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Merge pull request #94 from datajoint/run_kilosort
`run_kilosort` -> `main`
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‎.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
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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 Element 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
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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.org/python/community/02-Contribute.html
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about: Please make sure to review the DataJoint Contribution Guidelines

‎.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
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on the need for this feature and/or what could be improved. Ex. I'm always frustrated
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when [...]
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### Requirements
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A clear and concise description of the requirements to satisfy the new feature. Detail
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what you expect from a successful implementation of the feature. Ex. When using this
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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
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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
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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 Element 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
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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
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feature request.

‎CHANGELOG.md

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+ Update - Move common functions to `element-interface` package.
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+ Add - NWB export function
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## [0.1.0b4] - 2021-11-29
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### Added
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+ Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
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## [0.1.0b0] - 2021-05-07
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+ Update - First beta release

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[Support@DataJoint.com](mailto:support@datajoint.com).
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
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For answers to common questions about this code of conduct, see the FAQ at
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[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[homepage]: https://www.contributor-covenant.org
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
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[Mozilla CoC]: https://github.com/mozilla/diversity
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[FAQ]: https://www.contributor-covenant.org/faq
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[translations]: https://www.contributor-covenant.org/translations

‎README.md

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+ This repository features DataJoint pipeline design for extracellular array electrophysiology,
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with Neuropixels probe and Kilosort spike sorting method.
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+ The pipeline presented here is not a complete pipeline by itself, but rather a modular
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design of tables and dependencies specific to the extracellular electrophysiology workflow.
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+ This module is designed to be integrated into a complete data pipeline and provides
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data tables and computational dependencies specific to extracellular electrophysiology
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processing and analysis.
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+ This modular pipeline element can be flexibly attached downstream
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to any particular design of experiment session, thus assembling a fully functional
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ephys pipeline.
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+ This Element provides three schema options, selected via the DataJoint config file, with `dj.config['custom']['ephys_mode']`
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+ `acute` probe insertion, with curated clustering
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+ `chronic` probe insertion, with curated clustering
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+ `no-curation`, with kilosort triggered clustering
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+ See the [Element Array Electrophysiology documentation](https://elements.datajoint.org/description/array_ephys/) for the background information and development timeline.
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+ For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health.

‎element_array_ephys/__init__.py

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# ephys_acute as default
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import element_array_ephys.ephys_acute as ephys
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import datajoint as dj
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import logging
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import os
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dj.config['enable_python_native_blobs'] = True
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def get_logger(name):
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log = logging.getLogger(name)
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log.setLevel(os.getenv('LOGLEVEL', 'INFO'))
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return log
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from . import ephys_acute as ephys

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