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Merge pull request #165 from kabilar/patch
Patch issue with nullable attributes
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name: Release | ||
on: | ||
workflow_dispatch: | ||
jobs: | ||
make_github_release: | ||
uses: datajoint/.github/.github/workflows/make_github_release.yaml@main | ||
pypi_release: | ||
needs: make_github_release | ||
uses: datajoint/.github/.github/workflows/pypi_release.yaml@main | ||
secrets: | ||
TWINE_USERNAME: ${{secrets.TWINE_USERNAME}} | ||
TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}} | ||
with: | ||
UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}} | ||
mkdocs_release: | ||
uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main | ||
permissions: | ||
contents: write | ||
# devcontainer-build: | ||
# uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main | ||
# devcontainer-publish: | ||
# needs: | ||
# - devcontainer-build | ||
# uses: datajoint/.github/.github/workflows/devcontainer-publish.yaml@main | ||
# secrets: | ||
# DOCKERHUB_USERNAME: ${{secrets.DOCKERHUB_USERNAME}} | ||
# DOCKERHUB_TOKEN: ${{secrets.DOCKERHUB_TOKEN_FOR_ELEMENTS}} |
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name: Test | ||
on: | ||
push: | ||
pull_request: | ||
workflow_dispatch: | ||
jobs: | ||
# devcontainer-build: | ||
# uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main | ||
tests: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
py_ver: ["3.9", "3.10"] | ||
mysql_ver: ["8.0", "5.7"] | ||
include: | ||
- py_ver: "3.8" | ||
mysql_ver: "5.7" | ||
- py_ver: "3.7" | ||
mysql_ver: "5.7" | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python ${{matrix.py_ver}} | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: ${{matrix.py_ver}} | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install flake8 "black[jupyter]" | ||
- name: Run style tests | ||
run: | | ||
python_version=${{matrix.py_ver}} | ||
black element_array_ephys --check --verbose --target-version py${python_version//.} | ||
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# DataJoint Element - Array Electrophysiology Element | ||
[![PyPI version](https://badge.fury.io/py/element-array-ephys.svg)](http://badge.fury.io/py/element-array-ephys) | ||
|
||
DataJoint Element for extracellular array electrophysiology. DataJoint Elements | ||
collectively standardize and automate data collection and analysis for neuroscience | ||
experiments. Each Element is a modular pipeline for data storage and processing with | ||
corresponding database tables that can be combined with other Elements to assemble a | ||
fully functional pipeline. | ||
# DataJoint Element for Extracellular Electrophysiology | ||
|
||
![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg) | ||
DataJoint Element for extracellular array electrophysiology that processes data | ||
acquired with a polytrode probe | ||
(e.g. [Neuropixels](https://www.neuropixels.org), Neuralynx) using the | ||
[SpikeGLX](https://github.com/billkarsh/SpikeGLX) or | ||
[OpenEphys](https://open-ephys.org/gui) acquisition software and | ||
[MATLAB-based Kilosort](https://github.com/MouseLand/Kilosort) or [python-based | ||
Kilosort](https://github.com/MouseLand/pykilosort) spike sorting software. DataJoint | ||
Elements collectively standardize and automate data collection and analysis for | ||
neuroscience experiments. Each Element is a modular pipeline for data storage and | ||
processing with corresponding database tables that can be combined with other Elements | ||
to assemble a fully functional pipeline. | ||
|
||
Installation and usage instructions can be found at the | ||
[Element documentation](https://datajoint.com/docs/elements/element-array-ephys). | ||
## Experiment flowchart | ||
|
||
![flowchart](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg) | ||
|
||
## Data Pipeline Diagram | ||
|
||
![datajoint](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg) | ||
|
||
|
||
## Getting Started | ||
|
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+ Install from PyPI | ||
|
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```bash | ||
pip install element-array-ephys | ||
``` | ||
|
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+ [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-array-ephys#interactive-tutorial) | ||
|
||
+ [Documentation](https://datajoint.com/docs/elements/element-array-ephys) | ||
|
||
## Support | ||
|
||
+ If you need help getting started or run into any errors, please contact our team by email at [email protected]. |
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