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bw2 / ConfigArgParse

A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
MIT License
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ConfigArgParse

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Overview


Applications with more than a handful of user-settable options are best
configured through a combination of command line args, config files,
hard-coded defaults, and in some cases, environment variables.

Python's command line parsing modules such as argparse have very limited
support for config files and environment variables, so this module
extends argparse to add these features.

Available on PyPI: http://pypi.python.org/pypi/ConfigArgParse

Features

Example


*config_test.py*:

Script that defines 4 options and a positional arg and then parses and prints the values. Also,
it prints out the help message as well as the string produced by :code:`format_values()` to show
what they look like.

.. code:: py

   import configargparse

   p = configargparse.ArgParser(default_config_files=['/etc/app/conf.d/*.conf', '~/.my_settings'])
   p.add('-c', '--my-config', required=True, is_config_file=True, help='config file path')
   p.add('--genome', required=True, help='path to genome file')  # this option can be set in a config file because it starts with '--'
   p.add('-v', help='verbose', action='store_true')
   p.add('-d', '--dbsnp', help='known variants .vcf', env_var='DBSNP_PATH')  # this option can be set in a config file because it starts with '--'
   p.add('vcf', nargs='+', help='variant file(s)')

   options = p.parse_args()

   print(options)
   print("----------")
   print(p.format_help())
   print("----------")
   print(p.format_values())    # useful for logging where different settings came from

*config.txt:*

Since the script above set the config file as required=True, lets create a config file to give it:

.. code:: py

    # settings for config_test.py
    genome = HCMV     # cytomegalovirus genome
    dbsnp = /data/dbsnp/variants.vcf

*command line:*

Now run the script and pass it the config file:

.. code:: bash

    DBSNP_PATH=/data/dbsnp/variants_v2.vcf python config_test.py --my-config config.txt f1.vcf f2.vcf

*output:*

Here is the result:

.. code:: bash

    Namespace(dbsnp='/data/dbsnp/variants_v2.vcf', genome='HCMV', my_config='config.txt', v=False, vcf=['f1.vcf', 'f2.vcf'])
    ----------
    usage: config_test.py [-h] -c MY_CONFIG --genome GENOME [-v] [-d DBSNP]
                          vcf [vcf ...]

    Args that start with '--' (eg. --genome) can also be set in a config file
    (/etc/app/conf.d/*.conf or ~/.my_settings or specified via -c). Config file
    syntax allows: key=value, flag=true, stuff=[a,b,c] (for details, see syntax at
    https://goo.gl/R74nmi). If an arg is specified in more than one place, then
    commandline values override environment variables which override config file
    values which override defaults.

    positional arguments:
      vcf                   variant file(s)

    optional arguments:
      -h, --help            show this help message and exit
      -c MY_CONFIG, --my-config MY_CONFIG
                            config file path
      --genome GENOME       path to genome file
      -v                    verbose
      -d DBSNP, --dbsnp DBSNP
                            known variants .vcf [env var: DBSNP_PATH]

    ----------
    Command Line Args:   --my-config config.txt f1.vcf f2.vcf
    Environment Variables:
      DBSNP_PATH:        /data/dbsnp/variants_v2.vcf
    Config File (config.txt):
      genome:            HCMV

Special Values

Under the hood, configargparse handles environment variables and config file values by converting them to their corresponding command line arg. For example, "key = value" will be processed as if "--key value" was specified on the command line.

Also, the following special values (whether in a config file or an environment variable) are handled in a special way to support booleans and lists:

Config File Syntax


Only command line args that have a long version (eg. one that starts with '--')
can be set in a config file. For example, "--color" can be set by putting
"color=green" in a config file. The config file syntax depends on the constructor
arg: :code:`config_file_parser_class` which can be set to one of the provided
classes: :code:`DefaultConfigFileParser`, :code:`YAMLConfigFileParser`,
:code:`ConfigparserConfigFileParser` or to your own subclass of the
:code:`ConfigFileParser` abstract class.

*DefaultConfigFileParser*  - the full range of valid syntax is:

.. code:: yaml

        # this is a comment
        ; this is also a comment (.ini style)
        ---            # lines that start with --- are ignored (yaml style)
        -------------------
        [section]      # .ini-style section names are treated as comments

        # how to specify a key-value pair (all of these are equivalent):
        name value     # key is case sensitive: "Name" isn't "name"
        name = value   # (.ini style)  (white space is ignored, so name = value same as name=value)
        name: value    # (yaml style)
        --name value   # (argparse style)

        # how to set a flag arg (eg. arg which has action="store_true")
        --name
        name
        name = True    # "True" and "true" are the same

        # how to specify a list arg (eg. arg which has action="append")
        fruit = [apple, orange, lemon]
        indexes = [1, 12, 35 , 40]

*YAMLConfigFileParser*  - allows a subset of YAML syntax (http://goo.gl/VgT2DU)

