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Merge pull request #13 from kabilar/main
Add `Miniscope-DAQ-V4` and `CaImAn` trigger
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| --- | ||
| name: Bug report | ||
| about: Create a report to help us improve | ||
| title: '' | ||
| labels: 'bug' | ||
| 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 | ||
| Include: | ||
| - OS (WIN | MACOS | Linux) | ||
| - DataJoint Element Version | ||
| - MySQL Version | ||
| - MySQL Deployment Strategy (local-native | local-docker | remote) | ||
| - Minimum number of steps to reliably reproduce the issue | ||
| - Complete error stack as a result of evaluating the above steps | ||
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| ### Expected Behavior | ||
| A clear and concise description of what you expected to happen. | ||
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| ### Screenshots | ||
| If applicable, add screenshots to help explain your problem. | ||
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| ### Additional Research and Context | ||
| Add any additional research or context that was conducted in creating this report. | ||
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| For example: | ||
| - Related GitHub issues and PR's either within this repository or in other relevant | ||
| repositories. | ||
| - Specific links to specific lines or a focus within source code. | ||
| - Relevant summary of Maintainers development meetings, milestones, projects, etc. |
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| blank_issues_enabled: false | ||
| contact_links: | ||
| - name: DataJoint Contribution Guideline | ||
| url: https://docs.datajoint.org/python/community/02-Contribute.html | ||
| about: Please make sure to review the DataJoint Contribution Guidelines |
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| @@ -0,0 +1,57 @@ | ||
| --- | ||
| name: Feature request | ||
| about: Suggest an idea for a new feature | ||
| title: '' | ||
| labels: 'enhancement' | ||
| 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 | ||
| 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: | ||
| - OS (WIN | MACOS | Linux) | ||
| - DataJoint Element Version | ||
| - MySQL Version | ||
| - MySQL Deployment Strategy (local-native | local-docker | remote) | ||
| - Minimum number of steps to reliably reproduce the issue | ||
| - Complete error stack as a result of evaluating the above steps | ||
|
|
||
| ### Screenshots | ||
| If applicable, add screenshots to help explain your feature. | ||
|
|
||
| ### Additional Research and Context | ||
| Add any additional research or context that was conducted in creating this feature request. | ||
|
|
||
| For example: | ||
| - Related GitHub issues and PR's either within this repository or in other relevant | ||
| repositories. | ||
| - Specific links to specific lines or a focus within source code. | ||
| - Relevant summary of Maintainers development meetings, milestones, projects, etc. | ||
| - Any additional supplemental web references or links that would further justify this | ||
| feature request. |
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| name: Development | ||
| on: | ||
| pull_request: | ||
| push: | ||
| tags: | ||
| - '*.*.*' | ||
| jobs: | ||
| test-changelog: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Get changelog entry | ||
| id: changelog_reader | ||
| uses: guzman-raphael/changelog-reader-action@v5 | ||
| with: | ||
| path: ./CHANGELOG.md | ||
| - name: Verify changelog parsing | ||
| env: | ||
| TAG_NAME: ${{steps.changelog_reader.outputs.version}} | ||
| RELEASE_NAME: Release ${{steps.changelog_reader.outputs.version}} | ||
| BODY: ${{steps.changelog_reader.outputs.changes}} | ||
| PRERELEASE: ${{steps.changelog_reader.outputs.status == 'prereleased'}} | ||
| DRAFT: ${{steps.changelog_reader.outputs.status == 'unreleased'}} | ||
| run: | | ||
| echo "TAG_NAME=${TAG_NAME}" | ||
| echo "RELEASE_NAME=${RELEASE_NAME}" | ||
| echo "BODY=${BODY}" | ||
| echo "PRERELEASE=${PRERELEASE}" | ||
| echo "DRAFT=${DRAFT}" | ||
| build: | ||
| needs: test-changelog | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| include: | ||
| - py_ver: 3.8 | ||
| distro: alpine | ||
| image: djbase | ||
| env: | ||
| PY_VER: ${{matrix.py_ver}} | ||
| DISTRO: ${{matrix.distro}} | ||
| IMAGE: ${{matrix.image}} | ||
| DOCKER_CLIENT_TIMEOUT: "120" | ||
| COMPOSE_HTTP_TIMEOUT: "120" | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Compile image | ||
| run: | | ||
| export PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])") | ||
| export PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}') | ||
| export HOST_UID=$(id -u) | ||
| docker-compose -f docker-compose-build.yaml up --exit-code-from element --build | ||
| IMAGE=$(docker images --filter "reference=datajoint/${PKG_NAME}*" \ | ||
| --format "{{.Repository}}") | ||
| TAG=$(docker images --filter "reference=datajoint/${PKG_NAME}*" --format "{{.Tag}}") | ||
| docker save "${IMAGE}:${TAG}" | \ | ||
