conda-deps 0.0.2

Generate conda environment files from Python source code

Purpose

The goal of this script is to generate a conda yaml environment file as a result of the dependencies found in source code. Initially, this script will scan Python code only, but it would be great to have it working for other programming languages as well.

This script will translate import statements in Python source code like:

import numpy
import scipy

into a conda environment yaml file:

name: testenv

channels:
- conda-forge
- bioconda
- defaults

dependencies:
- numpy
- scipy

Installation

This script only works in Python 3 and will only scan properly Python 3 source code.

Here are a few commands to get the script up and running from scratch:

curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p conda-install
source conda-install/etc/profile.d/conda.sh 
conda update --all --yes
conda create -n conda_deps python=3
conda activate conda_deps
wget https://raw.githubusercontent.com/cgat-developers/conda_deps/master/{conda_deps.py,python_deps.json}
python conda_deps.py --help

Usage

Assuming you have conda_deps.py in your working directory, this is how you run the script:

python conda_deps.py </path/to/file.py>

The script can also scan folders with Python code within:

python conda_deps.py </path/to/folder/>

In case you want to exclude one or more subfolders, use the --exclude-folder option one or more times:

python conda_deps.py --exclude-folder </path/to/folder/folder1> </path/to/folder>

You may also want to scan additonal Python files of folders:

python conda_deps.py </path/to/folder> --include-py-files my-script.py --include-py-files </another/folder>

How it works

The script uses Python's Abstract Syntax Trees to parse Python files. It looks for import <module> statements, and discards the modules belonging to the Python Standard Library (e.g. import os). It assumes that <module> has a corresponding conda package with the same name (e.g. import numpy corresponds to conda install numpy). However, that is not always the case and you can provide a proper translation between the module name and its corresponding conda package (e.g. import yaml will require conda install pyyaml) via the python_deps.json file, which will be loaded into a dictionary at the beginning of the script. It looks like this:

{
    "Bio":"biopython",
    "Cython":"cython",
    "bs4":"beautifulsoup4",
    "bx":"bx-python",
    "lzo":"python-lzo",
    "pyBigWig":"pybigwig",
    "sklearn":"scikit-learn",
    "web":"web.py",
    "weblogolib":"python-weblogo",
    "yaml":"pyyaml"
}    

The key is the name in import <module> and the value is the name of the conda package.

The python_deps.json file is meant to be useful for generic use. However, it is possible to include additional json files specific to your project:

python conda_deps.py --include-json my_project.json </path/to/project/>

The translations in my_project.json will take priority over those in python_deps.json.

Related tools

• snakefood: a more comprehensive tool but it works only with Python 2.
• pipreqs: does a similar job but for requirements.txt files and pip.

References

• https://docs.python.org/3/library/ast.html#module-ast
• http://bit.ly/2rDf5xu
• http://bit.ly/2r0Uv9t
• https://github.com/titusjan/astviewer