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Merge pull request #144 from datajoint/dev
`dev` -> `master`
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‎.dockerignore‎

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pharus

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: 'bug'
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assignees: ''
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---
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## Bug Report
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### Description
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A clear and concise description of what is the overall operation that is intended to be performed that resulted in an error.
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### Reproducibility
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Include:
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- OS (WIN | MACOS | Linux)
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- DataJoint LabBook Version
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- MySQL Version
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- MySQL Deployment Strategy (local-native | local-docker | remote)
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- Minimum number of steps to reliably reproduce the issue
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- Complete error stack as a result of evaluating the above steps
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### Expected Behavior
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A clear and concise description of what you expected to happen.
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### Screenshots
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If applicable, add screenshots to help explain your problem.
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### Additional Research and Context
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Add any additional research or context that was conducted in creating this report.
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For example:
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- Related GitHub issues and PR's either within this repository or in other relevant repositories.
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- Specific links to specific lines or a focus within source code.
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- Relevant summary of Maintainers development meetings, milestones, projects, etc.

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false
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contact_links:
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- name: DataJoint Contribution Guideline
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url: https://docs.datajoint.io/python/community/02-Contribute.html
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about: Please make sure to review the DataJoint Contribution Guideline

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for a new feature
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title: ''
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labels: 'enhancement'
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assignees: ''
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---
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## Feature Request
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### Problem
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A clear and concise description how this idea has manifested and the context. Elaborate on the need for this feature and/or what could be improved. Ex. I'm always frustrated when [...]
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### Requirements
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A clear and concise description of the requirements to satisfy the new feature. Detail what you expect from a successful implementation of the feature. Ex. When using this feature, it should [...]
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### Justification
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Provide the key benefits in making this a supported feature. Ex. Adding support for this feature would ensure [...]
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### Alternative Considerations
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Do you currently have a work-around for this? Provide any alternative solutions or features you've considered.
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### Related Errors
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Add any errors as a direct result of not exposing this feature.
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Please include steps to reproduce provided errors as follows:
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- OS (WIN | MACOS | Linux)
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- DataJoint LabBook Version
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- MySQL Version
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- MySQL Deployment Strategy (local-native | local-docker | remote)
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- Minimum number of steps to reliably reproduce the issue
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- Complete error stack as a result of evaluating the above steps
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### Screenshots
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If applicable, add screenshots to help explain your feature.
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### Additional Research and Context
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Add any additional research or context that was conducted in creating this feature request.
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For example:
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- Related GitHub issues and PR's either within this repository or in other relevant repositories.
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- Specific links to specific lines or a focus within source code.
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- Relevant summary of Maintainers development meetings, milestones, projects, etc.
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- Any additional supplemental web references or links that would further justify this feature request.

