lili Wang
Life for Fun
Life Oriented Programming

Python Cooknotes 01 - reading configs from a file

Scenario

When python reading a common config file by configparser, for example, a config setting file for Scanpy:


has_spatial = True

...

marker = Human-CD163,Human-CD3,Human-CD19,Human-CD4

marker_types = {Tcell: [Human-CD3, Human-CD4], Bcell: [Human-CD19], Macrophages: [Human-CD163], Other: []}

...

, since configparser always return str object, this may results in potential issues should be considered:

  • bool(False) return True

  • return elements in a list that contains blank, quotation mark, line break and other special characters

config example

Solution

1. configparser

This is my personal not so “elegant” solution.

  • For bool dtype, using .getboolean() method
  • For list dtype, transformation using .split() and .strip()
  • For dict dtype, using internal ast library
def getConfig(filename, section, option, dtype=None):
    import ast

    conf = configparser.ConfigParser()
    conf.read(filename)
    if dtype == bool:
        config = conf[section].getboolean(option)
    elif dtype == list:
        config = conf[section][option]
        config = [c.strip() for c in config.split(',')]
    elif dtype == dict:
        config = conf[section][option]
        config = ast.literal_eval(config)
    else:
        config = conf[section][option]
        config = config.strip('"\n\t ') #eval()
    return config
Reference

2. yaml

Here list an example from pyyaml document to show its organization way. A block mapping may be nested in a block sequence:

# YAML
- name: PyYAML
  status: 4
  license: MIT
  language: Python
- name: PySyck
  status: 5
  license: BSD
  language: Python
  • read-in by python 
    # Python
[{'status': 4, 'language': 'Python', 'name': 'PyYAML', 'license': 'MIT'},
{'status': 5, 'license': 'BSD', 'name': 'PySyck', 'language': 'Python'}]
  • code-usage 
    import yaml
with open("./config/config.yaml", 'r') as stream: 
  config = yaml.safe_load(stream)
Reference

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