# Project Management

Labrat can create projects from Cookiecutter templates and record their paths in a local registry. This is useful when several analyses need the same initial directory structure and metadata.


# Create a project

Choose a template, a display name, a parent directory, and a description:

``` bash
labrat project new \
  --type computational-biology \
  --name "BMPR2 Variant Analysis" \
  --path ./projects \
  --description "Analyze BMPR2 variants in pulmonary hypertension"
```

The default template names are `computational-biology`, `data-science`, and `andymcdgeo-streamlit`. Templates are remote repositories, so first-time project creation requires network access.

`--path` identifies the parent directory. Cookiecutter creates the project inside that directory. Labrat replaces spaces in the submitted project name with underscores before passing it to the template. The template can still control the final directory name.


# Inspect your projects

``` bash
labrat project list
```

Labrat stores the absolute project path, description, project type, creation time, and last-modified time in `~/.labrat/config.json`. The project list records pointers to the original project directories.

Keep project files, version-control history, and separate backups as the authoritative records of an analysis.


# Use the Python API

``` python
from pathlib import Path

from labrat.project import ProjectManager

manager = ProjectManager(username="Dr. Jane Doe")
projects = manager.list_projects()

for project in projects:
    print(project["name"], Path(project["path"]))
```

The Python API also exposes methods to update timestamps, recursively list project files, add templates, and archive projects. See the generated [ProjectManager](../reference/project.ProjectManager.md#labrat.project.ProjectManager) API reference for their full signatures.


# Delete with an archive

``` bash
labrat project delete \
  --path ./projects/BMPR2_Analysis \
  --archive-dir ./project-archives
```

This command asks for confirmation. It copies and zips the project before recursively deleting the original directory and removing its registry entry. The archive parent directory must already exist.

> **Warning: Warning**
>
> Confirm that the archive was written to the intended filesystem before relying on it for recovery. Deleting a project removes the original directory tree.

To preserve the source directory while creating a backup, use `labrat archive`.