chore/issue1/update-metadata

.gitignore

@@ -1,3 +1,9 @@
+# data
+data/
+
+# scripts
+scripts/
+
 # experiments
 experiments/
 

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-mobi@childmind.org.
+<mobi@childmind.org>.
 
 All complaints will be reviewed and investigated promptly and fairly.
 
@@ -117,13 +117,13 @@ the community.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
-https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+<https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
 
 Community Impact Guidelines were inspired by [Mozilla's code of conduct
 enforcement ladder](https://github.com/mozilla/diversity).
 
 [homepage]: https://www.contributor-covenant.org
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

CONTRIBUTING.md

@@ -5,7 +5,9 @@ Pull requests are always welcome, and we appreciate any help you give. Note that
 When submitting a pull request, we ask you to check the following:
 
 1. **Unit tests**, **documentation**, and **code style** are in order.
-   See the Continuous Integration for up to date information on the current code style, tests, and any other requirements.
+   See the Continuous Integration for up-to-date information on the current code style, tests, and any other requirements.
+
+   See the following [Google Python style guide](https://google.github.io/styleguide/pyguide.html#3164-guidelines-derived-from-guidos-recommendations) for coding style guidelines.
 
    It is also OK to submit work in progress if you're unsure of what this exactly means, in which case you'll likely be asked to make some further changes.
 

README.md

@@ -1,32 +1,88 @@
 # Graphomotor Study Toolkit
 
+A Python toolkit for analysis of graphomotor data collected via Curious.
+
 [![Build](https://github.com/childmindresearch/graphomotor/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/graphomotor/actions/workflows/test.yaml?query=branch%3Amain)
 [![codecov](https://codecov.io/gh/childmindresearch/graphomotor/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/graphomotor)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![stability-experimental](https://img.shields.io/badge/stability-experimental-orange.svg)
 [![LGPL--2.1 License](https://img.shields.io/badge/license-LGPL--2.1-blue.svg)](https://github.com/childmindresearch/graphomotor/blob/main/LICENSE)
-[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/graphomotor)
+[![Documentation](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/graphomotor)
+
+Welcome to `graphomotor`, a specialized Python library for analyzing graphomotor data collected via [Curious](https://www.gettingcurious.com/). This toolkit provides comprehensive tools for processing, analyzing, and visualizing data from various graphomotor assessment tasks including spiral drawing, trails making, alphabetic writing, digit symbol substitution, and the Rey-Osterrieth Complex Figure Test.
+
+## Feature Extraction Capabilities
 
-A Python toolkit for the analysis of Graphomotor study.
+The toolkit extracts clinically relevant metrics from digitized drawing data. Currently implemented features include:
 
-## Progress
+- **Temporal Features**: Task completion duration
+- **Velocity Features**: Velocity analysis including linear, radial, and angular velocity components with statistical measures (sum, median, variation, skewness, kurtosis)
+- **Distance Features**: Spatial accuracy measurements using Hausdorff distance metrics with temporal normalizations and segment-specific analysis
+- **Drawing Error Features**: Area under the curve (AUC) calculations between drawn paths and ideal reference trajectories to quantify spatial accuracy
 
-| Task name | Preprocessing | Feature extraction | Visualization |
+> **Note:** This toolkit is under active development, with a primary focus on the spiral drawing task and planned expansion to additional graphomotor assessments in subsequent releases.
+
+## Development Progress
+
+| Task | Preprocessing | Feature Extraction | Visualization |
 | :--- | :---: | :---: | :---: |
-| Spiral | ![data_cleaning](https://img.shields.io/badge/pending-red) | ![feature_extraction](https://img.shields.io/badge/in_progress-yellow) | ![visualization](https://img.shields.io/badge/pending-red) |
-| Rey-Osterrieth Complex Figure | ![data_cleaning](https://img.shields.io/badge/pending-red) | ![feature_extraction](https://img.shields.io/badge/pending-red) | ![visualization](https://img.shields.io/badge/pending-red) |
-| Alphabetic Writing | ![data_cleaning](https://img.shields.io/badge/pending-red)|  ![feature_extraction](https://img.shields.io/badge/pending-red) | ![visualization](https://img.shields.io/badge/pending-red) |
-| Digit Symbol Substitute | ![data_cleaning](https://img.shields.io/badge/pending-red)|  ![feature_extraction](https://img.shields.io/badge/pending-red) | ![visualization](https://img.shields.io/badge/pending-red) |
-| Trails Making |  ![data_cleaning](https://img.shields.io/badge/pending-red) | ![feature_extraction](https://img.shields.io/badge/pending-red) | ![visualization](https://img.shields.io/badge/pending-red) |
+| Spiral | ![Spiral: Preprocessing Pending](https://img.shields.io/badge/pending-red) | ![Spiral: Feature Extraction In Progress](https://img.shields.io/badge/in_progress-yellow) | ![Spiral: Visualization Pending](https://img.shields.io/badge/pending-red) |
+| Rey-Osterrieth Complex Figure | ![Rey-Osterrieth: Preprocessing Pending](https://img.shields.io/badge/pending-red) | ![Rey-Osterrieth: Feature Extraction Pending](https://img.shields.io/badge/pending-red) | ![Rey-Osterrieth: Visualization Pending](https://img.shields.io/badge/pending-red) |
+| Alphabetic Writing | ![Alphabetic Writing: Preprocessing Pending](https://img.shields.io/badge/pending-red) | ![Alphabetic Writing: Feature Extraction Pending](https://img.shields.io/badge/pending-red) | ![Alphabetic Writing: Visualization Pending](https://img.shields.io/badge/pending-red) |
+| Digit Symbol Substitution | ![Digit Symbol Substitution: Preprocessing Pending](https://img.shields.io/badge/pending-red) | ![Digit Symbol Substitution: Feature Extraction Pending](https://img.shields.io/badge/pending-red) | ![Digit Symbol Substitution: Visualization Pending](https://img.shields.io/badge/pending-red) |
+| Trails Making | ![Trails Making: Preprocessing Pending](https://img.shields.io/badge/pending-red) | ![Trails Making: Feature Extraction Pending](https://img.shields.io/badge/pending-red) | ![Trails Making: Visualization Pending](https://img.shields.io/badge/pending-red) |
 
