NWB revisions - PR 2 of 3

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Report
+
+### Description
+
+A clear and concise description of what is the overall operation that is intended to be
+performed that resulted in an error.
+
+### 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
+
+### Expected Behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this report.
+
+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.

.github/ISSUE_TEMPLATE/config.yml

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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

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for a new feature
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request
+
+### Problem
+
+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 [...]
+
+### Requirements
+
+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 [...]
+
+### Justification
+
+Provide the key benefits in making this a supported feature. Ex. Adding support for this
+feature would ensure [...]
+
+### Alternative Considerations
+
+Do you currently have a work-around for this? Provide any alternative solutions or
+features you've considered.
+
+### Related Errors
+Add any errors as a direct result of not exposing this feature.
+
+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.

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
 
+## [0.1.0b4] - 2021-11-29
+### Added
++ Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
+
+
 ## [0.1.0b0] - 2021-05-07
 ### Added
 + First beta release

CODE_OF_CONDUCT.md

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

README.md

@@ -3,13 +3,19 @@
 + This repository features DataJoint pipeline design for extracellular array electrophysiology, 
 with Neuropixels probe and Kilosort spike sorting method. 
 
-+ The pipeline presented here is not a complete pipeline by itself, but rather a modular 
-design of tables and dependencies specific to the extracellular electrophysiology workflow. 
++ This module is designed to be integrated into a complete data pipeline and provides
+data tables and computational dependencies specific to extracellular electrophysiology
+processing and analysis.
 
 + This modular pipeline element can be flexibly attached downstream 
 to any particular design of experiment session, thus assembling a fully functional 
 ephys pipeline.
 
++ This Element provides three schema options, selected via the DataJoint config file, with `dj.config['custom']['ephys_mode']`
+  + `acute` probe insertion, with curated clustering
+  + `chronic` probe insertion, with curated clustering
+  + `no-curation`, with kilosort triggered clustering
+
 + See the [Element Array Electrophysiology documentation](https://elements.datajoint.org/description/array_ephys/) for the background information and development timeline.
 
 + 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
-import element_array_ephys.ephys_acute as ephys
+import datajoint as dj
+import logging
+import os
+
+
+dj.config['enable_python_native_blobs'] = True
+
+
+def get_logger(name):
+    log = logging.getLogger(name)
+    log.setLevel(os.getenv('LOGLEVEL', 'INFO'))
+    return log
+
+from . import ephys_acute as ephys