.. code:: yaml

        # a comment
        name1: value
        name2: true    # "True" and "true" are the same

        fruit: [apple, orange, lemon]
        indexes: [1, 12, 35, 40]
        colors:
          - green
          - red
          - blue

*ConfigparserConfigFileParser*  - allows a subset of python's configparser
module syntax (https://docs.python.org/3.7/library/configparser.html). In
particular the following configparser options are set:

.. code:: py

        config = configparser.ArgParser(
            delimiters=("=",":"),
            allow_no_value=False,
            comment_prefixes=("#",";"),
            inline_comment_prefixes=("#",";"),
            strict=True,
            empty_lines_in_values=False,
        )

Once configparser parses the config file all section names are removed, thus all
keys must have unique names regardless of which INI section they are defined
under. Also, any keys which have python list syntax are converted to lists by
evaluating them as python code using ast.literal_eval
(https://docs.python.org/3/library/ast.html#ast.literal_eval). To facilitate
this all multi-line values are converted to single-line values. Thus multi-line
string values will have all new-lines converted to spaces. Note, since key-value
pairs that have python dictionary syntax are saved as single-line strings, even
if formatted across multiple lines in the config file, dictionaries can be read
in and converted to valid python dictionaries with PyYAML's safe_load. Example
given below:

.. code:: py

        # inside your config file (e.g. config.ini)
        [section1]  # INI sections treated as comments
        system1_settings: { # start of multi-line dictionary
            'a':True,
            'b':[2, 4, 8, 16],
            'c':{'start':0, 'stop':1000},
            'd':'experiment 32 testing simulation with parameter a on'
            } # end of multi-line dictionary value

        .......

        # in your configargparse setup
        import configargparse
        import yaml

        parser = configargparse.ArgParser(
            config_file_parser_class=configargparse.ConfigparserConfigFileParser
        )
        parser.add_argument('--system1_settings', type=yaml.safe_load)

        args = parser.parse_args() # now args.system1 is a valid python dict

*IniConfigParser*  - INI parser with support for sections.

This parser somewhat ressembles ``ConfigparserConfigFileParser``. It uses configparser and apply the same kind of processing to 
values written with python list syntax. 

With the following additions: 
   - Must be created with argument to bind the parser to a list of sections.
   - Does not convert multiline strings to single line.
   - Optional support for converting multiline strings to list (if ``split_ml_text_to_list=True``). 
   - Optional support for quoting strings in config file 
      (useful when text must not be converted to list or when text 
      should contain trailing whitespaces).

This config parser can be used to integrate with ``setup.cfg`` files.

Example::

      # this is a comment
      ; also a comment
      [my_super_tool]
      # how to specify a key-value pair
      format-string: restructuredtext 
      # white space are ignored, so name = value same as name=value
      # this is why you can quote strings 
      quoted-string = '\thello\tmom...  '
      # how to set an arg which has action="store_true"
      warnings-as-errors = true
      # how to set an arg which has action="count" or type=int
      verbosity = 1
      # how to specify a list arg (eg. arg which has action="append")
      repeatable-option = ["https://docs.python.org/3/objects.inv",
                     "https://twistedmatrix.com/documents/current/api/objects.inv"]
      # how to specify a multiline text:
      multi-line-text = 
         Lorem ipsum dolor sit amet, consectetur adipiscing elit. 
         Vivamus tortor odio, dignissim non ornare non, laoreet quis nunc. 
         Maecenas quis dapibus leo, a pellentesque leo. 

If you use ``IniConfigParser(sections, split_ml_text_to_list=True)``::

      # the same rules are applicable with the following changes:
      [my-software]
      # how to specify a list arg (eg. arg which has action="append")
      repeatable-option = # Just enter one value per line (the list literal format can also be used)
         https://docs.python.org/3/objects.inv
         https://twistedmatrix.com/documents/current/api/objects.inv
      # how to specify a multiline text (you have to quote it):
      multi-line-text = '''
         Lorem ipsum dolor sit amet, consectetur adipiscing elit. 
         Vivamus tortor odio, dignissim non ornare non, laoreet quis nunc. 
         Maecenas quis dapibus leo, a pellentesque leo. 
         '''

Usage:

.. code:: py

   import configargparse
   parser = configargparse.ArgParser(
            default_config_files=['setup.cfg', 'my_super_tool.ini'],
            config_file_parser_class=configargparse.IniConfigParser(['tool:my_super_tool', 'my_super_tool']),
        )
   ...

*TomlConfigParser*  - TOML parser with support for sections.

`TOML <https://github.com/toml-lang/toml/blob/main/toml.md>`_ parser. This config parser can be used to integrate with ``pyproject.toml`` files.

