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Merge pull request #165 from kabilar/patch
Patch issue with nullable attributes
2 parents 1d30cb8 + 48a1e76 commit e4dd98a

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‎.github/workflows/development.yaml

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‎.github/workflows/release.yaml

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name: Release
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on:
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workflow_dispatch:
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jobs:
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make_github_release:
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uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
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pypi_release:
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needs: make_github_release
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uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
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secrets:
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TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
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TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
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with:
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UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
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mkdocs_release:
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uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
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permissions:
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contents: write
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# devcontainer-build:
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# uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
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# devcontainer-publish:
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# needs:
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# - devcontainer-build
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# uses: datajoint/.github/.github/workflows/devcontainer-publish.yaml@main
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# secrets:
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# DOCKERHUB_USERNAME: ${{secrets.DOCKERHUB_USERNAME}}
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# DOCKERHUB_TOKEN: ${{secrets.DOCKERHUB_TOKEN_FOR_ELEMENTS}}

‎.github/workflows/test.yaml

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name: Test
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on:
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push:
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pull_request:
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workflow_dispatch:
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jobs:
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# devcontainer-build:
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# uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
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tests:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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py_ver: ["3.9", "3.10"]
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mysql_ver: ["8.0", "5.7"]
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include:
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- py_ver: "3.8"
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mysql_ver: "5.7"
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- py_ver: "3.7"
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mysql_ver: "5.7"
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{matrix.py_ver}}
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uses: actions/setup-python@v4
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with:
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python-version: ${{matrix.py_ver}}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 "black[jupyter]"
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- name: Run style tests
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run: |
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python_version=${{matrix.py_ver}}
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black element_array_ephys --check --verbose --target-version py${python_version//.}
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‎.github/workflows/u24_element_before_release.yml

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‎.github/workflows/u24_element_release_call.yml

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‎.github/workflows/u24_element_tag_to_release.yml

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‎CHANGELOG.md

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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
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[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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## [Unreleased] - 2023-06-23
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## [0.2.11] - 2023-06-29
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+ Update - Improve kilosort triggering routine - better logging, remove temporary files, robust resumable processing
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+ Add - Null value for `package_version` to patch bug
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+ Update - GitHub Actions workflows
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+ Update - README instructions
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## [0.2.10] - 2023-05-26
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‎README.md

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# DataJoint Element - Array Electrophysiology Element
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[![PyPI version](https://badge.fury.io/py/element-array-ephys.svg)](http://badge.fury.io/py/element-array-ephys)
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DataJoint Element for extracellular array electrophysiology. DataJoint Elements
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collectively standardize and automate data collection and analysis for neuroscience
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experiments. Each Element is a modular pipeline for data storage and processing with
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corresponding database tables that can be combined with other Elements to assemble a
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fully functional pipeline.
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# DataJoint Element for Extracellular Electrophysiology
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![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
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DataJoint Element for extracellular array electrophysiology that processes data
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acquired with a polytrode probe
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(e.g. [Neuropixels](https://www.neuropixels.org), Neuralynx) using the
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[SpikeGLX](https://github.com/billkarsh/SpikeGLX) or
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[OpenEphys](https://open-ephys.org/gui) acquisition software and
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[MATLAB-based Kilosort](https://github.com/MouseLand/Kilosort) or [python-based
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Kilosort](https://github.com/MouseLand/pykilosort) spike sorting software. DataJoint
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Elements collectively standardize and automate data collection and analysis for
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neuroscience experiments. Each Element is a modular pipeline for data storage and
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processing with corresponding database tables that can be combined with other Elements
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to assemble a fully functional pipeline.
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Installation and usage instructions can be found at the
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[Element documentation](https://datajoint.com/docs/elements/element-array-ephys).
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## Experiment flowchart
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![flowchart](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
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## Data Pipeline Diagram
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![datajoint](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
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## Getting Started
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+ Install from PyPI
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```bash
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pip install element-array-ephys
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```
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+ [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-array-ephys#interactive-tutorial)
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+ [Documentation](https://datajoint.com/docs/elements/element-array-ephys)
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## Support
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+ If you need help getting started or run into any errors, please contact our team by email at support@datajoint.com.

‎element_array_ephys/ephys_acute.py

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raise ValueError(f"Unknown task mode: {task_mode}")
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creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
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self.insert1({**key, "clustering_time": creation_time})
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self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
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@schema

‎element_array_ephys/ephys_chronic.py

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raise ValueError(f"Unknown task mode: {task_mode}")
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creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
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self.insert1({**key, "clustering_time": creation_time})
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self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
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‎element_array_ephys/ephys_no_curation.py

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raise ValueError(f"Unknown task mode: {task_mode}")
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creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
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self.insert1({**key, "clustering_time": creation_time})
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self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
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