Merge branch 'master' into 2396-update-latest-archivedf-lowcell

Author: RasmusBurge-CG

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 63.2.13
+current_version = 63.5.14
 commit = True
 tag = True
 tag_name = v{new_version}

.github/workflows/build_and_publish.yml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"

.github/workflows/build_dockerfile_on_push.yml

@@ -7,28 +7,34 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
         run: echo "branch=$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})" >> $GITHUB_OUTPUT
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
+
+      - name: Suppress annotations during build
+        run: echo "::stop-commands::no-annotations"
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: ./
           file: ./Dockerfile
           push: true
           tags: "clinicalgenomics/cg-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/cg-stage:latest"
+
+      - name: Resume annotations
+        run: echo "::no-annotations::"

.github/workflows/build_dockerfile_on_release.yml

@@ -11,21 +11,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check Out Repo
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: ./
           file: ./Dockerfile

.github/workflows/build_publish_cli_image.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Prepare Branch Name
         id: prepare_branch_name
@@ -23,7 +23,7 @@ jobs:
           fi
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
@@ -50,7 +50,7 @@ jobs:
 
       - name: Build and Push Docker Image
         id: docker_cli_build
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: ./
           file: ./Dockerfile-cli

.github/workflows/installations.yml

@@ -12,7 +12,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -25,7 +25,7 @@ jobs:
           virtualenvs-create: false
 
       - name: Cache Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ${{ env.pythonLocation }}

.github/workflows/tests_and_coverage.yml

@@ -12,7 +12,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -25,7 +25,7 @@ jobs:
           virtualenvs-create: false
 
       - name: Cache dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ${{ env.pythonLocation }}
@@ -35,7 +35,7 @@ jobs:
         if: steps.cache.outputs.cache-hit != 'true'
         run: poetry install --no-interaction
 
-      - name: Test with pytest & Coveralls
+      - name: Test with Pytest & Coveralls
         run: |
           pytest -n logical --cov=cg/
           coveralls

alembic/versions/2024_09_27_d6474325c722_refactor_pacbio_models.py

@@ -0,0 +1,104 @@
+"""Refactor pacbio models
+
+Revision ID: d6474325c722
+Revises: 18dbadd8c436
+Create Date: 2024-09-27 15:40:49.040271
+
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "d6474325c722"
+down_revision = "18dbadd8c436"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # PacbioSequencingRun
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("barcoded_hifi_reads", sa.BIGINT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("barcoded_hifi_reads_percentage", sa.FLOAT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("barcoded_hifi_yield", sa.BIGINT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("barcoded_hifi_yield_percentage", sa.FLOAT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("barcoded_hifi_mean_read_length", sa.BIGINT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("run_name", type_=mysql.VARCHAR(64), nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("unbarcoded_hifi_reads", sa.BIGINT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("unbarcoded_hifi_yield", sa.BIGINT, nullable=True),
+    )
+    op.add_column(
+        table_name="pacbio_sequencing_run",
+        column=sa.Column("unbarcoded_hifi_mean_read_length", sa.BIGINT, nullable=True),
+    )
+
+    # PacbioSampleSequencingMetrics
+    op.add_column(
+        table_name="pacbio_sample_run_metrics",
+        column=sa.Column("polymerase_mean_read_length", sa.BIGINT, nullable=True),
+    )
+    op.drop_column(table_name="pacbio_sample_run_metrics", column_name="percent_reads_passing_q30")
+    op.drop_column(table_name="pacbio_sample_run_metrics", column_name="failed_reads")
+    op.drop_column(table_name="pacbio_sample_run_metrics", column_name="failed_yield")
+    op.drop_column(table_name="pacbio_sample_run_metrics", column_name="failed_mean_read_length")
+
+
+def downgrade():
+    # PacbioSequencingRun
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="barcoded_hifi_reads")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="barcoded_hifi_reads_percentage")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="barcoded_hifi_yield")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="barcoded_hifi_yield_percentage")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="barcoded_hifi_mean_read_length")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="run_name")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="unbarcoded_hifi_reads")
+    op.drop_column(table_name="pacbio_sequencing_run", column_name="unbarcoded_hifi_yield")
+    op.drop_column(
+        table_name="pacbio_sequencing_run", column_name="unbarcoded_hifi_mean_read_length"
+    )
+
+    # PacbioSampleSequencingMetrics
+    op.drop_column(
+        table_name="pacbio_sample_run_metrics", column_name="polymerase_mean_read_length"
+    )
+    op.add_column(
+        table_name="pacbio_sample_run_metrics",
+        column=sa.Column("percent_reads_passing_q30", sa.FLOAT, nullable=False),
+    )
+    op.add_column(
+        table_name="pacbio_sample_run_metrics",
+        column=sa.Column("failed_reads", sa.BIGINT, nullable=False),
+    )
+    op.add_column(
+        table_name="pacbio_sample_run_metrics",
+        column=sa.Column("failed_yield", sa.BIGINT, nullable=False),
+    )
+    op.add_column(
+        table_name="pacbio_sample_run_metrics",
+        column=sa.Column("failed_mean_read_length", sa.BIGINT, nullable=False),
+    )