From 091177a718ad66343a92a6043dacf7c9de69df75 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Oct 2023 16:04:13 -0400 Subject: [PATCH 1/5] chore: update docker base image to 2023.10.20 --- Dockerfile | 2 +- dev.Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 891d477..f4209c2 100644 --- a/Dockerfile +++ b/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"] diff --git a/dev.Dockerfile b/dev.Dockerfile index 551febc..196b3fa 100644 --- a/dev.Dockerfile +++ b/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='[{ \ From 036b0225a65171ea345b2bc331e3b9728cce39bf Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Oct 2023 16:04:31 -0400 Subject: [PATCH 2/5] chore: update cromwell to 86 --- Dockerfile | 2 +- dev.Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index f4209c2..d500dd8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,7 @@ RUN apt-get update -y && \ pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.21.0,<0.22.0" 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 diff --git a/dev.Dockerfile b/dev.Dockerfile index 196b3fa..857094d 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -22,7 +22,7 @@ RUN apt-get update -y && \ pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.21.0,<0.22.0" 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 From 83db554426d2aebadfd38543c5d23fdc8d916a86 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Oct 2023 16:04:42 -0400 Subject: [PATCH 3/5] chore: update pysam to 0.22 --- Dockerfile | 2 +- dev.Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index d500dd8..8d029a0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,7 +8,7 @@ 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=86 diff --git a/dev.Dockerfile b/dev.Dockerfile index 857094d..23d60d1 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -19,7 +19,7 @@ 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=86 From 9ab794ec86345641214ec12122f2586e4a23bce6 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Oct 2023 16:04:52 -0400 Subject: [PATCH 4/5] chore: update lockfile dependencies --- poetry.lock | 1171 ++++++++++++++++++++++++++------------------------- 1 file changed, 596 insertions(+), 575 deletions(-) diff --git a/poetry.lock b/poetry.lock index 28c4836..56a32c9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,98 +2,98 @@ [[package]] name = "aiohttp" -version = "3.8.5" +version = "3.8.6" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.6" files = [ - {file = 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"sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"}, ] [[package]] From aefbfe599b614903e909029c3dcea77cbc4accb7 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 27 Oct 2023 16:06:26 -0400 Subject: [PATCH 5/5] ci: update action versions + poetry version --- .github/workflows/build.yml | 4 ++-- .github/workflows/lint.yml | 2 +- .github/workflows/test.yml | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index da6ade3..7b83e47 100644 --- a/.github/workflows/build.yml +++ b/.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/bento_build_action@v0.11.0 + uses: bento-platform/bento_build_action@v0.11.1 with: registry: ghcr.io registry-username: ${{ github.actor }} diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index f931316..7e03440 100644 --- a/.github/workflows/lint.yml +++ b/.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: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 66f82bc..60d7f64 100644 --- a/.github/workflows/test.yml +++ b/.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