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Merge pull request #21 from ttngu207/main
GitHub Action for release process
2 parents 4cced0e + 6120883 commit 283fad0

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‎.github/workflows/development.yaml

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name: Development
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on:
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pull_request:
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push:
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tags:
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- '*.*.*'
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jobs:
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test-changelog:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Get changelog entry
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id: changelog_reader
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uses: guzman-raphael/changelog-reader-action@v5
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with:
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path: ./CHANGELOG.md
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- name: Verify changelog parsing
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env:
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TAG_NAME: ${{steps.changelog_reader.outputs.version}}
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RELEASE_NAME: Release ${{steps.changelog_reader.outputs.version}}
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BODY: ${{steps.changelog_reader.outputs.changes}}
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PRERELEASE: ${{steps.changelog_reader.outputs.status == 'prereleased'}}
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DRAFT: ${{steps.changelog_reader.outputs.status == 'unreleased'}}
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run: |
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echo "TAG_NAME=${TAG_NAME}"
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echo "RELEASE_NAME=${RELEASE_NAME}"
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echo "BODY=${BODY}"
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echo "PRERELEASE=${PRERELEASE}"
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echo "DRAFT=${DRAFT}"
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build:
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needs: test-changelog
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- py_ver: 3.8
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distro: alpine
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image: djbase
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env:
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PY_VER: ${{matrix.py_ver}}
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DISTRO: ${{matrix.distro}}
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IMAGE: ${{matrix.image}}
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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steps:
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- uses: actions/checkout@v2
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- name: Compile image
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run: |
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export PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])")
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export PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}')
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export HOST_UID=$(id -u)
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docker-compose -f docker-compose-build.yaml up --exit-code-from element --build
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IMAGE=$(docker images --filter "reference=datajoint/${PKG_NAME}*" \
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--format "{{.Repository}}")
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TAG=$(docker images --filter "reference=datajoint/${PKG_NAME}*" --format "{{.Tag}}")
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docker save "${IMAGE}:${TAG}" | \
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gzip > "image-${PKG_NAME}-${PKG_VERSION}-py${PY_VER}-${DISTRO}.tar.gz"
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echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV
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echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV
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- name: Add image artifact
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uses: actions/upload-artifact@v2
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with:
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name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
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path: "image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-\
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${{matrix.distro}}.tar.gz"
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retention-days: 1
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- if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
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name: Add pip artifacts
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uses: actions/upload-artifact@v2
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with:
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name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}
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path: dist
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retention-days: 1
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publish-release:
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if: github.event_name == 'push'
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needs: build
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runs-on: ubuntu-latest
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env:
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TWINE_USERNAME: ${{secrets.twine_test_username}}
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TWINE_PASSWORD: ${{secrets.twine_test_password}}
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outputs:
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release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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steps:
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- uses: actions/checkout@v2
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- name: Determine package version
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run: |
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PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])")
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SDIST_PKG_NAME=$(echo ${PKG_NAME} | sed 's|_|-|g')
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PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}')
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echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV
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echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV
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echo "SDIST_PKG_NAME=${SDIST_PKG_NAME}" >> $GITHUB_ENV
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- name: Get changelog entry
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id: changelog_reader
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uses: guzman-raphael/changelog-reader-action@v5
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with:
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path: ./CHANGELOG.md
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version: ${{env.PKG_VERSION}}
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- name: Create GH release
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id: create_gh_release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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tag_name: ${{steps.changelog_reader.outputs.version}}
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release_name: Release ${{steps.changelog_reader.outputs.version}}
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body: ${{steps.changelog_reader.outputs.changes}}
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prerelease: ${{steps.changelog_reader.outputs.status == 'prereleased'}}
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draft: ${{steps.changelog_reader.outputs.status == 'unreleased'}}
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- name: Fetch image artifact
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uses: actions/download-artifact@v2
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with:
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name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py3.8-alpine
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- name: Fetch pip artifacts
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uses: actions/download-artifact@v2
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with:
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name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}
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path: dist
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- name: Publish pip release
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run: |
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export HOST_UID=$(id -u)
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docker load < "image-${{env.PKG_NAME}}-${PKG_VERSION}-py3.8-alpine.tar.gz"
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docker-compose -f docker-compose-build.yaml run \
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-e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} element \
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sh -lc "pip install twine && python -m twine upload --repository testpypi dist/*"
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- name: Determine pip artifact paths
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run: |
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echo "PKG_WHEEL_PATH=$(ls dist/${PKG_NAME}-*.whl)" >> $GITHUB_ENV
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echo "PKG_SDIST_PATH=$(ls dist/${SDIST_PKG_NAME}-*.tar.gz)" >> $GITHUB_ENV
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- name: Upload pip wheel asset to release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: ${{env.PKG_WHEEL_PATH}}
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asset_name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}.whl
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asset_content_type: application/zip
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- name: Upload pip sdist asset to release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: ${{env.PKG_SDIST_PATH}}
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asset_name: pip-${{env.SDIST_PKG_NAME}}-${{env.PKG_VERSION}}.tar.gz
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asset_content_type: application/gzip

