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Merge pull request Duke-GCB#177 from fabricebrito/calrissian-172
Addresses issue Duke-GCB#172 introducing hatch and pyproject.toml
2 parents 4ee2108 + 98af45d commit 62093d9

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Diff for: ‎.github/workflows/build-and-test.yaml

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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name: Build & Tests
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on: [push, pull_request]
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permissions:
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contents: read
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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cache: "pip"
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- name: Install dependencies
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run: |
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# python -m pip install --upgrade pip
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pip install hatch
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- name: Cache Hatch
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id: cache-hatch
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uses: actions/cache@v3
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with:
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path: /home/runner/.local/share/hatch/env/virtual/
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key: ${{ runner.os }}-hatch
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- name: Build
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run: hatch build
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- name: Test
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run: |
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hatch -e test run nose2 --verbose

Diff for: ‎.github/workflows/build.yaml

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This file was deleted.

Diff for: ‎.github/workflows/package.yaml

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name: package
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name: Publish to PyPI
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on:
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release:
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types: [created]
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permissions:
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contents: read
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jobs:
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deploy:
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version:
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runs-on: ubuntu-latest
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outputs:
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app-version: ${{ steps.set-version.outputs.version }}
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steps:
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- uses: actions/checkout@v4
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- run: echo "APP_VERSION=$(python setup.py --version)" >> $GITHUB_ENV
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- run: echo app version is $APP_VERSION
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- id: set-version
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run: echo "::set-output name=version::$APP_VERSION"
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deploy:
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runs-on: ubuntu-latest
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environment: release
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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python-version: '3.10'
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python3 -m venv venv
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. venv/bin/activate
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pip install setuptools wheel twine
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pip install -r requirements.txt
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- name: verify git tag vs. version
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run: |
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python3 -m venv venv
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. venv/bin/activate
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python setup.py verify
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- name: Build
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run: |
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. venv/bin/activate
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python setup.py bdist_wheel --universal
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- name: Publish
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.PYPI_APIKEY }}
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run: |
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. venv/bin/activate
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twine upload dist/*
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container-build:
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needs: version
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: echo version ${{needs.version.outputs.app-version}}
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- run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
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- name: build & push image
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run: |
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IMAGE_ID=ghcr.io/duke-gcb/calrissian/calrissian
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docker build . --file Dockerfile --tag calrissian
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docker tag calrissian $IMAGE_ID:${{needs.version.outputs.app-version}}
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docker push $IMAGE_ID:${{needs.version.outputs.app-version}}
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# python -m pip install --upgrade pip
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pip install hatch
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- name: Build package
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run: hatch build
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- name: Test package
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run: hatch -e test run nose2 --verbose
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- name: Publish package distributions to Test PyPI
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if: github.ref != 'refs/heads/main'
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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repository-url: https://test.pypi.org/legacy/
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- name: Publish package distributions to PyPI
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if: github.ref == 'refs/heads/main'
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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repository-url: https://upload.pypi.org/legacy/

Diff for: ‎.gitignore

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*.whl
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*.zip
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env-calrissian*
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*.tar.gz

Diff for: ‎CHANGELOG.md

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The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
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## [v0.18.0] - 2024-12-13
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### Changes
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- Drop setup.py and requirements.txt in favour of PEP 517 and 518 by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/177
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## [v0.17.2] - 2024-05-02
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### Changes
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- calls `setup_kubernetes` before `_setup` to set `cudaDeviceCount` by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/170
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## [v0.17.1] - 2024-05-02
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### Changes
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## [v0.17.0] - 2024-05-02
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- broken release
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### Changes
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- Create codemeta.json by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/163
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- Conformance 1.2.1 by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/164
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- Update README.md by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/165
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- adds `cudaVersionMin`, `cudaComputeCapability` in `CUDARequirement` by @fabricebrito in https://github.com/Duke-GCB/calrissian/pull/168
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## [v0.16.0] - 2023-11-23
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### Changes

Diff for: ‎Dockerfile

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FROM python:3.10.0-slim-buster
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LABEL maintainer="[email protected]"
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# Stage 1: Build stage
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FROM rockylinux:9.3-minimal AS build
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# cwltool requires nodejs
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RUN apt-get update && apt-get install -y nodejs
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# Install necessary build tools
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RUN microdnf install -y curl tar
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RUN mkdir -p /app
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COPY . /app
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RUN pip install /app
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WORKDIR /app
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# Download the hatch tar.gz file from GitHub
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RUN curl -L https://github.com/pypa/hatch/releases/latest/download/hatch-x86_64-unknown-linux-gnu.tar.gz -o /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz
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# Extract the hatch binary
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RUN tar -xzf /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz -C /tmp/
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# Stage 2: Final stage
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FROM rockylinux:9.3-minimal
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# Install runtime dependencies
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RUN microdnf install -y --nodocs nodejs && \
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microdnf clean all
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# Create a default user and home directory
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# Set up a default user and home directory
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ENV HOME=/home/calrissian
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# home dir is created by useradd with group (g=0) to comply with
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# https://docs.openshift.com/container-platform/3.11/creating_images/guidelines.html#openshift-specific-guidelines
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# Create a user with UID 1001, group root, and a home directory
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RUN useradd -u 1001 -r -g 0 -m -d ${HOME} -s /sbin/nologin \
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-c "Default Calrissian User" calrissian && \
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chown -R 1001:0 /app && \
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chmod g+rwx ${HOME}
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-c "Default Calrissian User" calrissian && \
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mkdir -p /app && \
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mkdir -p /prod && \
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chown -R 1001:0 /app && \
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chmod g+rwx ${HOME} /app
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# Copy the hatch binary from the build stage
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COPY --from=build /tmp/hatch /usr/bin/hatch
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# Ensure the hatch binary is executable
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RUN chmod +x /usr/bin/hatch
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# Switch to the non-root user
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USER calrissian
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# Copy the application files into the /app directory
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COPY --chown=1001:0 . /tmp
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WORKDIR /tmp
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# Set up virtual environment paths
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ENV VIRTUAL_ENV=/app/envs/calrissian
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ENV PATH="$VIRTUAL_ENV/bin:$PATH"
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# Prune any existing environments and create a new production environment
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RUN cd /tmp && hatch env prune && \
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hatch env create prod && \
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rm -fr /tmp/* /tmp/.git /tmp/.pytest_cache
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WORKDIR /app
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# Set the default command to run when the container starts
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CMD ["calrissian"]

Diff for: ‎README.md

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- `RETRY_MIN`: Default `5`. Minimum interval between retries.
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- `RETRY_MAX`: Default `1200`. Maximum interval between retries.
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- `RETRY_ATTEMPTS`: Default `10`. Max number of retries before giving up.
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## For developers
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### Installing for Development
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Note that for development you can just use [Hatch] directly as described below.
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### Installing Hatch
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The main tool that is used for development is [Hatch]. It manages dependencies (in a virtualenv that is created on the fly) and is also the command runner.
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So first, [install it][install Hatch]. Ideally in an isolated way with **`pipx install hatch`** (after [installing `pipx`]), or just `pip install hatch` as a more well-known way.
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### Running tests
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```
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hatch run test:test
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```
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Verbose:
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```
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hatch run test:testv
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```
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### Running test coverage
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```
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hatch run test:cov
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```
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### Running calrissian
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```
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hatch run calrissian
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```
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### Serve the documentation
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```
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hatch run docs:serve
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```

Diff for: ‎calrissian/__about__.py

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version="0.18.0"

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