| gzip > "image-${PKG_NAME}-${PKG_VERSION}-py${PY_VER}-${DISTRO}.tar.gz" | ||
| echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV | ||
| echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV | ||
| - name: Add image artifact | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}} | ||
| path: "image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-\ | ||
| ${{matrix.distro}}.tar.gz" | ||
| retention-days: 1 | ||
| - if: matrix.py_ver == '3.8' && matrix.distro == 'alpine' | ||
| name: Add pip artifacts | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}} | ||
| path: dist | ||
| retention-days: 1 | ||
| publish-release: | ||
| if: github.event_name == 'push' | ||
| needs: build | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| TWINE_USERNAME: ${{secrets.twine_username}} | ||
| TWINE_PASSWORD: ${{secrets.twine_password}} | ||
| outputs: | ||
| release_upload_url: ${{steps.create_gh_release.outputs.upload_url}} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Determine package version | ||
| run: | | ||
| PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])") | ||
| SDIST_PKG_NAME=$(echo ${PKG_NAME} | sed 's|_|-|g') | ||
| PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}') | ||
| echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV | ||
| echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV | ||
| echo "SDIST_PKG_NAME=${SDIST_PKG_NAME}" >> $GITHUB_ENV | ||
| - name: Get changelog entry | ||
| id: changelog_reader | ||
| uses: guzman-raphael/changelog-reader-action@v5 | ||
| with: | ||
| path: ./CHANGELOG.md | ||
| version: ${{env.PKG_VERSION}} | ||
| - name: Create GH release | ||
| id: create_gh_release | ||
| uses: actions/create-release@v1 | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| with: | ||
| tag_name: ${{steps.changelog_reader.outputs.version}} | ||
| release_name: Release ${{steps.changelog_reader.outputs.version}} | ||
| body: ${{steps.changelog_reader.outputs.changes}} | ||
| prerelease: ${{steps.changelog_reader.outputs.status == 'prereleased'}} | ||
| draft: ${{steps.changelog_reader.outputs.status == 'unreleased'}} | ||
| - name: Fetch image artifact | ||
| uses: actions/download-artifact@v2 | ||
| with: | ||
| name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py3.8-alpine | ||
| - name: Fetch pip artifacts | ||
| uses: actions/download-artifact@v2 | ||
| with: | ||
| name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}} | ||
| path: dist | ||
| - name: Publish pip release | ||
| run: | | ||
| export HOST_UID=$(id -u) | ||
| docker load < "image-${{env.PKG_NAME}}-${PKG_VERSION}-py3.8-alpine.tar.gz" | ||
| docker-compose -f docker-compose-build.yaml run \ | ||
| -e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} element \ | ||
| sh -lc "pip install twine && python -m twine upload dist/*" | ||
| - name: Determine pip artifact paths | ||
| run: | | ||
| echo "PKG_WHEEL_PATH=$(ls dist/${PKG_NAME}-*.whl)" >> $GITHUB_ENV | ||
| echo "PKG_SDIST_PATH=$(ls dist/${SDIST_PKG_NAME}-*.tar.gz)" >> $GITHUB_ENV | ||
| - name: Upload pip wheel asset to release | ||
| uses: actions/upload-release-asset@v1 | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| with: | ||
| upload_url: ${{steps.create_gh_release.outputs.upload_url}} | ||
| asset_path: ${{env.PKG_WHEEL_PATH}} | ||
| asset_name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}.whl | ||
| asset_content_type: application/zip | ||
| - name: Upload pip sdist asset to release | ||
| uses: actions/upload-release-asset@v1 | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| with: | ||
| upload_url: ${{steps.create_gh_release.outputs.upload_url}} | ||
| asset_path: ${{env.PKG_SDIST_PATH}} | ||
| asset_name: pip-${{env.SDIST_PKG_NAME}}-${{env.PKG_VERSION}}.tar.gz | ||
| asset_content_type: application/gzip |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| # Changelog | ||
|
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| Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. | ||
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| ## Unreleased - 2022-04-25 | ||
| + Add - Load data acquired with Miniscope-DAQ-V4 | ||
| + Add - Load data analyzed with CaImAn | ||
| + Add - Trigger CaImAn analysis | ||
| + Remove - Load data analyzed with MiniscopeAnalysis | ||
|
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| ## 0.1.1 - 2021-04-01 | ||
| + Add - Load data acquired with Miniscope-DAQ-V3 | ||
| + Add - Load data analyzed with MiniscopeAnalysis |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,15 @@ | ||
| ARG PY_VER | ||
| ARG DISTRO | ||
| ARG IMAGE | ||
| ARG PKG_NAME | ||
| ARG PKG_VERSION | ||
|
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| FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO} | ||
| COPY --chown=anaconda:anaconda ./requirements.txt ./setup.py \ | ||
| /main/ | ||
| COPY --chown=anaconda:anaconda ./${PKG_NAME} /main/${PKG_NAME} | ||
| RUN \ | ||
| cd /main && \ | ||
| pip install . && \ | ||
| rm -R /main/* | ||
| WORKDIR /main |
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