‎.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-docs:
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needs: test-changelog
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runs-on: ubuntu-latest
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env:
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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 docs static artifacts
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run: |
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export DJ_LABBOOK_VERSION=$(awk 'FNR==3' package.json | \
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awk '{split($0,a,":"); print a[2]}' | \
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awk -F'"' '{$0=$2}1')
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docker-compose -f docker-compose-docs.yaml up --exit-code-from docs-build --build
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echo "DJ_LABBOOK_VERSION=${DJ_LABBOOK_VERSION}" >> $GITHUB_ENV
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- name: Add docs static artifacts
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uses: actions/upload-artifact@v2
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with:
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name: docs-static-djlabbook-${{env.DJ_LABBOOK_VERSION}}
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path: docs/build/html
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retention-days: 1
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build:
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needs: test-changelog
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runs-on: ubuntu-latest
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env:
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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 static artifacts
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run: |
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export DJLABBOOK_VERSION=$(cat package.json | grep \"version\" | \
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awk -F\" '{print $4}')
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export HOST_UID=$(id -u)
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mkdir build
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docker-compose -f docker-compose-build.yaml up \
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--exit-code-from datajoint-labbook --build
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echo "DJLABBOOK_VERSION=${DJLABBOOK_VERSION}" >> $GITHUB_ENV
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- name: Add static artifacts
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uses: actions/upload-artifact@v2
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with:
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name: static-djlabbook-${{env.DJLABBOOK_VERSION}}
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path: build
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retention-days: 1
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test:
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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: ${{matrix.image}}
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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- name: Determine package version
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run: |
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DJLABBOOK_VERSION=$(cat package.json | grep \"version\" | awk -F\" '{print $4}')
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echo "DJLABBOOK_VERSION=${DJLABBOOK_VERSION}" >> $GITHUB_ENV
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- name: Run primary tests
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run: |
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export PHARUS_VERSION=$(cat pharus/pharus/version.py | tail -1 | \
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awk -F\' '{print $2}')
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export HOST_UID=$(id -u)
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docker-compose -f docker-compose-dev.yaml run -e CI=true datajoint-labbook \
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npm test -- --coverage
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publish-release:
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if: github.event_name == 'push'
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needs:
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- build
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- build-docs
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- test
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runs-on: ubuntu-latest
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outputs:
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release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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steps:
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- uses: actions/checkout@v2
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- name: Determine package version
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run: |
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DJLABBOOK_VERSION=$(cat package.json | grep \"version\" | awk -F\" '{print $4}')
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echo "DJLABBOOK_VERSION=${DJLABBOOK_VERSION}" >> $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: ${{env.DJLABBOOK_VERSION}}
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- name: Fetch static artifacts
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uses: actions/download-artifact@v2
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with:
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name: static-djlabbook-${{env.DJLABBOOK_VERSION}}
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path: build
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- name: Compress static site artifacts
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run: zip -r static-djlabbook-${DJLABBOOK_VERSION}.zip build
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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: Upload static site 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: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: static-djlabbook-${{env.DJLABBOOK_VERSION}}.zip
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asset_name: static-djlabbook-${{env.DJLABBOOK_VERSION}}.zip
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asset_content_type: application/zip
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- name: Upload deploy docker environment
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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: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: docker-compose-deploy.yaml
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asset_name: docker-compose-deploy.yaml
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asset_content_type: application/yaml
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publish-docs:
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if: github.event_name == 'push'
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needs: publish-release
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Determine package version
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run: |
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export DJLABBOOK_VERSION=$(cat package.json | grep \"version\" | \
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awk -F\" '{print $4}')
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echo "DJLABBOOK_VERSION=${DJLABBOOK_VERSION}" >> $GITHUB_ENV
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- name: Fetch docs static artifacts
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uses: actions/download-artifact@v2
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with:
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name: docs-static-djlabbook-${{env.DJLABBOOK_VERSION}}
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path: docs/build/html
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- name: Commit documentation changes
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run: |
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git clone https://github.com/${GITHUB_REPOSITORY}.git \
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--branch gh-pages --single-branch gh-pages
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rm -R gh-pages/*
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cp -r docs/build/html/* gh-pages/
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cp .gitignore gh-pages/
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touch gh-pages/.nojekyll
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cd gh-pages
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Action"
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git add . --all
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git commit -m "Update documentation" -a || true
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# The above command will fail if no changes were present, so we ignore
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# the return code.
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- name: Push changes
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uses: ad-m/github-push-action@master
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with:
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branch: gh-pages
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directory: gh-pages
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github_token: ${{secrets.GITHUB_TOKEN}}
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- name: Compress docs static site artifacts
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run: zip -r docs-static-djlabbook-${DJLABBOOK_VERSION}.zip docs/build/html
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- name: Upload docs static site 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: ${{needs.publish-release.outputs.release_upload_url}}
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asset_path: "docs-static-djlabbook-${{env.DJLABBOOK_VERSION}}.zip"
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asset_name: "docs-static-djlabbook-${{env.DJLABBOOK_VERSION}}.zip"
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asset_content_type: application/zip
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# fail_on_unmatched_files: true

‎.gitignore‎

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# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
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# docs
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/docs/build
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/docs/sphinx/_static/typedocs
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# dependencies
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/node_modules
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yarn-debug.log*
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yarn-error.log*
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.eslintcache
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.eslintcache
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.env
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docker-compose.y*ml
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.vscode

‎.gitmodules‎

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[submodule "pharus"]
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path = pharus
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url = [email protected]:datajoint/pharus.git
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branch = master

‎.vscode/settings.json‎

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