_request'
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: Docker image tag(s) pushed
 
-      - name: docker push (branch name)
-        if: env.BRANCH_NAME != '' && env.BRANCH_NAME != 'master'
-        run: docker push rnacentral/r2dt:${{ env.BRANCH_NAME }}
+      - name: Create or update comment for image tags
+        uses: peter-evans/create-or-update-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            Docker image tag(s) pushed:
+            ```text
+            ${{ steps.docker_meta.outputs.tags }}
+            ```
+            Labels added to images:
+            ```text
+            ${{ steps.docker_meta.outputs.labels }}
+            ```
+          edit-mode: replace
 
   final-notification:
     runs-on: ubuntu-latest
     needs: create-docker-tag
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Final notification
         uses: rtCamp/action-slack-notify@v2

diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,11 @@ output/*
 headers.txt
 traveler-input.fasta
 tests/results
-tests/*.html
+tests/html
+tests/**/*.png
 .vscode
 docs/_build/*
+results/**
+1.4/**
+.idea/**
+.python-version
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,6 +18,9 @@ repos:
     rev: v2.15.6
     hooks:
     -   id: pylint
+        args:
+            - --rcfile=.pylintrc
+            - --disable=F0401,W0402,E1101,C0114
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks: