Install opendvp

Install opendvp#

Quick start#

$ conda create --name opendvp -y python=3.12
$ conda activate opendvp
$ pip install opendvp

or

$ uv add opendvp

Installing with conda/mamba#

Mamba is a fast, drop-in replacement for the conda package manager. It significantly speeds up installing packages and resolving environment dependencies, making it a great tool for any data scientist or Python developer. 🐍

This tutorial will guide you through installing Mamba on your system.

If you are new here is a nice post explaining the main Concepts (<5min read)

Install conda/mamba environment manager#

  1. Check and download the most recent Conda-forge Installer release for your OS here: Downloads.

  2. Follow instructions on website for your OS

  3. For Windows only: use the Miniforge Prompt

  4. Run conda init

  5. Run conda install mamba -n base -c conda-forge to install mamba

Install opendvp with conda#

$ conda create --name opendvp -y python=3.12
$ conda activate opendvp
$ pip install opendvp

Test install#

$ python
>>> import opendvp
>>> print(opendvp.__version__)
0.7.1

Make sure you always activate the environment to use opendvp.

Install with uv#

Assuming that most proteomics analysts use R, I have made this small tutorial to get you started with environment creation in python. uv is an extremely fast Python package and project manager, it has many great features and it is a great skill to have if you need python for anything. Check their documentation.

Installing uv in Windows#

Use this line to download the latest stable uv version

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Unfortunately, there are many things that can go wrong in this step, depending on your computer setup. I am afraid I cannot explain all of these. I suggest you ask ChatGPT for help :)

Installing uv in Linux and MacOS#

Use curl to download the script and execute it with sh:

curl -LsSf https://astral.sh/uv/install.sh | sh

or brew

brew install uv

Check uv works by running uv in the command line#

$ uv
An extremely fast Python package manager.

Usage: uv [OPTIONS] <COMMAND>

Commands:
  run      Run a command or script
  init     Create a new project
  add      Add dependencies to the project
  remove   Remove dependencies from the project
  version  Read or update the project's version
  sync     Update the project's environment
  lock     Update the project's lockfile
  ... (10 lines hidden)

Install opendvp with uv#

  1. Create a new directory.

uv works by creating directory specific environments. Therefore you should create a new directory for each different project. This might seems like separating a lot of things, but will keep your projects tidy, and you should only have what you need for each specific project.

  1. Open directory in VSCode

  2. Use uv to create your python (3.12) environment

$ uv init --python 3.12
Initialized project `temp`

  1. Use uv to install opendvp

$ uv add opendvp

Check opendvp is installed#

> uv pip show opendvp
Name: opendvp
Version: 0.7.1
... (hidden 3 lines)

Showing you what version is installed where

Use openDVP with jupyter notebooks#

  • Create a new jupyter notebook, or a new file with suffix .ipynb

  • Choose Select kernel in VSCode, and pick the Python environment that matches your directory name.

Try importing opendvp, it will take some time the first time you do this.

import opendvp as dvp

Use this to check the version from within python

print(dvp.__version__)

Troubleshooting#

  • Python version cannot yet be >=3.13 ; this will cause install to fail. Use python 3.11 or 3.12.

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