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Work around a packaging issue in biopython. #64

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Jun 28, 2024
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Work around a packaging issue in biopython. #64

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5e80225
Work around a packaging issue in biopython.
jgadling Jun 26, 2024
6e601bc
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jgadling Jun 27, 2024
20d16c1
add ver.
jgadling Jun 27, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
FROM python:3.12-slim-bookworm AS build

RUN apt update && \
apt install -y make gcc && \
apt install -y make gcc git && \
apt clean

COPY requirements.txt .
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2 changes: 1 addition & 1 deletion Dockerfile.dev
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@@ -1,6 +1,6 @@
FROM python:3.12-slim-bookworm AS build
RUN apt-get update && \
apt-get install -y vim wget nginx nginx-extras procps ripgrep make gcc && \
apt-get install -y vim wget nginx nginx-extras procps ripgrep make gcc git && \
apt-get clean

ENV POETRY_VERSION=1.8
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126 changes: 57 additions & 69 deletions poetry.lock
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3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -29,6 +29,8 @@ httpx = "^0.24.1"
[tool.poetry.dependencies]
python = "^3.12"
fastapi = "^0.110.0"
# biopython 1.83 fails installation on m1 macs. The issue is fixed upstream so we're pinning to a specific commit until the next release.
biopython = { git = "https://github.com/biopython/biopython.git", rev = "e0731edc892b653dee10b1f68acf795086e6f3f0" }
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maybe add a comment or TODO here as why ^1.82 version failed and to upgrade when next build is available.

asyncpg = "^0.28.0"
alembic = "^1.11.1"
sgqlc = "^16.3"
Expand All @@ -47,7 +49,6 @@ strcase = "^1.0.0"
linkml-runtime = "^1.6.0"
sqlalchemy_utils = "^0.41.1"
strawberry-graphql = "^0.217.0"
biopython = "^1.82"

[build-system]
requires = ["poetry-core"]
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