Cleaned up the documentation for the hedpy

.github/workflows/mdformat.yaml

@@ -27,7 +27,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install mdformat>=0.7.0 mdformat-myst>=0.1.5 mdformat-tables>=0.4.0
+          pip install mdformat>=0.7.0 mdformat-myst>=0.1.5
 
       - name: Run mdformat (check only)
         run: |

README.md

@@ -1,4 +1,4 @@
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8056010.svg)](https://doi.org/10.5281/zenodo.8056010) [![Maintainability](https://qlty.sh/gh/hed-standard/projects/hed-python/maintainability.svg)](https://qlty.sh/gh/hed-standard/projects/hed-python) [![Code Coverage](https://qlty.sh/gh/hed-standard/projects/hed-python/coverage.svg)](https://qlty.sh/gh/hed-standard/projects/hed-python) ![Python3](https://img.shields.io/badge/python-%3E=3.10-yellow.svg) ![PyPI - Status](https://img.shields.io/pypi/v/hedtools) [![Documentation](https://img.shields.io/badge/docs-hed--python-blue.svg)](https://www.hedtags.org/hed-python)
+![PyPI - Status](https://img.shields.io/pypi/v/hedtools) ![Python3](https://img.shields.io/badge/python-%3E=3.10-yellow.svg) [![Maintainability](https://qlty.sh/gh/hed-standard/projects/hed-python/maintainability.svg)](https://qlty.sh/gh/hed-standard/projects/hed-python) [![Code Coverage](https://qlty.sh/gh/hed-standard/projects/hed-python/coverage.svg)](https://qlty.sh/gh/hed-standard/projects/hed-python) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8056010.svg)](https://doi.org/10.5281/zenodo.8056010) [![Docs](https://img.shields.io/badge/docs-hed--python-blue.svg)](https://www.hedtags.org/hed-python)
 
 # HEDTools - Python
 

docs/user_guide.md

@@ -279,16 +279,15 @@ HEDTools provides a unified command-line interface (CLI) using a **git-style com
 
 ### Available commands
 
-| Command                        | Description                                                 |
-| ------------------------------ | ----------------------------------------------------------- |
-| **Annotation management**      |                                                             |
-| `hedpy validate-bids`          | Validate HED annotations in BIDS datasets                   |
-| `hedpy extract-sidecar`        | Extract JSON sidecar template from tabular (`.tsv`) files   |
-| **Schema management**          |                                                             |
-| `hedpy schema validate`        | Validate HED schema files                                   |
-| `hedpy schema convert`         | Convert schemas between formats (XML, MEDIAWIKI, TSV, JSON) |
-| `hedpy schema add-ids`         | Add unique HED IDs to schema terms                          |
-| `hedpy schema create-ontology` | Generate OWL ontology files from HED schemas                |
+| Command                       | Description                                                 |
+| ----------------------------- | ----------------------------------------------------------- |
+| **Annotation management**     |                                                             |
+| `hedpy validate bids-dataset` | Validate HED annotations in BIDS datasets                   |
+| `hedpy extract bids-sidecar`  | Extract JSON sidecar template from tabular (`.tsv`) files   |
+| **Schema management**         |                                                             |
+| `hedpy schema validate`       | Validate HED schema files                                   |
+| `hedpy schema convert`        | Convert schemas between formats (XML, MEDIAWIKI, TSV, JSON) |
+| `hedpy schema add-ids`        | Add unique HED IDs to schema terms                          |
 
 ### Installation and basic usage
 
@@ -305,7 +304,7 @@ Get help on available commands:
 hedpy --help
 
 # Help for a specific command
-hedpy validate-bids --help
+hedpy validate bids-dataset --help
 
 # Help for command groups
 hedpy schema --help
@@ -321,35 +320,35 @@ ______________________________________________________________________
 
 ### BIDS validation
 
-Validate HED annotations in BIDS datasets using `hedpy validate-bids`.
+Validate HED annotations in BIDS datasets using `hedpy validate bids-dataset`.
 
