Metadata-Version: 2.4
Name: aind-data-transfer-lite
Version: 0.4.0
Summary: Generated from aind-library-template
Author: Allen Institute for Neural Dynamics
License: MIT
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: aind-data-access-api
Requires-Dist: aind-data-schema-models<5.0
Requires-Dist: awscli
Requires-Dist: boto3
Requires-Dist: magic-class>=0.7.0
Requires-Dist: magicgui==0.10.1
Requires-Dist: pydantic<2.12,>=2.0
Requires-Dist: pydantic-settings<3.0,>=2.8.0
Requires-Dist: PyQt5>=5.15.11
Provides-Extra: dev
Requires-Dist: black; extra == "dev"
Requires-Dist: coverage; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Requires-Dist: interrogate; extra == "dev"
Requires-Dist: isort; extra == "dev"
Requires-Dist: Sphinx; extra == "dev"
Requires-Dist: furo; extra == "dev"
Dynamic: license-file

# aind-data-transfer-lite

[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
![Code Style](https://img.shields.io/badge/code%20style-black-black)
[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)

## Getting Started

### Who is this for?

You want to upload data to AIND's Cloud Storage platform on AWS.

### Prerequisites
Authentication for write permissions to aind-open-data bucket. Please reach out to AIND Scientific Computing for access.

## Installation
Install directly from PyPI. We recommend installing into a virtual environment or conda environment.
```bash
pip install aind-data-transfer-lite
```

## Usage

You can interact with AIND Data Transfer Lite in two ways:

1. Launch the GUI window for visual interaction.
2. Run Python scripts or the command-line interface to perform data uploads programmatically.

### Launching the UI

- Ensure dependencies are installed.

- Either:
  - Open the file `src/aind_data_transfer_lite/ui.py` in VS Code and click "Run" in the upper right-hand corner.

  - Or run the following in the terminal:
    ```bash
    python -m aind_data_transfer_lite.ui
    ```

- You should see a window titled "AIND Data Transfer Lite" appear.

<p align="center">
  <img src="docs/examples/expected_ui_popup.png" alt="Expected UI popup" />
</p>

#### Logging and Output

During an upload job, high-level progress and status messages are displayed in the Output panel of the UI. For full, detailed logs (including validation steps and upload diagnostics), refer to the terminal where the application was launched.

### Example Python Script

```python
from pathlib import Path
import os
from aind_data_transfer_lite.models import JobSettings
from aind_data_transfer_lite.upload_data import UploadDataJob

# Assuming running from same directory as this README file
cwd = os.getcwd()
behavior_path = Path(cwd) / "tests" / "resources" / "behavior_data"
ecephys_path = Path(cwd) / "tests" / "resources" / "ecephys_data"
metadata_path = Path(cwd) / "tests" / "resources" / "metadata_dir"

modality_directories = {
  "behavior": behavior_path,
  "ecephys": ecephys_path
}

metadata_directory = metadata_path

job_settings = JobSettings(
  dry_run=True,
  modality_directories=modality_directories,
  metadata_directory=metadata_directory,
  s3_bucket="aind-open-data-dev"
)

job = UploadDataJob(job_settings=job_settings)
job.run_job()
```

### Example Command Line (Linux and MacOs)
```bash
python -m aind_data_transfer_lite.upload_data \
--metadata_directory "./tests/resources/metadata_dir" \
--modality_directories '{"behavior": "./tests/resources/behavior_data", "ecephys": "./tests/resources/ecephys_data"}' \
--dry_run "True"
```

### Example Command Line (PowerShell)
```bash
python -m aind_data_transfer_lite.upload_data `
--metadata_directory "./tests/resources/metadata_dir" `
--modality_directories '{\"behavior\": \"./tests/resources/behavior_data\", \"ecephys\": \"./tests/resources/ecephys_data\"}' `
--dry_run "True"
```

## Contributing

For code development, clone the repo and install as
```bash
pip install -e ".[dev]"
```

### Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:

```bash
coverage run -m unittest discover && coverage report
```

- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:

```bash
interrogate .
```

- Use **flake8** to check that code is up to standards (no unused imports, etc.):
```bash
flake8 .
```

- Use **black** to automatically format the code into PEP standards:
```bash
black .
```

- Use **isort** to automatically sort import statements:
```bash
isort .
```

### Pull requests

For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
```text
<type>(<scope>): <short summary>
```

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
- **docs**: Documentation only changes
- **feat**: A new feature
- **fix**: A bugfix
- **perf**: A code change that improves performance
- **refactor**: A code change that neither fixes a bug nor adds a feature
- **test**: Adding missing tests or correcting existing tests

### Semantic Release

The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):

| Commit message                                                                                                                                                                                   | Release type                                                                                                    |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
| `fix(pencil): stop graphite breaking when too much pressure applied`                                                                                                                             | ~~Patch~~ Fix Release, Default release                                                                          |
| `feat(pencil): add 'graphiteWidth' option`                                                                                                                                                       | ~~Minor~~ Feature Release                                                                                       |
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
