Project Title

Short description of the research code, analysis workflow, or computational tool.

Replace this title and description before public release, manuscript submission, or DOI archiving.

Purpose

This repository contains reproducible research code and documentation for lab research projects, including:

• data processing
• analysis workflows
• figure and table generation
• notebook-based methods
• reusable scripts or Python modules
• validation or quality-control checks

Replace this section with a project-specific description before public release or manuscript submission.

Repository structure

.
├── .github/
│   ├── CODEOWNERS
│   ├── dependabot.yml
│   ├── pull_request_template.md
│   ├── ISSUE_TEMPLATE/
│   │   ├── bug_report.yml
│   │   ├── config.yml
│   │   └── documentation_update.yml
│   └── workflows/
│       └── README.md
├── data/
│   └── README.md
├── docs/
│   ├── README.md
│   ├── user_guide.md
│   └── output_dictionary.md
├── examples/
│   └── README.md
├── notebooks/
│   └── README.md
├── results/
│   └── README.md
├── scripts/
│   └── README.md
├── src/
│   └── README.md
├── tests/
│   └── README.md
├── README.md
├── CHANGELOG.md
├── CONTRIBUTING.md
├── CITATION.cff
├── CODE_OF_CONDUCT.md
├── DATA_AVAILABILITY_TEMPLATE.md
├── GOVERNANCE.md
├── LICENSE_NOTICE.md
├── MAINTAINERS.md
├── NEW_REPOSITORY_SETUP_CHECKLIST.md
├── RELEASE_CHECKLIST.md
├── ROADMAP.md
├── SECURITY.md
├── environment.yml
├── pyproject.toml
└── requirements.txt

Getting started

Clone the repository:

git clone https://github.com/VCU-Soft-Functional-Materials-Lab/REPOSITORY-NAME.git
cd REPOSITORY-NAME

Create the environment using Conda:

conda env create -f environment.yml
conda activate PROJECT_ENV_NAME

Or install dependencies using pip:

pip install -r requirements.txt

For notebook-based projects, place notebooks in notebooks/.

For reusable scripts, place command-line or helper scripts in scripts/.

For reusable Python modules, place package code in src/.

For tests or validation checks, use tests/.

Reproducibility

Before using this repository for a manuscript, poster, thesis, report, public release, or DOI archive, document:

• input data sources
• software version
• package dependencies
• analysis settings
• expected outputs
• release tag
• DOI/archive link, if applicable

Use RELEASE_CHECKLIST.md before creating a public release or archive.

Use NEW_REPOSITORY_SETUP_CHECKLIST.md when creating a new project repository from this template.

Data availability

Large raw data files should generally not be stored directly in this repository.

Use an approved archive such as Zenodo, OSF, institutional storage, or another PI-approved repository.

Add project-specific data availability information here before public release or manuscript submission.

Citation

If this repository supports a publication, cite the associated paper and archived software release.

Update CITATION.cff before public release or DOI archiving.

License

Add a formal license only after confirming the lab/project policy with the PI or project lead.

Until a formal license is selected, see LICENSE_NOTICE.md.

Governance and contribution

Project governance expectations are described in GOVERNANCE.md.

Maintainer information should be updated in MAINTAINERS.md.

Contribution expectations are described in CONTRIBUTING.md.

Security reporting expectations are described in SECURITY.md.

Contact

Maintained by the VCU Soft Functional Materials Lab.

Update this section with project-specific contact information before public release.