‎.gitignore

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# dotenv
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./.env
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.env
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# virtualenv
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.venv
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**/*~
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**/#*#
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**/.#*
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docker-compose.yml
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docker-compose.y*ml

‎CHANGELOG.md

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# Changelog
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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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## [Unreleased]
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### Added
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+ Added GitHub Action release process
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+ `probe` and `ephys` elements
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+ Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
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+ Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
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[Unreleased]: https://github.com/datajoint/element-array-ephys/releases/tag/HEAD

‎Dockerfile

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ARG PY_VER
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ARG DISTRO
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ARG IMAGE
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ARG PKG_NAME
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ARG PKG_VERSION
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FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
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COPY --chown=dja:anaconda ./requirements.txt ./setup.py \
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/main/
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COPY --chown=dja:anaconda ./${PKG_NAME} /main/${PKG_NAME}
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RUN \
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cd /main && \
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pip install . && \
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rm -R /main/*
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WORKDIR /main

‎docker-compose-build.yaml

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# PY_VER=3.8 IMAGE=djbase DISTRO=alpine PKG_NAME=$(python -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])") PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__/ {print $2}') HOST_UID=$(id -u) docker-compose -f docker-compose-build.yaml up --exit-code-from element --build
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#
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# Intended for updating dependencies and docker image.
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# Used to build release artifacts.
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version: "2.4"
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services:
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element:
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build:
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context: .
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args:
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- PY_VER
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- DISTRO
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- IMAGE
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- PKG_NAME
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- PKG_VERSION
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image: datajoint/${PKG_NAME}:${PKG_VERSION}
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user: ${HOST_UID}:anaconda
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volumes:
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- .:/main
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command:
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- sh
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- -lc
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- |
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set -e
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rm -R build dist *.egg-info || echo "No prev build"
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python setup.py bdist_wheel sdist

‎element_array_ephys/ephys.py

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class ClusterQualityLabel(dj.Lookup):
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definition = """
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# Quality
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cluster_quality_label : varchar(100)
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cluster_quality_label: varchar(100)
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---
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cluster_quality_description : varchar(4000)
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cluster_quality_description: varchar(4000)
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"""
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contents = [
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('good', 'single unit'),
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-> ClusteringTask
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---
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clustering_time: datetime # time of generation of this set of clustering results
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package_version='': varchar(16)
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"""
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def make(self, key):

‎element_array_ephys/version.py

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"""Package metadata."""
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__version__ = '0.1.0a2'
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__version__ = '0.1.0a3'

‎setup.py

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from setuptools import setup, find_packages
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from os import path
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pkg_name = 'element_array_ephys'
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pkg_name = [p for p in find_packages() if '.' not in p][0]
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here = path.abspath(path.dirname(__file__))
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long_description = """"
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DataJoint Element for Extracellular Array Electrophysiology with Neuropixels probe
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"""
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with open(path.join(here, 'README.md'), 'r') as f:
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long_description = f.read()
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with open(path.join(here, 'requirements.txt')) as f:
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requirements = f.read().splitlines()
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exec(f.read())
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setup(
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name='element-array-ephys',
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name=pkg_name.replace('_', '-'),
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version=__version__,
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description="DataJoint Element for Extracellular Array Electrophysiology",
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long_description=long_description,
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author='DataJoint NEURO',
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author_email='info@vathes.com',
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license='MIT',
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url='https://github.com/datajoint/element-array-ephys',
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url=f'https://github.com/datajoint/{pkg_name.replace("_", "-")}',
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keywords='neuroscience electrophysiology science datajoint',
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packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
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scripts=[],

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