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kabilarkabilar
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Merge branch 'main' of https://github.com/datajoint/element-array-ephys into main
2 parents f69e491 + f2ac602 commit 1ce53f3

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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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## [0.1.0a3] - 2021-04-26
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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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[0.1.0a3]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a3

‎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/__init__.py

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__author__ = "DataJoint NEURO"
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__date__ = "December 15, 2020"
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__version__ = "0.0.1"
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import datajoint as dj
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import pathlib
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__all__ = ['__author__', '__version__', '__date__']
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dj.config['enable_python_native_blobs'] = True
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def find_full_path(root_directories, relative_path):
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"""
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Given a relative path, search and return the full-path
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from provided potential root directories (in the given order)
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:param root_directories: potential root directories
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:param relative_path: the relative path to find the valid root directory
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:return: root_directory (pathlib.Path object)
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"""
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relative_path = pathlib.Path(relative_path)
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if relative_path.exists():
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return relative_path
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# turn to list if only a single root directory is provided
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if isinstance(root_directories, (str, pathlib.Path)):
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root_directories = [root_directories]
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for root_dir in root_directories:
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if (pathlib.Path(root_dir) / relative_path).exists():
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return pathlib.Path(root_dir) / relative_path
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raise FileNotFoundError('No valid full-path found (from {})'
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' for {}'.format(root_directories, relative_path))
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def find_root_directory(root_directories, full_path):
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"""
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Given multiple potential root directories and a full-path,
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search and return one directory that is the parent of the given path
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:param root_directories: potential root directories
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:param full_path: the relative path to search the root directory
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:return: full-path (pathlib.Path object)
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"""
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full_path = pathlib.Path(full_path)
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if not full_path.exists():
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raise FileNotFoundError(f'{full_path} does not exist!')
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# turn to list if only a single root directory is provided
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if isinstance(root_directories, (str, pathlib.Path)):
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root_directories = [root_directories]
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try:
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return next(pathlib.Path(root_dir) for root_dir in root_directories
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if pathlib.Path(root_dir) in set(full_path.parents))
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except StopIteration:
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raise FileNotFoundError('No valid root directory found (from {})'
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' for {}'.format(root_directories, full_path))

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