From 08835cec701ce2b68089ff6b8adc161aa73bbfab Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 Feb 2023 14:56:57 -0800 Subject: [PATCH 1/4] fix up Dockerfile to work with poetry --- Dockerfile | 39 ++++++++++++++++++++++++++++++--------- 1 file changed, 30 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index c793e2a7..9383e696 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,17 +1,38 @@ -FROM python:3.9 -MAINTAINER Sierra Moxon "smoxon@lbl.gov" +FROM python:3.9-bullseye as builder -# Clone repository -RUN git clone https://github.com/biolink/kgx +# https://stackoverflow.com/questions/53835198/integrating-python-poetry-with-docker +ENV PYTHONFAULTHANDLER=1 \ + PYTHONUNBUFFERED=1 \ + PYTHONHASHSEED=random \ + PIP_NO_CACHE_DIR=off \ + PIP_DISABLE_PIP_VERSION_CHECK=on \ + PIP_DEFAULT_TIMEOUT=100 \ + POETRY_VERSION=1.2.1 -# Setup -RUN cd kgx && git checkout tags/2.0.0 && pip install -r requirements.txt -&& python setup.py install +# Install Poetry +RUN pip install "poetry==$POETRY_VERSION" +RUN poetry self add "poetry-dynamic-versioning[plugin]" +WORKDIR /code -# Make data directory -RUN mkdir data +# Build project. The .git directory is needed for poetry-dynamic-versioning +COPY ./.git ./.git +COPY pyproject.toml poetry.lock README.md . +COPY kgx kgx/ +RUN poetry build + +####################################### +FROM python:3.9-slim-bullseye as runner +RUN useradd --create-home kgxuser WORKDIR /kgx +RUN mkdir data +USER kgxuser +ENV PATH="${PATH}:/home/kgxuser/.local/bin" + +COPY --from=builder /code/dist/*.whl /tmp +RUN pip install --user /tmp/*.whl + +# command to run on container start CMD ["/bin/bash"] From c4432211d45d253d5bb4b5e2beeab10475294571 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 14 Feb 2023 15:45:00 -0800 Subject: [PATCH 2/4] fixing token --- .github/workflows/pypi-release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi-release.yml b/.github/workflows/pypi-release.yml index e982da92..d002ce3a 100644 --- a/.github/workflows/pypi-release.yml +++ b/.github/workflows/pypi-release.yml @@ -28,4 +28,4 @@ jobs: uses: pypa/gh-action-pypi-publish@v1.2.2 with: user: __token__ - password: ${{ secrets.KGX_PYPI }} + password: ${{ secrets.KGX_PYPI_TOKEN }} From 562e93d74ddcfdbff0faf327b67b13b0d12bd631 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 23 Feb 2023 20:00:05 +0000 Subject: [PATCH 3/4] Bump markdown-it-py from 2.1.0 to 2.2.0 Bumps [markdown-it-py](https://github.com/executablebooks/markdown-it-py) from 2.1.0 to 2.2.0. - [Release notes](https://github.com/executablebooks/markdown-it-py/releases) - [Changelog](https://github.com/executablebooks/markdown-it-py/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/markdown-it-py/compare/v2.1.0...v2.2.0) --- updated-dependencies: - dependency-name: markdown-it-py dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 3253 ++++++++++++++++++++++++++------------------------- 1 file changed, 1628 insertions(+), 1625 deletions(-) diff --git a/poetry.lock b/poetry.lock index eaae49a3..82edb42e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] name = "aiohttp" version = "2.3.10" @@ -5,6 +7,30 @@ description = "Async http client/server framework (asyncio)" category = "main" optional = false python-versions = ">=3.4.2" +files = [ + {file = "aiohttp-2.3.10-cp34-cp34m-macosx_10_10_x86_64.whl", hash = "sha256:834f687b806fbf49cb135b5a208b5c27338e19c219d6e09e9049936e01e8bea8"}, + {file = "aiohttp-2.3.10-cp34-cp34m-macosx_10_11_x86_64.whl", hash = "sha256:6b8c5a00432b8a5a083792006e8fdfb558b8b10019ce254200855264d3a25895"}, + {file = "aiohttp-2.3.10-cp34-cp34m-macosx_10_12_x86_64.whl", hash = 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