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Merged
VisLab merged 1 commit into from
Jan 27, 2026
Merged

Removed the remodeling tools (issue #1180) #1196

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47 changes: 39 additions & 8 deletions README.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 |

Expand Down
4 changes: 4 additions & 0 deletions docs/index.rst
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@@ -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
===============

Expand Down
9 changes: 9 additions & 0 deletions docs/overview.md
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@@ -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
Expand Down
9 changes: 9 additions & 0 deletions docs/user_guide.md
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@@ -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
Expand Down
27 changes: 1 addition & 26 deletions hed/tools/__init__.py
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@@ -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
Expand All @@ -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
Expand All @@ -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
5 changes: 0 additions & 5 deletions hed/tools/remodeling/__init__.py
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