 ## Installation
 
-Install the newest development version via :
+Install the graphomotor package from PyPI:
+
+```sh
+pip install graphomotor
+```
+
+Or install the latest development version directly from GitHub:
 
 ```sh
 pip install git+https://github.com/childmindresearch/graphomotor
 ```
 
-## Links or References
+## Quick Start
+
+Currently, `graphomotor` is available as an importable Python library. CLI functionality is planned for future releases.
+
+### Extracting Features from Spiral Drawing Data
+
+```python
+from graphomotor.core import orchestrator
+
+# Path to your spiral drawing data file
+input_file = "path/to/your/spiral_data.csv"
+
+# Directory where extracted features will be saved
+output_dir = "path/to/output/directory"
+
+# Run the analysis pipeline
+features = orchestrator.run_pipeline(
+    input_path=input_file,
+    output_path=output_dir
+)
+
+# Features are returned as a dictionary and saved as CSV
+print(f"Successfully extracted {len(features)} feature categories")
+```
+
+For detailed configuration options and additional parameters, refer to the [`run_pipeline` documentation](https://childmindresearch.github.io/graphomotor/graphomotor/core/orchestrator.html#run_pipeline).
+
+> **Note:** Currently, only single file processing is supported, with batch processing planned for future releases.
+
+## Future Directions
+
+The Graphomotor Study Toolkit is under active development. For more detailed information about upcoming features and development plans, please refer to the [GitHub Issues](https://github.com/childmindresearch/graphomotor/issues) page.
+
+## Contributing
+
+We welcome contributions from the community! If you're interested in contributing, please review our [Contributing Guidelines](CONTRIBUTING.md) for information on how to get started, coding standards, and the pull request process.
+
+## References
 
-- [A very important resource](https://www.youtube.com/watch?v=dQw4w9WgXcQ)
+1. Messan, K. S., Kia, S. M., Narayan, V. A., Redmond, S. J., Kogan, A., Hussain, M. A., McKhann, G. M. II, & Vahdat, S. (2022). Assessment of Smartphone-Based Spiral Tracing in Multiple Sclerosis Reveals Intra-Individual Reproducibility as a Major Determinant of the Clinical Utility of the Digital Test. Frontiers in Medical Technology, 3, 714682. [https://doi.org/10.3389/fmedt.2021.714682](https://doi.org/10.3389/fmedt.2021.714682)

SECURITY.md

@@ -1,22 +1,13 @@
-# This file is a placeholder, will be updated later.
-
 # Security
 
 Child Mind Institute values the security of our users, data, and servers. We take the security of our systems seriously and encourage users to report any suspected security vulnerabilities promptly.
 
 ## Supported Versions
 
-MODIFY:
-
-Note which version(s) will receive security updates. For example:
-
-| Version | Supported          |
-| ------- | ------------------ |
-| 1.0.x   | :white_check_mark: |
-| 0.9.x   | :x:                |
+Only the latest minor version will receive security updates. All older minor versions should be considered unmaintained.
 
 ## Reporting Vulnerabilities
 
-To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at mobi@childmind.org. Please refrain from using other communication channels.
+To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at <mobi@childmind.org>. Please refrain from using other communication channels.
 
 For non-security-related issues, we welcome your input and feedback on our issues page. Feel free to share your ideas and suggestions to help us improve our services.

pyproject.toml

@@ -1,9 +1,10 @@
 [project]
 name = "graphomotor"
 version = "0.1.0"
-description = "Toolkit for analysis of Graphomotor study tasks"
+description = "A Python toolkit for analysis of graphomotor data collected via Curious"
 authors = [
-  {name = "Alp Erkent", email = "alp.erkent@childmind.org"}
+  {name = "Alp Erkent", email = "alp.erkent@childmind.org"},
+  {name = "Adam Santorelli", email = "adam.santorelli@childmind.org"}
 ]
 license = "LGPL-2.1"
 readme = "README.md"
@@ -39,7 +40,7 @@ src = ["src"]
 target-version = "py312"
 
 [tool.ruff.lint]
-select = ["ANN", "D", "E", "F", "I"]
+select = ["ANN", "D", "E", "F", "I", "INP"]
 ignore = []
 fixable = ["ALL"]
 unfixable = []