Removed the remodeling tools (issue hed-standard#1180)

Author: VisLab

README.md

@@ -18,12 +18,13 @@ HED (Hierarchical Event Descriptors) is a framework for systematically describin
 
 - Validate HED annotations against schema specifications
 - Analyze and summarize HED-tagged datasets
-- Transform and remodel event data
 - Full HED support in BIDS (Brain Imaging Data Structure)
 - HED support in NWB (Neurodata Without Borders) when used the [ndx-hed](https://github.com/hed-standard/ndx-hed) extension.
 - Platform-independent and data-neutral
 - Command-line tools and Python API
 
+**Note:** Table remodeling tools have been moved to a separate package. See [table-remodeler](https://pypi.org/project/table-remodeler/) on PyPI or visit [https://www.hedtags.org/table-remodeler](https://www.hedtags.org/table-remodeler) for more information.
+
 ## Quick start
 
 ```{index} quick start, getting started, installation
@@ -59,6 +60,38 @@ Or install from GitHub (latest):
 pip install git+https://github.com/hed-standard/hed-python/@main
 ```
 
+### Development installation
+
+```{index} development installation, editable install, optional dependencies
+```
+
+For development work or to access optional features, install from the cloned repository:
+
+```bash
+# Clone the repository
+git clone https://github.com/hed-standard/hed-python.git
+cd hed-python
+
+# Install in editable mode with base dependencies
+pip install -e .
+
+# Install with optional dependency groups
+pip install -e ".[dev]"       # Development tools (ruff, black, codespell)
+pip install -e ".[docs]"      # Documentation tools (sphinx, furo)
+pip install -e ".[test]"      # Testing tools (coverage)
+pip install -e ".[examples]"  # Jupyter notebook support
+
+# Install all optional dependencies
+pip install -e ".[dev,docs,test,examples]"
+```
+
+**Optional dependency groups:**
+
+- `dev` - Code quality tools: ruff (linter), black (formatter), codespell, mdformat
+- `docs` - Documentation generation: sphinx, furo theme, myst-parser
+- `test` - Code coverage reporting: coverage
+- `examples` - Jupyter notebook support: jupyter, notebook, ipykernel
+
 ### Basic usage
 
 ```{index} usage examples, HedString, load_schema_version, validation example
@@ -111,9 +144,10 @@ hedpy schema convert /path/to/schema.xml
 ```bash
 validate_bids /path/to/dataset
 hed_validate_schemas /path/to/schema.xml
-run_remodel /path/to/data /path/to/config.json
 ```
 
+**Note:** The `run_remodel` command has been removed. Table remodeling functionality is now available in the separate [table-remodeler](https://pypi.org/project/table-remodeler/) package.
+
 For more examples, see the [user guide](https://www.hedtags.org/hed-python/user_guide.html).
 
 ### Jupyter notebook examples
@@ -172,14 +206,10 @@ pip install -e .[docs]
 # Build the documentation
 cd docs
 sphinx-build -b html . _build/html
-
-# Or use the make command (if available)
-make html
-
-# View the built documentation
-# Open docs/_build/html/index.html in your browser
 ```
 
+To iew the built documentation open `docs/_build/html/index.html` in your browser
+
 ### Formatting with Black
 
 ```{index} Black, code formatting, style guide
@@ -229,6 +259,7 @@ The HED ecosystem consists of several interconnected repositories:
 | [hed-resources](https://github.com/hed-standard/hed-resources)         | Tutorials and other HED resources                |
 | [hed-specification](https://github.com/hed-standard/hed-specification) | Official HED specification documents             |
 | [hed-schemas](https://github.com/hed-standard/hed-schemas)             | Official HED schema repository                   |
+| [table-remodeler](https://github.com/hed-standard/table-remodeler)     | Table transformation and remodeling tools        |
 | [ndx-hed](https://github.com/hed-standard/ndx-hed)                     | HED support for NWB                              |
 | [hed-javascript](https://github.com/hed-standard/hed-javascript)       | JavaScript HED validation tools                  |
 

docs/index.rst

@@ -1,3 +1,7 @@
+.. meta::
+   :description: Python tools for HED (Hierarchical Event Descriptors) validation, analysis, and BIDS integration in neuroscience
+   :keywords: HED, hierarchical event descriptors, Python, validation, BIDS, neuroscience, event annotation, metadata, analysis tools
+
 Python HEDTools
 ===============
 

docs/overview.md

@@ -1,3 +1,12 @@
+```{meta}
+---
+description: Overview of Python HEDTools - validation, analysis, and processing 
+  tools for Hierarchical Event Descriptors (HED) in neuroscience
+keywords: HED overview, Python tools, event descriptors, BIDS, NWB, 
+  neuroscience, validation, schema
+---
+```
+
 # Python HEDTools overview
 
 ```{index} single: HED; overview

docs/user_guide.md

@@ -1,3 +1,12 @@
+```{meta}
+---
+description: Complete user guide for Python HEDTools - validation, BIDS 
+  integration, analysis, and command-line tools for HED annotations
+keywords: HED tutorial, Python guide, validation examples, BIDS datasets, 
+  sidecar files, command-line interface, Jupyter notebooks
+---
+```
+
 # Python HEDTools guide
 
 ```{index} user guide, tutorial, getting started

hed/tools/__init__.py

@@ -1,4 +1,4 @@
-"""HED remodeling, analysis and summarization tools."""
+"""HED analysis and summarization tools."""
 
 from .analysis.event_manager import EventManager
 from .analysis.file_dictionary import FileDictionary
@@ -19,27 +19,6 @@
 from .bids.bids_tabular_file import BidsTabularFile
 from .bids.bids_util import parse_bids_filename
 
-from .remodeling.dispatcher import Dispatcher
-from .remodeling.backup_manager import BackupManager
-from .remodeling.operations.base_summary import BaseSummary
-from .remodeling.operations.base_op import BaseOp
-from .remodeling.operations.factor_column_op import FactorColumnOp
-from .remodeling.operations.factor_hed_tags_op import FactorHedTagsOp
-from .remodeling.operations.factor_hed_type_op import FactorHedTypeOp
-from .remodeling.operations.merge_consecutive_op import MergeConsecutiveOp
-from .remodeling.operations.number_groups_op import NumberGroupsOp
-from .remodeling.operations.number_rows_op import NumberRowsOp
-from .remodeling.operations import valid_operations
-from .remodeling.operations.remap_columns_op import RemapColumnsOp
-from .remodeling.operations.remove_columns_op import RemoveColumnsOp
-from .remodeling.operations.remove_rows_op import RemoveRowsOp
-from .remodeling.operations.rename_columns_op import RenameColumnsOp
-from .remodeling.operations.reorder_columns_op import ReorderColumnsOp
-from .remodeling.operations.split_rows_op import SplitRowsOp
-from .remodeling.operations.summarize_column_names_op import SummarizeColumnNamesOp
-from .remodeling.operations.summarize_column_values_op import SummarizeColumnValuesOp
-from .remodeling.operations.summarize_hed_type_op import SummarizeHedTypeOp
-
 from .util.data_util import get_new_dataframe, get_value_dict, replace_values, reorder_columns
 from .util.io_util import check_filename, clean_filename, extract_suffix_path, get_file_list, make_path
 from .util.io_util import get_path_components
@@ -55,7 +34,3 @@
     strs_to_sidecar,
     to_strlist,
 )
-
-from .remodeling.cli import run_remodel
-from .remodeling.cli import run_remodel_backup
-from .remodeling.cli import run_remodel_restore