Reproducibly/automatically download data from the DepMap.
Project description
DepMap Downloader
Reproducibly/automatically download data from the Cancer Dependency Map.
💪 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
.
Get the Achilles gene dependencies:
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:
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 with:
$ pip install depmap_downloader
The most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/depmap_downloader.git
To install in development mode, use the following:
$ 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 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's cookiecutter package using @cthoyt's 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:
$ tox
Additionally, these tests are automatically re-run with each commit in a GitHub Action .
📦 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:
$ tox -e finish
This script does the following:
- Uses BumpVersion to switch the version number in the
setup.cfg
andsrc/depmap_downloader/version.py
to not have the-dev
suffix - Packages the code in both a tar archive and a wheel
- Uploads to PyPI using
twine
. Be sure to have a.pypirc
file configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for depmap_downloader-0.0.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 01ce198387694b35c041608ce9d978b0231e7ff203ce66dcf13a372b1a379031 |
|
MD5 | c8f9f83005dbdc51b602ae28bcc11435 |
|
BLAKE2b-256 | b15518be0f9185487cf19b7b967346faebfc3da9193ed3ab73b235b235680d17 |