 #### Basic validation
 
 ```bash
 # Validate a BIDS dataset
-hedpy validate-bids /path/to/bids/dataset
+hedpy validate bids-dataset /path/to/bids/dataset
 
 # Include warnings in addition to errors
-hedpy validate-bids /path/to/bids/dataset -w
+hedpy validate bids-dataset /path/to/bids/dataset -w
 
 # Enable verbose output
-hedpy validate-bids /path/to/bids/dataset -v
+hedpy validate bids-dataset /path/to/bids/dataset -v
 ```
 
 #### Output options
 
 ```bash
 # Save results to a file
-hedpy validate-bids /path/to/bids/dataset -o validation_results.txt
+hedpy validate bids-dataset /path/to/bids/dataset -o validation_results.txt
 
 # Output in compact JSON format (array of issues only)
-hedpy validate-bids /path/to/bids/dataset -f json -o results.json
+hedpy validate bids-dataset /path/to/bids/dataset -f json -o results.json
 
 # Pretty-printed JSON with version metadata (recommended for saving)
-hedpy validate-bids /path/to/bids/dataset -f json_pp -o results.json
+hedpy validate bids-dataset /path/to/bids/dataset -f json_pp -o results.json
 
 # Print to stdout AND save to file
-hedpy validate-bids /path/to/bids/dataset -o results.txt -p
+hedpy validate bids-dataset /path/to/bids/dataset -o results.txt -p
 ```
 
 **Output format differences:**
@@ -362,83 +361,83 @@ hedpy validate-bids /path/to/bids/dataset -o results.txt -p
 
 ```bash
 # Validate specific file types (default: events, participants)
-hedpy validate-bids /path/to/bids/dataset -s events -s participants -s sessions
+hedpy validate bids-dataset /path/to/bids/dataset -s events -s participants -s sessions
 
 # Exclude certain directories (default: sourcedata, derivatives, code, stimuli)
-hedpy validate-bids /path/to/bids/dataset -x derivatives -x sourcedata -x mydata
+hedpy validate bids-dataset /path/to/bids/dataset -x derivatives -x sourcedata -x mydata
 
 # Limit number of errors reported per error type
-hedpy validate-bids /path/to/bids/dataset -ec 5
+hedpy validate bids-dataset /path/to/bids/dataset -el 5
 
 # Apply error limit per file instead of overall
-hedpy validate-bids /path/to/bids/dataset -ec 5 -ef
+hedpy validate bids-dataset /path/to/bids/dataset -el 5 -ef
 ```
 
 #### Logging options
 
 ```bash
 # Set log level
-hedpy validate-bids /path/to/bids/dataset -l DEBUG
+hedpy validate bids-dataset /path/to/bids/dataset -l DEBUG
 
 # Save logs to file
-hedpy validate-bids /path/to/bids/dataset -lf validation.log
+hedpy validate bids-dataset /path/to/bids/dataset -lf validation.log
 
 # Save logs to file without stderr output
-hedpy validate-bids /path/to/bids/dataset -lf validation.log -lq
+hedpy validate bids-dataset /path/to/bids/dataset -lf validation.log -lq
 ```
 
 #### Complete example
 
 ```bash
 # Comprehensive validation with all options
-hedpy validate-bids /path/to/bids/dataset \
+hedpy validate bids-dataset /path/to/bids/dataset \
   -w \
   -v \
   -f json_pp \
   -o validation_results.json \
   -s events \
   -x derivatives \
-  -ec 10 \
+  -el 10 \
   -lf validation.log
 ```
 
 ______________________________________________________________________
 
 ### Sidecar template extraction
 
-Extract a JSON sidecar template from BIDS event files using `hedpy extract-sidecar`.
+Extract a JSON sidecar template from BIDS event files using `hedpy extract bids-sidecar`.
 
