Skip to main content

An open-source Python package of the AlphaPept ecosystem

Project description

Pip installation GUI and PyPi releases Downloads Downloads Downloads

AlphaBase

AlphaBase provides all basic python functionalities for AlphaPept ecosystem from the Mann Labs at the Max Planck Institute of Biochemistry and the University of Copenhagen. To enable all hyperlinks in this document, please view it at GitHub.


About

An open-source Python package of the AlphaPept ecosystem from the Mann Labs at the Max Planck Institute of Biochemistry and the University of Copenhagen. It provides basic functionalities for AlphaPept ecosystem.


License

AlphaBase was developed by the Mann Labs at the Max Planck Institute of Biochemistry and the University of Copenhagen and is freely available with an Apache License. External Python packages (available in the requirements folder) have their own licenses, which can be consulted on their respective websites.


Installation

AlphaBase can be installed and used on all major operating systems (Windows, macOS and Linux). There are two different types of installation possible:

  • Pip installer: Choose this installation if you want to use AlphaBase as a Python package in an existing Python 3.8 environment (e.g. a Jupyter notebook).
  • Developer installer: Choose this installation if you are familiar with conda and Python. This installation allows access to all available features of AlphaBase and even allows to modify its source code directly. Generally, the developer version of AlphaBase outperforms the precompiled versions which makes this the installation of choice for high-throughput experiments.

Pip

AlphaBase can be installed in an existing Python 3.8 environment with a single bash command. This bash command can also be run directly from within a Jupyter notebook by prepending it with a !:

pip install alphabase

Installing AlphaBase like this avoids conflicts when integrating it in other tools, as this does not enforce strict versioning of dependancies. However, if new versions of dependancies are released, they are not guaranteed to be fully compatible with AlphaBase. While this should only occur in rare cases where dependencies are not backwards compatible, you can always force AlphaBase to use dependancy versions which are known to be compatible with:

pip install "alphabase[stable]"

NOTE: You might need to run pip install pip==21.0 before installing AlphaBase like this. Also note the double quotes ".

For those who are really adventurous, it is also possible to directly install any branch (e.g. @development) with any extras (e.g. #egg=alphabase[stable,development-stable]) from GitHub with e.g.

pip install "git+https://github.com/MannLabs/alphabase.git@development#egg=alphabase[stable,development-stable]"

Developer

AlphaBase can also be installed in editable (i.e. developer) mode with a few bash commands. This allows to fully customize the software and even modify the source code to your specific needs. When an editable Python package is installed, its source code is stored in a transparent location of your choice. While optional, it is advised to first (create and) navigate to e.g. a general software folder:

mkdir ~/folder/where/to/install/software
cd ~/folder/where/to/install/software

The following commands assume you do not perform any additional cd commands anymore.

Next, download the AlphaBase repository from GitHub either directly or with a git command. This creates a new AlphaBase subfolder in your current directory.

git clone https://github.com/MannLabs/alphabase.git

For any Python package, it is highly recommended to use a separate conda virtual environment, as otherwise dependancy conflicts can occur with already existing packages.

conda create --name alphabase python=3.8 -y
conda activate alphabase

Finally, AlphaBase and all its dependancies need to be installed. To take advantage of all features and allow development (with the -e flag), this is best done by also installing the development dependencies instead of only the core dependencies:

pip install -e "./alphabase[development]"

By default this installs loose dependancies (no explicit versioning), although it is also possible to use stable dependencies (e.g. pip install -e "./alphabase[stable,development-stable]").

By using the editable flag -e, all modifications to the AlphaBase source code folder are directly reflected when running AlphaBase. Note that the AlphaBase folder cannot be moved and/or renamed if an editable version is installed. In case of confusion, you can always retrieve the location of any Python module with e.g. the command import module followed by module.__file__.


Usage

AlphaBase can be imported as a Python package into any Python script or notebook with the command import alphabase.

A brief Jupyter notebook tutorial on how to use the API is also present in the nbs folder.


Troubleshooting

In case of issues, check out the following:

  • Issues: Try a few different search terms to find out if a similar problem has been encountered before
  • Discussions: Check if your problem or feature requests has been discussed before.

Citations

There are currently no plans to draft a manuscript.


How to contribute

If you like this software, you can give us a star to boost our visibility! All direct contributions are also welcome. Feel free to post a new issue or clone the repository and create a pull request with a new branch. For an even more interactive participation, check out the discussions and the the Contributors License Agreement.


Changelog

See the HISTORY.md for a full overview of the changes made in each version.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

alphabase-0.1.0.tar.gz (166.7 kB view details)

Uploaded Source

Built Distribution

alphabase-0.1.0-py3-none-any.whl (184.1 kB view details)

Uploaded Python 3

File details

Details for the file alphabase-0.1.0.tar.gz.

File metadata

  • Download URL: alphabase-0.1.0.tar.gz
  • Upload date:
  • Size: 166.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.9.13

File hashes

Hashes for alphabase-0.1.0.tar.gz
Algorithm Hash digest
SHA256 a68cee30883f4c2c691ebb3df1e65a3083165306c0ed94904666582674d600ec
MD5 d1484142ba5c316fe55f5786211cc2fd
BLAKE2b-256 2036c1099f91326c19d0325e3608f39e8843bed53d7460cfe41daf57597a71c2

See more details on using hashes here.

File details

Details for the file alphabase-0.1.0-py3-none-any.whl.

File metadata

  • Download URL: alphabase-0.1.0-py3-none-any.whl
  • Upload date:
  • Size: 184.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.9.13

File hashes

Hashes for alphabase-0.1.0-py3-none-any.whl
Algorithm Hash digest
SHA256 ca9c4dc65013aedf0d8ec1fbecef6fe4e37a914746535c9b1390bfb380500438
MD5 5c992774b6c62e4ca8914571d58ca591
BLAKE2b-256 957a100a9f6d97fc997f89c7f46fc8fe9b1ac22ed731cf61a5df3a7b2e2c9c68

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page