From c3d31aa50341f6b4982b566147a6f835a70e9b85 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 12 Aug 2024 10:43:49 -0400 Subject: [PATCH] chore: update base image, dependencies; bump to 0.14.3 --- .github/workflows/build.yml | 2 +- Dockerfile | 2 +- container.requirements.txt | 8 +- dev.Dockerfile | 2 +- poetry.lock | 773 +++++++++++++++++++----------------- pyproject.toml | 12 +- 6 files changed, 419 insertions(+), 380 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7b83e47..1123ff1 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -22,7 +22,7 @@ jobs: uses: actions/checkout@v4 - name: Run Bento build action - uses: bento-platform/bento_build_action@v0.11.1 + uses: bento-platform/bento_build_action@v1.0.0 with: registry: ghcr.io registry-username: ${{ github.actor }} diff --git a/Dockerfile b/Dockerfile index 2ff5d84..66b6e7a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -47,7 +47,7 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x WORKDIR / -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.07.09 AS base-deps +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.08.12 AS base-deps SHELL ["/bin/bash", "-c"] diff --git a/container.requirements.txt b/container.requirements.txt index 219fbcd..550ba64 100644 --- a/container.requirements.txt +++ b/container.requirements.txt @@ -1,4 +1,4 @@ -gunicorn==22.0.0 -gevent==23.9.1 -pysam>=0.22.0,<0.23.0 -fasta-checksum-utils>=0.4.1,<0.5 +gunicorn==23.0.0 +gevent==24.2.1 +pysam>=0.22.1,<0.23.0 +fasta-checksum-utils>=0.4.3,<0.5 diff --git a/dev.Dockerfile b/dev.Dockerfile index f323aaf..6cb598e 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -47,7 +47,7 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x WORKDIR / -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.07.09 AS base-deps +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.08.12 AS base-deps LABEL org.opencontainers.image.description="Local development image for Bento WES." 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