Merge branch 'master' into wgs-whole-region-deleted-v2.3.1

.circleci/config.yml

@@ -8,7 +8,7 @@ jobs:
     docker:
       # specify the version you desire here
       # use `-browsers` prefix for selenium tests, e.g. `3.6.1-browsers`
-      - image: kclem/crispresso2vpy3
+      - image: pinellolab/crispresso2:v2.3.0
 
       # Specify service dependencies here if necessary
       # CircleCI maintains a library of pre-built images

.github/envs/test_env.yml

@@ -0,0 +1,18 @@
+name: test_env
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - pip
+  - fastp
+  - numpy<2
+  - cython
+  - jinja2
+  - tbb=2020.2
+  - pyparsing=2.3.1
+  - scipy
+  - matplotlib=3.8.4
+  - pandas>2
+  - pip:
+    - ydiff

.github/workflows/.pylintrc

@@ -0,0 +1,7 @@
+[FORMAT]
+max-line-length=150
+max-args=15
+max-locals=40
+
+[MESSAGES CONTROL]
+disable = E0401, W0719

.github/workflows/aws_ecr.yml

@@ -0,0 +1,47 @@
+name: Push Docker image to Amazon ECR
+
+on:
+  release:
+    types:
+      - edited
+      - released
+    branches:
+      - master
+
+jobs:
+  build-and-push:
+    name: Build and Push Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - id: get_version
+      name: Get version
+      uses: jannemattila/get-version-from-tag@v3
+
+    - name: Configure AWS credentials
+      uses: aws-actions/configure-aws-credentials@v1
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-east-1
+
+    - name: Login to Amazon ECR
+      id: login-ecr
+      uses: aws-actions/amazon-ecr-login@v1
+
+    - name: Build, tag, and push the image to Amazon ECR
+      id: build-image
+      env:
+        AWS_ACCOUNT: ${{ secrets.AWS_ACCOUNT_ID }}
+        ECR_REPOSITORY: 'crispresso2'
+        AWS_REGION: 'us-east-1'
+        IMAGE_TAG: v${{ steps.get_version.outputs.version }}
+      run: |
+        # Build a docker container and push it to ECR 
+        docker build -t $AWS_ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/$ECR_REPOSITORY:$IMAGE_TAG .
+        echo "Pushing image to ECR..."
+        docker push $AWS_ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/$ECR_REPOSITORY:$IMAGE_TAG
+        echo "::set-output name=image::$AWS_ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/$ECR_REPOSITORY:$IMAGE_TAG"

.github/workflows/integration_tests.yml

@@ -0,0 +1,135 @@
+name: Run Integration Tests
+
+on:
+  push:
+
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy
+
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Conda Env
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test_env
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          use-mamba: true
+
+      - name: Get Date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda Env
+        id: cache-env
+        uses: actions/cache@v3
+        env:
+          # Increase this number to reset the cache if envs/test_env.yml hasn't changed
+          CACHE_NUMBER: 0
+        with:
+          path: /usr/share/miniconda/envs/test_env
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/envs/test_env.yml') }}
+
+      - name: Update Conda Env
+        run: |
+          conda env update -n test_env -f .github/envs/test_env.yml
+        if: steps.cache-env.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
+          conda list
+
+      - name: Create directory for files
+        run: |
+          mkdir ../CRISPResso2_copy
+          cp -r * ../CRISPResso2_copy
+
+      - name: Copy C2_tests repo
+        uses: actions/checkout@v3
+        with:
+          repository: edilytics/CRISPResso2_tests
+          # ref: '<BRANCH-NAME>' # update to specific branch
+
+      - name: Run Basic
+        run: |
+          make basic test print
+
+      - name: Run Params
+        if: success() || failure()
+        run: |
+          make params test print
+
+      - name: Run Prime Editor
+        if: success() || failure()
+        run: |
+          make prime-editor test print
+
+      - name: Run BAM Input
+        if: success() || failure()
+        run: |
+          make bam test print
+
+      - name: Run BAM Output
+        if: success() || failure()
+        run: |
+          make bam-out test print
+
+      - name: Run BAM Genome Output
+        if: success() || failure()
+        run: |
+          make bam-out-genome test print
+
+      - name: Run Batch
+        if: success() || failure()
+        run: |
+          make batch test print
+
+      - name: Run Pooled
+        if: success() || failure()
+        run: |
+          make pooled test print
+
+      - name: Run Pooled Mixed Mode
+        if: success() || failure()
+        run: |
+          make pooled-mixed-mode test print
+
+      - name: Run Pooled Mixed Mode Demux
+        if: success() || failure()
+        run: |
+          make pooled-mixed-mode-genome-demux test print
+
+      - name: Run Pooled Paired Sim
+        if: success() || failure()
+        run: |
+          make pooled-paired-sim test print
+
+      - name: Run WGS
+        if: success() || failure()
+        run: |
+          make wgs test print
+
+      - name: Run Compare
+        if: success() || failure()
+        run: |
+          make compare test print
+
+      - name: Run Aggregate
+        if: success() || failure()
+        run: |
+          make aggregate test print

.github/workflows/pylint.yml

@@ -0,0 +1,27 @@
+name: Pylint
+
+on:
+  push:
+
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint --fail-under=6.2 $(git ls-files '*.py') --rcfile=/home/runner/work/CRISPResso2/CRISPResso2/.github/workflows/.pylintrc

.github/workflows/pytest.yml

@@ -0,0 +1,45 @@
+name: Run Pytest
+
+on:
+  push:
+
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          activate-environment: test_env
+          environment-file: .github/envs/test_env.yml
+
+    - name: Install apt dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
+
+    - name: Install Pytest
+      run: |
+        pip install pytest pytest-cov
+
+    - name: Install CRISPResso
+      run: |
+        pip install -e .
+
+    - name: Run Pytest
+      run: |
+        pytest tests --cov CRISPResso2