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Merge branch 'main' of datajoint/element-interface
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‎.gitignore‎

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# User data
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.DS_Store
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temp*
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user_data/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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**/*~
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**/#*#
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**/.#*
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docker-compose.y*ml

‎.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"
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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

‎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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## [0.3.1] - Unreleased
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## [0.5.4] - 2023-05-14
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+ Fix - DANDI URL for uploads where `staging=False`.
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## [0.5.3] - 2023-05-11
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+ Fix - `.ipynb` dark mode output for all notebooks.
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+ Fix - Remove `GOOGLE_ANALYTICS_KEY` from `u24_element_release_call.yml`.
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## [0.5.2] - 2023-04-28
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+ Fix - `.ipynb` output in tutorials is not visible in dark mode.
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## [0.5.1] - 2023-03-15
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+ Fix - ingestion routine for multiple Z devices in `prairieviewreader.py`.
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## [0.5.0] - 2023-01-09
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+ Remove - `recursive_search` function
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+ Add - pre-commit checks to the repo to observe flake8, black, isort
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+ Add - `value_to_bool` and `QuietStdOut` utilities
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## [0.4.2] - 2022-12-16
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+ Update - PrairieView loader checks for multi-plane vs single-plane scans.
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## [0.4.1] - 2022-12-15
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+ Update - PrairieView loader now reads recording start time from metadata file
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## [0.4.0] - 2022-12-14
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+ Add - mkdocs documentation
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+ Add - improved docstrings for mkdocs
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+ Add - EXTRACT trigger and loader tools
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## [0.3.0] - 2022-10-7
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+ Add - Function `prairieviewreader` to parse metadata from Bruker PrarieView acquisition system
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+ Add - Function `prairieviewreader` to parse metadata from Bruker PrarieView acquisition
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system
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+ Update - Changelog with tag links
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## [0.2.1] - 2022-07-13
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+ Add - Adopt `black` formatting
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+ Add - Function `run_caiman` to trigger CNMF algorithm.
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+ Add - Function `ingest_csv_to_table` to insert data from CSV files into tables.
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+ Add - Function `recursive_search` to search through nested dictionary for a key.
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+ Add - Function `upload_to_dandi` to upload Neurodata Without Borders file to the DANDI platform.
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+ Add - Function `upload_to_dandi` to upload Neurodata Without Borders file to the DANDI
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platform.
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+ Update - Remove `extras_require` feature to allow this package to be published to PyPI.
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## [0.1.0a1] - 2022-01-12
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+ Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
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[0.5.4]: https://github.com/datajoint/element-interface/releases/tag/0.5.4
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[0.5.3]: https://github.com/datajoint/element-interface/releases/tag/0.5.3
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[0.5.2]: https://github.com/datajoint/element-interface/releases/tag/0.5.2
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[0.5.1]: https://github.com/datajoint/element-interface/releases/tag/0.5.1
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[0.5.0]: https://github.com/datajoint/element-interface/releases/tag/0.5.0
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[0.4.2]: https://github.com/datajoint/element-interface/releases/tag/0.4.2
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[0.4.1]: https://github.com/datajoint/element-interface/releases/tag/0.4.1
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[0.4.0]: https://github.com/datajoint/element-interface/releases/tag/0.4.0
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[0.3.0]: https://github.com/datajoint/element-interface/releases/tag/0.3.0
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[0.2.1]: https://github.com/datajoint/element-interface/releases/tag/0.2.1
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[0.2.0]: https://github.com/datajoint/element-interface/releases/tag/0.2.0

‎CONTRIBUTING.md‎

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# Contribution Guidelines
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This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/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.

‎LICENSE‎

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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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fully functional pipeline. Element Interface is home to a number of utilities that make
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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-interface).

‎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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],
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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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],
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"words": [
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"isort",
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"Bruker",
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"Neurodata",
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"Prairie",
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"CNMF",
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"deconvolution"
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]
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}

‎docs/docker-compose.yaml‎

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# MODE="LIVE|QA|PUSH" PACKAGE=element_interface UPSTREAM_REPO=https://github.com/datajoint/element-interface.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
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#
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# navigate to http://localhost/
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version: "2.4"
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services:
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docs:
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build:
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dockerfile: docs/.docker/Dockerfile
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context: ../
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args:
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- PACKAGE
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image: ${PACKAGE}-docs
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environment:
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- PACKAGE
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- UPSTREAM_REPO
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- MODE
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- GOOGLE_ANALYTICS_KEY
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- PATCH_VERSION
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volumes:
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- ../docs:/main/docs
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- ../${PACKAGE}:/main/${PACKAGE}
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user: ${HOST_UID}:anaconda
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ports:
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- 80:80
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command:
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- sh
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- -c
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- |
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git config --global --add safe.directory /main
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set -e
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export PATCH_VERSION=$$(cat /main/$${PACKAGE}/version.py | grep -oE '\d+\.\d+\.[a-z0-9]+')
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if echo "$${MODE}" | grep -i live &>/dev/null; then
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mkdocs serve --config-file ./docs/mkdocs.yaml -a 0.0.0.0:80
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elif echo "$${MODE}" | grep -iE "qa|push" &>/dev/null; then
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echo "INFO::Delete gh-pages branch"
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git branch -D gh-pages || true
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echo "INFO::Fetch upstream gh-pages"
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git fetch $${UPSTREAM_REPO} gh-pages:gh-pages && git switch gh-pages || git switch --orphan gh-pages && git commit --allow-empty -m "init commit"
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echo "INFO::mike"
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mike deploy --config-file ./docs/mkdocs.yaml -u $$(grep -oE '\d+\.\d+' /main/$${PACKAGE}/version.py) latest
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mike set-default --config-file ./docs/mkdocs.yaml latest
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if echo "$${MODE}" | grep -i qa &>/dev/null; then
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mike serve --config-file ./docs/mkdocs.yaml -a 0.0.0.0:80
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elif echo "$${MODE}" | grep -i push &>/dev/null; then
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echo "INFO::Push gh-pages to upstream"
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git push $${UPSTREAM_REPO} gh-pages
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fi
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else
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echo "Unexpected mode..."
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exit 1
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fi

‎docs/src/.overrides/assets/stylesheets/extra.css‎

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/* --md-footer-fg-color: var(--dj-white); */
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}
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[data-md-color-scheme="slate"] td,
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th {
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color: var(--dj-black)
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}

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