Merge pull request #5 from sunbeam-labs/4-containerize-and-version

Containerize and version

.github/workflows/docker.yml

@@ -0,0 +1,60 @@
+name: Push to DockerHub
+
+on:
+  workflow_call:
+
+  workflow_dispatch:
+
+jobs:
+    build-and-push-to-dockerhub:
+        name: Push Docker image to Docker Hub
+        runs-on: ubuntu-latest
+
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+
+            - name: Get sbx version
+              shell: bash
+              run: |
+                SBX_VER=$(cat VERSION)
+                echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
+            
+            - name: Log in to Docker Hub
+              uses: docker/login-action@v3
+              with:
+                username: ${{ secrets.DOCKERHUB_USERNAME }}
+                password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+            - name: Extract metadata (tags, labels) for Docker
+              id: meta
+              uses: docker/metadata-action@v5
+              with:
+                images: sunbeamlabs/sbx_assembly
+
+            - name: Build and push Docker image for annotation
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_annotation.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-annotation
+                labels: ${{ steps.meta.outputs.labels }}
+
+            - name: Build and push Docker image for assembly
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_assembly.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-assembly
+                labels: ${{ steps.meta.outputs.labels }}
+
+            - name: Build and push Docker image for coverage
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_coverage.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-coverage
+                labels: ${{ steps.meta.outputs.labels }}

.github/workflows/pr.yml

@@ -0,0 +1,12 @@
+name: Tests
+
+on:
+    pull_request:
+      branches:
+        - main
+
+jobs:
+    run-tests:
+        uses: ./.github/workflows/tests.yml
+        secrets: inherit
+

.github/workflows/release.yml

@@ -0,0 +1,79 @@
+name: Release
+
+on:
+    release:
+      types: [published]
+
+    workflow_dispatch:
+
+jobs:
+    run-tests:
+        uses: ./.github/workflows/tests.yml
+        secrets: inherit
+
+    check-version:
+        runs-on: ubuntu-latest
+        steps:
+          - name: Checkout
+            uses: actions/checkout@v4
+
+          - name: Get sbx version
+            shell: bash
+            run: |
+              SBX_VER=$(cat VERSION)
+              echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
+
+          - id: get_version
+            uses: battila7/get-version-action@v2
+
+          - name: Check version
+            shell: bash
+            run: |
+              RELEASE_VERSION=${{ steps.get_version.outputs.version-without-v }}
+              echo "Release version: ${RELEASE_VERSION}"
+              echo "Sbx version: ${{ env.SBX_VER }}"
+
+              if [[ $RELEASE_VERSION == ${{ env.SBX_VER }} ]]; then
+                  echo "Versions match, continuing..."
+              else
+                  echo "Versions don't match, exiting..."
+                  exit 1
+              fi
+
+    push-to-dockerhub:
+        uses: ./.github/workflows/docker.yml
+        secrets: inherit
+        needs:
+          - run-tests
+          - check-version
+
+    test-apptainer:
+      name: Apptainer Test
+      runs-on: ubuntu-latest
+      needs: push-to-dockerhub
+
+      steps:
+        - name: Checkout Code
+          uses: actions/checkout@v4
+
+        - name: Set test env
+          run: echo "SUNBEAM_TEST_PROFILE=apptainer" >> $GITHUB_ENV
+
+        - uses: eWaterCycle/setup-apptainer@v2
+          with:
+            apptainer-version: 1.1.2
+
+        - name: Test with Sunbeam
+          uses: sunbeam-labs/sbx_test_action@v1
+          with:
+            test-directory: ".tests/e2e/"
+
+        - name: Dump Logs
+          shell: bash
+          if: always()
+          run: tail -n +1 logs/*
+
+        - name: Dump Stats
+          shell: bash
+          if: always()
+          run: cat stats/*

.github/workflows/tests.yml

@@ -1,31 +1,73 @@
 name: Tests
 
 on:
-  pull_request:
-    branches: [ master, main ]
   push:
     branches: [ master, main ]
+  workflow_call:
+  workflow_dispatch:
   schedule:
     - cron: "0 13 * * 1"
 
-jobs:  
+jobs:
+  lint:
+    name: Lint Code
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+            python-version: 3.12
+
+      - name: Install Dependencies
+        run: pip install black snakefmt
+
+      - name: Run Linter
+        run: |
+          black --check .
+          snakefmt --check *.smk
+
+  test-unit:
+    name: Run Extension Unit Tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+            python-version: 3.12
+
+      - name: Install Dependencies
+        run: pip install pytest
+
+      - name: Run Unit Tests
+        run: true #pytest .tests/unit/
+        # This'll require having a lib within scripts with internal tests
+
   test-e2e:
     name: Test Extension with Sunbeam
     runs-on: ubuntu-latest
+    needs:
+      - test-unit
+      - lint
 
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Test with Sunbeam
         uses: sunbeam-labs/sbx_test_action@v1
-          
-      - name: Dump Logs
-        shell: bash
-        if: always()
-        run: tail -n +1 logs/*
+
+      #- name: Dump Logs
+      #  shell: bash
+      #  if: always()
+      #  run: tail -n +1 logs/*
 
-      - name: Dump Stats
-        shell: bash
-        if: always()
-        run: cat stats/*
+      #- name: Dump Stats
+      #  shell: bash
+      #  if: always()
+      #  run: cat stats/*

.gitignore

@@ -0,0 +1 @@
+__pycache__

README.md

@@ -4,7 +4,7 @@
 
 <!-- Begin badges -->
 [![Tests](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml)
-[![Super-Linter](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml)
+[![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_assembly)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_assembly/)
 <!-- End badges -->
 
 A [Sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for assembly of contigs using Megahit, gene annotation using Prodigal, and annotation using [Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi) and [Diamond](https://github.com/bbuchfink/diamond). It can also map reads to contigs and calculat per-base coverage using [Minimap2](https://github.com/lh3/minimap2) and [samtools](https://github.com/samtools/samtools).

VERSION

@@ -0,0 +1 @@
+0.0.0

envs/sbx_annotation.Dockerfile

@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_assembly_env
+
+COPY envs/sbx_annotation.yml ./
+
+# Install environment
+RUN mamba env create --file sbx_annotation.yml --name sbx_annotation
+
+ENV PATH="/opt/conda/envs/sbx_annotation/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_annotation", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"

envs/sbx_assembly.Dockerfile

@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_assembly_env
+
+COPY envs/sbx_assembly.yml ./
+
+# Install environment
+RUN mamba env create --file sbx_assembly.yml --name sbx_assembly
+
+ENV PATH="/opt/conda/envs/sbx_assembly/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_assembly", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"