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Fixed co-pilot suggestions
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‎docs/user_guide.md‎

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@@ -7,8 +7,8 @@ This guide provides step-by-step instructions for using the HED Python tools for
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- 📚 [API Reference](api/index.html)
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- 📓 [Jupyter notebooks](https://github.com/hed-standard/hed-python/tree/main/examples)
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- 🐛 [GitHub issues](https://github.com/hed-standard/hed-python/issues)
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- � [HED resources](https://www.hedtags.org/hed-resources)
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- �📖 [HED specification](https://www.hedtags.org/hed-specification)
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- 🎓 [HED resources](https://www.hedtags.org/hed-resources)
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- 📖 [HED specification](https://www.hedtags.org/hed-specification)
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- 🌐 [Online tools](https://hedtools.org/hed)
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## Table of contents
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hed_string = HedString(hed_str, schema)
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issues += hed_string.validate()
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if issues:
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print(get_printable_issues_string(issues))
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print(get_printable_issue_string(issues))
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```
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## Working with BIDS datasets
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# Include warnings in validation
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issues = dataset.validate(check_for_warnings=True)
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```
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Since a BIDS dataset includes the HED version in its `dataset_description.json`, a HED version is not necessary for validation. The `BidsDataset` only holds information about the relevant `.tsv` and `.json` files, not the imaging data. The constructor has a number of parameters that restrict which of these files are considered. The relevant JSON files are all read in, but the `.tsv` contents is only loaded when needed.
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Since a BIDS dataset includes the HED version in its `dataset_description.json`, a HED version is not necessary for validation. The `BidsDataset` only holds information about the relevant `.tsv` and `.json` files, not the imaging data. The constructor has a number of parameters that restrict which of these files are considered. The relevant JSON files are all read in, but the `.tsv` content is only loaded when needed.
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### Working with individual event files
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## Jupyter notebooks
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The [**examples**](https://github.com/hed-standard/hed-python/tree/main/examples) directory[**hed-python**](https://github.com/hed-standard/hed-python) GitHub repository contains Jupyter notebooks for BIDS annotation workflows. These notebooks are **not included in the PyPI package**.
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The [**examples**](https://github.com/hed-standard/hed-python/tree/main/examples) directory in the GitHub [**hed-python**](https://github.com/hed-standard/hed-python) repository contains Jupyter notebooks for BIDS annotation workflows. These notebooks are **not included in the PyPI package**.
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### Available notebooks
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| Notebook | Purpose |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------- |
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| [extract_json_template.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/extract_json_template.ipynb) | Create JSON sidecar template from all event files |
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| [find_event_combinations.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/find_event_combinations.ipynb) | Extract unique combinations of column values |
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| [merge_spreadsheet_into_sidecar.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/merge_spreadsheet_into_sidecar.ipynb) | Merge edited spreadsheet of HED annotations back into JSON sidecar |
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| [sidecar_to_spreadsheet.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/sidecar_to_spreadsheet.ipynb) | Convert JSON sidecar to spreadsheet for editing |
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| [summarize_events.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/summarize_events.ipynb) | Summarize event file contents and value distributions |
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| [validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_dataset.ipynb) | Validate HED annotations in a BIDS dataset |
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| [validate_bids_dataset_with_libraries.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_dataset_with_libraries.ipynb) | Validate with HED library schemas |
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| [validate_bids_datasets.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_datasets.ipynb) | Batch validate multiple BIDS datasets |
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| Notebook | Purpose |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------ |
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| [extract_json_template.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/extract_json_template.ipynb) | Create JSON sidecar template from all event files |
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| [find_event_combinations.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/find_event_combinations.ipynb) | Extract unique combinations of column values |
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| [merge_spreadsheet_into_sidecar.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/merge_spreadsheet_into_sidecar.ipynb) | Merge edited spreadsheet of HED annotations back into JSON sidecar |
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| [sidecar_to_spreadsheet.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/sidecar_to_spreadsheet.ipynb) | Convert JSON sidecar to spreadsheet for editing |
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| [summarize_events.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/summarize_events.ipynb) | Summarize event file contents and value distributions |
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| [validate_bids_dataset.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_dataset.ipynb) | Validate HED annotations in a BIDS dataset |
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| [validate_bids_dataset_with_libraries.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_dataset_with_libraries.ipynb) | Validate with HED library schemas |
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| [validate_bids_datasets.ipynb](https://github.com/hed-standard/hed-python/blob/main/examples/validate_bids_datasets.ipynb) | Batch validate multiple BIDS datasets |
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### Getting the notebooks
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| ------------------------------ | ----------------------------------------------------------- |
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| **Annotation management** | |
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| `hedpy validate-bids` | Validate HED annotations in BIDS datasets |
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| `hedpy extract-sidecar` | Extract JSON sidecar template from tabular (`.tsv`) files |
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| `hedpy extract-sidecar` | Extract JSON sidecar template from tabular (`.tsv`) files |
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| **Schema management** | |
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| `hedpy schema validate` | Validate HED schema files |
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| `hedpy schema convert` | Convert schemas between formats (XML, MEDIAWIKI, TSV, JSON) |
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hedpy --version
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```
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---
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______________________________________________________________________
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### BIDS validation
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```
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**Output format differences:**
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- `text`: Human-readable format with issue counts and descriptions (default)
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- `json`: Compact JSON array of issues only, suitable for piping or programmatic processing
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- `json_pp`: Pretty-printed JSON object with `issues` array and `hedtools_version` metadata, with proper indentation for readability
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-lf validation.log
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```
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______________________________________________________________________
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### Sidecar template extraction
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-v
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______________________________________________________________________
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### Schema development
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- `.tsv` - TSV (tab-separated value) format
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- `.json` - JSON format
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______________________________________________________________________
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### Schema release
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5. Verify that the created ontology is valid using [**Protégé**](https://protege.stanford.edu/)
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6. Commit changes to version control before moving to stable release
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______________________________________________________________________
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### Legacy script access
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**However, the `hedpy` CLI is the recommended interface** as it provides a more consistent and discoverable command structure.
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______________________________________________________________________
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### Common workflows
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```
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______________________________________________________________________
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### Debugging tips
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1. **Don't modify released schemas** - they're immutable and shared
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2. **Check and recheck schema validity** - once released its permanent
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3. **Compare with schema with previous version** - make sure not its not a breaking change (major semantic version change)
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2. **Check and recheck prerelease schema validity** - once released it's permanent
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3. **Compare the schema with previous version** - make sure that changes are not breaking (major semantic version change)
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### Validation workflow
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2. **Use `#` placeholders** for value columns with continuous data
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4. **Use the latest versions of the schemas** later versions have improved linkage
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4. **Document your annotations** using descriptions in the sidecar
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5. **Document your annotations** using descriptions in the sidecar
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If you are annotated an NWB dataset, the instructions are somewhat similar but haven't been finalized.
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‎examples/README.md‎

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- **BIDS structure required**: These notebooks expect standard BIDS directory structure
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- **Inheritance handling**: Automatically processes BIDS sidecar inheritance
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- **Exclude directories**: Always exclude `derivatives`, `code`, `stimuli`, `sourcedata`
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- **Skip solumns**: Typically skip `onset`, `duration`, `sample` (BIDS-predefined)
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- **Skip columns**: Typically skip `onset`, `duration`, `sample` (BIDS-predefined)
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- **Value columns**: Columns with continuous data (annotated with `#` placeholder)

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