Example::

   # this is a comment
   [tool.my-software] # TOML section table.
   # how to specify a key-value pair
   format-string = "restructuredtext" # strings must be quoted
   # how to set an arg which has action="store_true"
   warnings-as-errors = true
   # how to set an arg which has action="count" or type=int
   verbosity = 1
   # how to specify a list arg (eg. arg which has action="append")
   repeatable-option = ["https://docs.python.org/3/objects.inv",
                  "https://twistedmatrix.com/documents/current/api/objects.inv"]
   # how to specify a multiline text:
   multi-line-text = '''
      Lorem ipsum dolor sit amet, consectetur adipiscing elit. 
      Vivamus tortor odio, dignissim non ornare non, laoreet quis nunc. 
      Maecenas quis dapibus leo, a pellentesque leo. 
      '''

Usage:

.. code:: py

   import configargparse
   parser = configargparse.ArgParser(
            default_config_files=['pyproject.toml', 'my_super_tool.toml'],
            config_file_parser_class=configargparse.TomlConfigParser(['tool.my_super_tool']),
        )
   ...

*CompositeConfigParser*  - Create a config parser to understand multiple formats.

This parser will successively try to parse the file with each parser, until it succeeds, 
else fail showing all encountered error messages.

The following code will make configargparse understand both TOML and INI formats. 
Making it easy to integrate in both ``pyproject.toml`` and ``setup.cfg``.

.. code:: py

   import configargparse
   my_tool_sections = ['tool.my_super_tool', 'tool:my_super_tool', 'my_super_tool']
                    # pyproject.toml like section, setup.cfg like section, custom section
   parser = configargparse.ArgParser(
            default_config_files=['setup.cfg', 'my_super_tool.ini'],
            config_file_parser_class=configargparse.CompositeConfigParser(
               [configargparse.TomlConfigParser(my_tool_sections), 
                configargparse.IniConfigParser(my_tool_sections, split_ml_text_to_list=True)]
               ),
        )
   ...

Note that it's required to put the TOML parser first because the INI syntax basically would accept anything whereas TOML. 

ArgParser Singletons

To make it easier to configure different modules in an application, configargparse provides globally-available ArgumentParser instances via configargparse.get_argument_parser('name') (similar to logging.getLogger('name')).

Here is an example of an application with a utils module that also defines and retrieves its own command-line args.

main.py

.. code:: py

import configargparse
import utils

p = configargparse.get_argument_parser()
p.add_argument("-x", help="Main module setting")
p.add_argument("--m-setting", help="Main module setting")
options = p.parse_known_args()   # using p.parse_args() here may raise errors.

utils.py

.. code:: py

import configargparse
p = configargparse.get_argument_parser()
p.add_argument("--utils-setting", help="Config-file-settable option for utils")

if __name__ == "__main__":
   options = p.parse_known_args()

Help Formatters


:code:`ArgumentDefaultsRawHelpFormatter` is a new HelpFormatter that both adds
default values AND disables line-wrapping. It can be passed to the constructor:
:code:`ArgParser(.., formatter_class=ArgumentDefaultsRawHelpFormatter)`

Aliases

The configargparse.ArgumentParser API inherits its class and method names from argparse and also provides the following shorter names for convenience:

HelpFormatters:

API Documentation


You can review the generated API Documentation for the ``configargparse`` module: `HERE <https://bw2.github.io/ConfigArgParse/>`_

Design Notes

Unit tests:

tests/test_configargparse.py contains custom unittests for features specific to this module (such as config file and env-var support), as well as a hook to load and run argparse unittests (see the built-in test.test_argparse module) but on configargparse in place of argparse. This ensures that configargparse will work as a drop in replacement for argparse in all usecases.

Previously existing modules (PyPI search keywords: config argparse):

Design choices:

  1. all options must be settable via command line. Having options that can only be set using config files or env. vars adds complexity to the API, and is not a useful enough feature since the developer can split up options into sections and call a section "config file keys", with command line args that are just "--" plus the config key.
  2. config file and env. var settings should be processed by appending them to the command line (another benefit of #1). This is an easy-to-implement solution and implicitly takes care of checking that all "required" args are provided, etc., plus the behavior should be easy for users to understand.
  3. configargparse shouldn't override argparse's convert_arg_line_to_args method so that all argparse unit tests can be run on configargparse.
  4. in terms of what to allow for config file keys, the "dest" value of an option can't serve as a valid config key because many options can have the same dest. Instead, since multiple options can't use the same long arg (eg. "--long-arg-x"), let the config key be either "--long-arg-x" or "long-arg-x". This means the developer can allow only a subset of the command-line args to be specified via config file (eg. short args like -x would be excluded). Also, that way config keys are automatically documented whenever the command line args are documented in the help message.
  5. don't force users to put config file settings in the right .ini [sections]. This doesn't have a clear benefit since all options are command-line settable, and so have a globally unique key anyway. Enforcing sections just makes things harder for the user and adds complexity to the implementation. NOTE: This design choice was preventing configargparse from integrating with common Python project config files like setup.cfg or pyproject.toml, so additional parser classes were added that parse only a subset of the values defined in INI or TOML config files.
  6. if necessary, config-file-only args can be added later by implementing a separate add method and using the namespace arg as in appsettings_v0.5

Relevant sites:

Versioning



This software follows `Semantic Versioning`_

.. _Semantic Versioning: http://semver.org/