 #### Basic extraction
 
 ```bash
 # Extract template for events files
-hedpy extract-sidecar /path/to/bids/dataset -s events
+hedpy extract bids-sidecar /path/to/bids/dataset -s events
 
 # Save to specific file
-hedpy extract-sidecar /path/to/bids/dataset -s events -o task_events.json
+hedpy extract bids-sidecar /path/to/bids/dataset -s events -o task_events.json
 ```
 
 #### Column handling
 
 ```bash
 # Specify value columns (use single annotation for column with # placeholder)
-hedpy extract-sidecar /path/to/bids/dataset -s events \
+hedpy extract bids-sidecar /path/to/bids/dataset -s events \
   -vc response_time -vc accuracy -vc subject_id
 
 # Skip specific columns (default: onset, duration, sample)
-hedpy extract-sidecar /path/to/bids/dataset -s events \
+hedpy extract bids-sidecar /path/to/bids/dataset -s events \
   -sc onset -sc duration -sc trial_type
 
 # Exclude certain directories
-hedpy extract-sidecar /path/to/bids/dataset -s events \
+hedpy extract bids-sidecar /path/to/bids/dataset -s events \
   -x derivatives -x pilot_data
 ```
 
 #### Complete example
 
 ```bash
 # Extract events template with custom column handling
-hedpy extract-sidecar /path/to/bids/dataset \
+hedpy extract bids-sidecar /path/to/bids/dataset \
   -s events \
   -vc response_time \
   -vc reaction_time \
@@ -517,23 +516,6 @@ hedpy schema add-ids /path/to/hed-schemas score 2.2.0
 - Modifies all schema formats (XML, MEDIAWIKI, TSV, JSON) in-place
 - Should be run after all schema content changes are finalized
 
-#### Create ontology
-
-Generate OWL (Web Ontology Language) ontology files from HED schemas for semantic web applications and ontology-based tools.
-
-```bash
-# Create ontology for a standard schema
-hedpy schema create-ontology /path/to/hed-schemas standard 8.4.0
-
-# Create ontology for a library schema with custom output location
-hedpy schema create-ontology /path/to/hed-schemas score 2.1.0 \
-  --dest /path/to/output
-
-# Create ontology with all outputs in specific directory
-hedpy schema create-ontology /path/to/hed-schemas lang 1.1.0 \
-  --dest ./ontologies
-```
-
 **Best practices:**
 
 1. Validate schema thoroughly before adding IDs
@@ -575,7 +557,7 @@ Each command provides help at several levels
 hedpy --help
 
 # Command-specific help
-hedpy validate-bids --help
+hedpy validate bids-dataset --help
 hedpy schema validate --help
 
 # Command group help
@@ -586,16 +568,16 @@ hedpy schema --help
 
 ```bash
 # Step 1: Extract sidecar template
-hedpy extract-sidecar /path/to/dataset -s events -o events.json
+hedpy extract bids-sidecar /path/to/dataset -s events -o events.json
 
 # Step 2: Edit events.json to add HED tags
 # (manual editing step)
 
 # Step 3: Validate with warnings
-hedpy validate-bids /path/to/dataset -w -v -o validation.txt
+hedpy validate bids-dataset /path/to/dataset -w -v -o validation.txt
 
 # Step 4: Fix issues and re-validate
-hedpy validate-bids /path/to/dataset -w
+hedpy validate bids-dataset /path/to/dataset -w
 ```
 
 #### Workflow 3: Schema development and testing
@@ -614,11 +596,8 @@ hedpy schema validate my_schema.xml --add-all-extensions
 #### Workflow 4: Preparing for schema release
 
 ```bash
-# Step 1: Add HED IDs
+# Add HED IDs
 hedpy schema add-ids /path/to/hed-schemas my_library 1.0.0
-
-# Step 2: Generate ontology
-hedpy schema create-ontology /path/to/hed-schemas my_library 1.0.0
 ```
 
 ______________________________________________________________________