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Worked on the new format of the documentation
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‎.github/workflows/docs.yml‎

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name: Deploy Documentation
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on:
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push:
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branches: [ main, master ]
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pull_request:
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branches: [ main, master ]
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Cache dependencies
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r docs_new/requirements.txt
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pip install -e .
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- name: Configure Git for GitHub Pages
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run: |
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git config user.name github-actions
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git config user.email github-actions@github.com
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- name: Build documentation
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run: mkdocs build --strict
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- name: Setup Pages
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uses: actions/configure-pages@v3
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v2
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with:
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path: site
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v2

‎.gitignore‎

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tests/scratch
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tests/test_output
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Sphinx documentation
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docs/_build/
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site/
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#machine specific files
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.vimrc

‎README.md‎

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Starting with `hedtools 0.2.0` local copies of the most recent schema versions
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are stored within the code modules for easy access.
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### Other links of interest
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### Building the docs locally
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You can build the documentation locally by executing the following commands in the hed-python repository root directory:
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```bash
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# Build the documentation
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mkdocs build
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# Serve locally with live reload
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mkdocs serve
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```
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The API documentation can be viewed at [ http://localhost:8000]( http://localhost:8000).
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Code climate reports: [https://codeclimate.com/github/hed-standard/hed-python](https://codeclimate.com/github/hed-standard/hed-python).

‎build_docs.py‎

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‎docs_new/api/errors.md‎

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# Errors
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Error handling and exception classes for HED validation and processing.
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## Exception Classes
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### HedFileError
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::: hed.errors.exceptions.HedFileError
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options:
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show_source: true
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### HedExceptions
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::: hed.errors.exceptions.HedExceptions
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options:
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show_source: true
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## Error Reporting
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### ErrorHandler
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::: hed.errors.error_reporter.ErrorHandler
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options:
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show_source: true
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### ErrorContext
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::: hed.errors.error_types.ErrorContext
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options:
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show_source: true
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## Error Types
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### ErrorSeverity
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::: hed.errors.error_types.ErrorSeverity
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options:
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show_source: true
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### ValidationErrors
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::: hed.errors.error_types.ValidationErrors
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options:
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show_source: true
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### SidecarErrors
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::: hed.errors.error_types.SidecarErrors
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options:
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show_source: true
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## Schema Error Messages
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::: hed.errors.schema_error_messages
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options:
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show_source: true

‎docs_new/api/index.md‎

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# API Reference
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This section provides comprehensive documentation for all HED Python tools modules and classes.
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## Core Modules
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### [Models](models.md)
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Core data models for working with HED data:
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- **HedString**: Represents and validates HED annotation strings
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- **HedTag**: Individual HED tag manipulation
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- **HedGroup**: Grouped HED annotations
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- **Sidecar**: BIDS sidecar file handling
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- **TabularInput**: Spreadsheet and tabular data processing
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### [Schema](schema.md)
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HED schema management and validation:
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- **HedSchema**: Main schema class for loading and querying schemas
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- **HedSchemaIO**: Schema input/output operations
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- **SchemaComparer**: Compare different schema versions
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### [Validator](validator.md)
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Validation tools and error handling:
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- **HedValidator**: Main validation engine
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- **ErrorReporter**: Error collection and reporting
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- **ValidationContext**: Validation state management
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### [Tools](tools.md)
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Utility tools and scripts:
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- **BidsTabularSummary**: BIDS dataset analysis
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- **ReorderColumns**: Spreadsheet manipulation
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- **TagCompareUtil**: Tag comparison utilities
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### [Errors](errors.md)
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Error handling and exception classes:
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- **HedFileError**: File-related errors
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- **HedExceptions**: General HED exceptions
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- **ErrorMessages**: Error message definitions
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## Quick Reference
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### Loading and Using Schemas
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::: hed.load_schema
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options:
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show_source: true
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### Basic Validation
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::: hed.HedString
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options:
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show_source: true
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members:
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- __init__
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- validate
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- remove_definitions
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### Working with BIDS Data
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::: hed.models.Sidecar
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options:
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show_source: true
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members:
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- __init__
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- validate
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- extract_definitions

‎docs_new/api/models.md‎

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# Models
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Core data models for working with HED data structures.
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## HedString
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::: hed.models.hed_string.HedString
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options:
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show_source: true
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## HedTag
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::: hed.models.hed_tag.HedTag
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options:
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show_source: true
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## HedGroup
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::: hed.models.hed_group.HedGroup
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options:
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show_source: true
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## Sidecar
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::: hed.models.sidecar.Sidecar
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options:
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show_source: true
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## TabularInput
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::: hed.models.tabular_input.TabularInput
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options:
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show_source: true
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## SpreadsheetInput
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::: hed.models.spreadsheet_input.SpreadsheetInput
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options:
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show_source: true
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## BaseInput
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::: hed.models.base_input.BaseInput
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options:
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show_source: true
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## ColumnMapper
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::: hed.models.column_mapper.ColumnMapper
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options:
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show_source: true
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## DefinitionDict
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::: hed.models.definition_dict.DefinitionDict
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options:
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show_source: true

‎docs_new/api/schema.md‎

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# Schema
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HED schema management, loading, and validation functionality.
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## HedSchema
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::: hed.schema.hed_schema.HedSchema
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options:
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show_source: true
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## Schema I/O
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::: hed.schema.hed_schema_io
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options:
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show_source: true
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## HedSchemaEntry
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::: hed.schema.hed_schema_entry.HedSchemaEntry
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options:
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show_source: true
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## HedSchemaGroup
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::: hed.schema.hed_schema_group.HedSchemaGroup
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options:
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show_source: true
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## Schema Comparison
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::: hed.schema.schema_comparer
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options:
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show_source: true
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## HED Cache Functions
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::: hed.schema.hed_cache
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options:
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show_source: true
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## Schema Validation Utilities
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::: hed.schema.schema_validation_util
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options:
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show_source: true

‎docs_new/api/tools.md‎

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# Tools
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Utility tools and scripts for working with HED data.
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## Analysis Tools
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### TabularSummary
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::: hed.tools.analysis.tabular_summary.TabularSummary
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options:
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show_source: true
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### Annotation Utilities
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::: hed.tools.analysis.annotation_util
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options:
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show_source: true
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## Remodeling Operations
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### Base Operations
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::: hed.tools.remodeling.operations.base_op
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options:
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show_source: true
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### Remove Columns
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::: hed.tools.remodeling.operations.remove_columns_op
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options:
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show_source: true
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### Rename Columns
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::: hed.tools.remodeling.operations.rename_columns_op
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options:
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show_source: true
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## BIDS Tools
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### BIDS Dataset Processing
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::: hed.tools.bids
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options:
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show_source: true

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