https://github.com/cthoyt/depmap_downloader

Reproducibly download the latest version of various DepMap datasets
https://github.com/cthoyt/depmap_downloader

Last synced: about 1 month ago
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Reproducibly download the latest version of various DepMap datasets

• Host: GitHub
• URL: https://github.com/cthoyt/depmap_downloader
• Owner: cthoyt
• License: mit
• Created: 2021-11-15T16:33:36.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2022-02-12T11:05:38.000Z (almost 3 years ago)
• Last Synced: 2024-09-17T05:08:55.620Z (about 2 months ago)
• Language: Python
• Size: 27.3 KB
• Stars: 2
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

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README

        




  DepMap Downloader





    

        

    

    

         

    

    

        

    

    

        

    

    

        

    

    

        

    

    

        

    



Reproducibly/automatically download data from

the [Cancer Dependency Map](https://depmap.org).

## 💪 Getting Started

The DepMap has a secret API that this package wraps, so you can always get the

latest version of some select datasets

using [`pystow`](https://github.com/cthoyt/pystow).

Get the Achilles gene dependencies:

```python

from depmap_downloader import ensure_achilles_gene_dependencies

# With a version

path = ensure_achilles_gene_dependencies(version="DepMap Public 21Q4")

# Get the latest

path = ensure_achilles_gene_dependencies()

```

Same for the CRISPR gene dependencies:

```python

from depmap_downloader import ensure_crispr_gene_dependencies

# With a version

path = ensure_crispr_gene_dependencies(version="DepMap Public 21Q4")

# Get the latest

path = ensure_crispr_gene_dependencies()

```

## 🚀 Installation

The most recent release can be installed from

[PyPI](https://pypi.org/project/depmap_downloader/) with:

```bash

$ pip install depmap_downloader

```

The most recent code and data can be installed directly from GitHub with:

```bash

$ pip install git+https://github.com/cthoyt/depmap_downloader.git

```

To install in development mode, use the following:

```bash

$ git clone git+https://github.com/cthoyt/depmap_downloader.git

$ cd depmap_downloader

$ pip install -e .

```

## 👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are

appreciated. See

[CONTRIBUTING.rst](https://github.com/cthoyt/depmap_downloader/blob/master/CONTRIBUTING.rst)

for more information on getting involved.

## 👋 Attribution

### ⚖️ License

The code in this package is licensed under the MIT License.

### 🍪 Cookiecutter

This package was created

with [@audreyfeldroy](https://github.com/audreyfeldroy)'s

[cookiecutter](https://github.com/cookiecutter/cookiecutter) package

using [@cthoyt](https://github.com/cthoyt)'s

[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)

template.

## 🛠️ For Developers

  See developer instrutions

The final section of the README is for if you want to get involved by making a

code contribution.

### ❓ Testing

After cloning the repository and installing `tox` with `pip install tox`, the

unit tests in the `tests/` folder can be run reproducibly with:

```shell

$ tox

```

Additionally, these tests are automatically re-run with each commit in

a [GitHub Action](https://github.com/cthoyt/depmap_downloader/actions?query=workflow%3ATests)

.

### 📦 Making a Release

After installing the package in development mode and installing

`tox` with `pip install tox`, the commands for making a new release are

contained within the `finish` environment in `tox.ini`. Run the following from

the shell:

```shell

$ tox -e finish

```

This script does the following:

1. Uses BumpVersion to switch the version number in the `setup.cfg` and

   `src/depmap_downloader/version.py` to not have the `-dev` suffix

2. Packages the code in both a tar archive and a wheel

3. Uploads to PyPI using `twine`. Be sure to have a `.pypirc` file configured to

   avoid the need for manual input at this step

4. Push to GitHub. You'll need to make a release going with the commit where the

   version was bumped.

5. Bump the version to the next patch. If you made big changes and want to bump

   the version by minor, you can use `tox -e bumpversion minor` after.