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chore: update service/workflow dependencies + base img #65

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merged 2 commits into from
Jan 8, 2024
Merged

chore: update service/workflow dependencies + base img #65

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0b5dbcd
chore: update service/workflow dependencies + base img
davidlougheed Jan 8, 2024
507160a
ci: update action version + poetry
davidlougheed Jan 8, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/lint.yml
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Expand Up @@ -9,7 +9,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
name: Set up Python
with:
python-version: "3.10"
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4 changes: 2 additions & 2 deletions .github/workflows/test.yml
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Expand Up @@ -22,12 +22,12 @@ jobs:
--health-retries 5
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
name: Set up Python
with:
python-version: ${{ matrix.python-version }}
- name: Install Poetry
run: python -m pip install poetry==1.6.1
run: python -m pip install poetry==1.7.1
- name: Install dependencies
run: python -m poetry install
- name: Test
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2 changes: 1 addition & 1 deletion Dockerfile
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@@ -1,4 +1,4 @@
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.12.01 AS base-deps
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 AS base-deps

SHELL ["/bin/bash", "-c"]

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2 changes: 1 addition & 1 deletion container.requirements.txt
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@@ -1,4 +1,4 @@
gunicorn==21.2.0
gevent==23.9.1
pysam>=0.22.0,<0.23.0
fasta-checksum-utils>=0.3.1,<0.4
fasta-checksum-utils>=0.4.0,<0.5
2 changes: 1 addition & 1 deletion dev.Dockerfile
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@@ -1,4 +1,4 @@
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.12.01 AS base-deps
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 AS base-deps

LABEL org.opencontainers.image.description="Local development image for Bento WES."
LABEL devcontainer.metadata='[{ \
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648 changes: 290 additions & 358 deletions poetry.lock
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "bento_wes"
version = "0.12.5"
version = "0.12.6"
description = "Workflow execution service for the Bento platform."
authors = [
"David Lougheed <[email protected]>",
Expand All @@ -24,7 +24,7 @@ classifiers = [

[tool.poetry.dependencies]
python = "^3.10.0"
bento-lib = {extras = ["fastapi"], version = "^11.1.1"}
bento-lib = {extras = ["flask"], version = "^11.2.0"}
celery = {extras = ["redis"], version = "^5.2.7"}
requests = "^2.28.1"
Flask = "~2.2.5"
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