Merge pull request #56 from bento-platform/chore/update-deps

chore: update dependencies

.github/workflows/build.yml

@@ -19,10 +19,10 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Run Bento build action
-        uses: bento-platform/[email protected].0
+        uses: bento-platform/[email protected].1
         with:
           registry: ghcr.io
           registry-username: ${{ github.actor }}

.github/workflows/lint.yml

@@ -8,7 +8,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         name: Set up Python
         with:

.github/workflows/test.yml

@@ -21,13 +21,13 @@ jobs:
           --health-timeout 5s
           --health-retries 5
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         name: Set up Python
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Poetry
-        run: python -m pip install poetry==1.3.2
+        run: python -m pip install poetry==1.6.1
       - name: Install dependencies
         run: python -m poetry install
       - name: Test

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.08.30 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 AS base-deps
 
 SHELL ["/bin/bash", "-c"]
 
@@ -8,10 +8,10 @@ SHELL ["/bin/bash", "-c"]
 RUN apt-get update -y && \
     apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
     rm -rf /var/lib/apt/lists/* && \
-    pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.21.0,<0.22.0"
+    pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.22.0,<0.23.0"
 
 WORKDIR /
-ENV CROMWELL_VERSION=85
+ENV CROMWELL_VERSION=86
 RUN curl -L \
     https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
     -o cromwell.jar

dev.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.08.30 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 AS base-deps
 
 LABEL org.opencontainers.image.description="Local development image for Bento WES."
 LABEL devcontainer.metadata='[{ \
@@ -19,10 +19,10 @@ SHELL ["/bin/bash", "-c"]
 RUN apt-get update -y && \
     apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
     rm -rf /var/lib/apt/lists/* && \
-    pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.21.0,<0.22.0"
+    pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.22.0,<0.23.0"
 
 WORKDIR /
-ENV CROMWELL_VERSION=85
+ENV CROMWELL_VERSION=86
 RUN curl -L \
     https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
     -o cromwell.jar