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Merge pull request #23 from CBroz1/main
Add linters, update docs
2 parents d68a61c + 2d89282 commit 662eb82

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‎.gitignore‎

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*nwb
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#mkdocs documentation
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site
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site
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docs/src/tutorials/*ipynb

‎.markdownlint.yaml‎

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# Markdown Linter configuration for docs
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# https://github.com/DavidAnson/markdownlint
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# https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
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MD009: false # permit trailing spaces
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MD007: false # List indenting - permit 4 spaces
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MD013:
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line_length: "88" # Line length limits
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tables: false # disable for tables
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headings: false # disable for headings
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MD030: false # Number of spaces after a list
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MD033: # HTML elements allowed
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allowed_elements:
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- "br"
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MD034: false # Permit bare URLs
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MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
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MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling

‎.pre-commit-config.yaml‎

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default_stages: [commit, push]
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exclude: (^.github/|^docs/|^images/)
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files # prevent giant files from being committed
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- id: requirements-txt-fixer
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- id: mixed-line-ending
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args: ["--fix=lf"]
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description: Forces to replace line ending by the UNIX 'lf' character.
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# black
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- repo: https://github.com/psf/black
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rev: 22.12.0
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hooks:
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- id: black
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- id: black-jupyter
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args:
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- --line-length=88
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# isort
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- repo: https://github.com/pycqa/isort
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rev: 5.11.2
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hooks:
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- id: isort
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args: ["--profile", "black"]
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description: Sorts imports in an alphabetical order
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# flake8
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- repo: https://github.com/pycqa/flake8
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rev: 4.0.1
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hooks:
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- id: flake8
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args: # arguments to configure flake8
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# making isort line length compatible with black
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- "--max-line-length=88"
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- "--max-complexity=18"
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- "--select=B,C,E,F,W,T4,B9"
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# these are errors that will be ignored by flake8
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# https://www.flake8rules.com/rules/{code}.html
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- "--ignore=E203,E501,W503,W605,E402"
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# E203 - Colons should not have any space before them.
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# Needed for list indexing
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# E501 - Line lengths are recommended to be no greater than 79 characters.
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# Needed as we conform to 88
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# W503 - Line breaks should occur after the binary operator.
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# Needed because not compatible with black
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# W605 - a backslash-character pair that is not a valid escape sequence now
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# generates a DeprecationWarning. This will eventually become a SyntaxError.
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# Needed because we use \d as an escape sequence
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# E402 - Place module level import at the top.
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# Needed to prevent circular import error

‎CHANGELOG.md‎

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# 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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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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## [0.1.3] - Unreleased
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+ Add - Notebook rendering in docs
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+ Add - Pre-commit, cspell, and markdown linters
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## [0.1.2] - 2022-10-21
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+ Add - mkdocs deployment with workflow API docs
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## [0.1.1] - 2022-10-11
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### Added
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+ CICD workflows for PyPI release
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+ Add - CICD workflows for PyPI release
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## [0.1.0] - 2022-05-10
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### Added
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+ Table architecture reflecting precursor projects
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+ Loaders for CCF atlas and channel locations json files
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+ Adopted black formatting into code base
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+ Add - Table architecture reflecting precursor projects
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+ Add - Loaders for CCF atlas and channel locations json files
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+ Add - Adopted black formatting into code base
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[0.1.3]: https://github.com/datajoint/element-electrode-localization/releases/tag/0.1.3
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[0.1.2]: https://github.com/datajoint/element-electrode-localization/releases/tag/0.1.2
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[0.1.1]: https://github.com/datajoint/element-electrode-localization/releases/tag/0.1.1
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[0.1.0]: https://github.com/datajoint/element-electrode-localization/releases/tag/0.1.0

‎CONTRIBUTING.md‎

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# Contribution Guidelines
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This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.org/python/community/02-Contribute.html). Please reference the link for more full details.
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This project follows the
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[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
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Please reference the link for more full details.

‎Dockerfile‎

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cd /main && \
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pip install . && \
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rm -R /main/*
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WORKDIR /main
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WORKDIR /main

‎LICENSE‎

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MIT License
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Copyright (c) 2022 DataJoint
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Copyright (c) 2023 DataJoint
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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SOFTWARE.

‎README.md‎

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![diagram](https://raw.githubusercontent.com/datajoint/element-electrode-localization/main/images/diagram_flowchart.svg)
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Installation and usage instructions can be found at the
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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-electrode-localization).

‎cspell.json‎

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// cSpell Settings
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//https://github.com/streetsidesoftware/vscode-spell-checker
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{
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"version": "0.2", // Version of the setting file. Always 0.2
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"language": "en", // language - current active spelling language
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"enabledLanguageIds": [
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"markdown",
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"yaml",
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"python"
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],
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// flagWords - list of words to be always considered incorrect
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// This is useful for offensive words and common spelling errors.
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// For example "hte" should be "the"
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"flagWords": [],
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"allowCompoundWords": true,
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"ignorePaths": [
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"./*.egg-info/*",
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"./images/*"
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],
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"words": [
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"amygdalar",
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"Andreas",
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"astype",
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"Axona",
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"Ayres",
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"Binarize",
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"Brody",
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"Buccino",
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"Chans",
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"cingulate",
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"DANDI",
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"DISTRO",
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"djtooltip",
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"djtooltiptext",
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"dtype",
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"elec",
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"eloc",
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"Ephys",
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"Feng",
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"Hawrylycz",
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"iblapps",
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"inlinehilite",
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"ipynb",
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"iterrows",
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"jupytext",
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"Lein",
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"Lesnar",
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"linenums",
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"Mesoscale",
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"mkdocstrings",
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"Moser",
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"nbconvert",
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"nbformat",
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"NEURO",
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"neuroanatomy",
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"neuroconv",
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"Neurodata",
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"neuroinformatics",
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"Neuropix",
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"NeuroPixels",
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"nrrd",
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"NWBHDF",
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"PSTH",
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"Purkinje",
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"pymdownx",
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"Reimer",
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"Roboto",
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"RRID",
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"Rxiv",
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"Sasaki",
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"Shen",
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"Siegle",
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"Sitonic",
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"Tolias",
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"tqdm",
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"Voxel",
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"xlink",
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"Yatsenko"
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]
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}

‎docker-compose-build.yaml‎

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- |
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set -e
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rm -R build dist *.egg-info || echo "No prev build"
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python setup.py bdist_wheel sdist
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python setup.py bdist_wheel sdist

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