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martinkilbingermartinkilbinger
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Merge pull request #40 from martinkilbinger/args
read param script
2 parents 397604a + c277a68 commit 5308909

9 files changed

Lines changed: 355 additions & 8 deletions

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‎cs_util/__init__.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,4 +23,4 @@
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from warnings import warn
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__version__ = "0.0.7"
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__version__ = "0.0.8"

‎cs_util/args.py‎

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"""ARGS.
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:Description: Handling of command line arguments.
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:Author: Martin Kilbinger <martin.kilbinger@cea.fr>
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"""
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import sys
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import os
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from optparse import OptionParser
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def parse_options(p_def, short_options, types, help_strings, args=None):
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"""Parse command line options.
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Parameters
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----------
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p_def : dict
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default parameter values
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short_options : dict
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command line options short (one character) versions
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types : dict
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command line options types
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help_strings : dict
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command line options help strings
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args : list, optional
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list of arguments, default is None, in which case sys.args[1:]
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is used
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Returns
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-------
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options: tuple
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Command line options
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"""
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if args is None:
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args = sys.argv[1:]
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usage = "%prog [OPTIONS]"
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parser = OptionParser(usage=usage)
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# Loop over default parameter values
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for key in p_def:
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# Process if help string exists
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if key in help_strings:
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# Set short option
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short = short_options[key] if key in short_options else ""
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# Set type
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typ = types[key] if key in types else "string"
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# Special case: bool type
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if typ == "bool":
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parser.add_option(
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f"{short}",
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f"--{key}",
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dest=key,
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default=False,
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action="store_true",
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help=help_strings[key].format(p_def[key]),
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)
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else:
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parser.add_option(
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short,
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f"--{key}",
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dest=key,
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type=typ,
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default=p_def[key],
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help=help_strings[key].format(p_def[key]),
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)
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# Add verbose option
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parser.add_option(
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"-v",
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"--verbose",
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dest="verbose",
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action="store_true",
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help="verbose output",
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)
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options_values, my_args = parser.parse_args(args)
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# Transform parameter values to dict
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options = {
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key: getattr(options_values, key) for key in vars(options_values)
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}
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# Add other default values which do not have argument option
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for key in p_def:
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if key not in options:
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options[key] = p_def[key]
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return options
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def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
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"""My String Split.
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Split a *string* into a list of strings. Choose as separator
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the first in the list [space, underscore] that occurs in the string.
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(Thus, if both occur, use space.)
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Parameters
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----------
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string : str
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Input string
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num : int
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Required length of output list of strings, -1 if no requirement.
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verbose : bool
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Verbose output
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stop : bool
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Stop programs with error if True, return None and continues otherwise
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sep : bool
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Separator, try ' ', '_', and '.' if None (default)
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Raises
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------
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ValueError
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If number of elements in string and num are different, for stop=True
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If no separator found in string
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Returns
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-------
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list
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List of string on success, and None if failed
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"""
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if string is None:
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return None
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if sep is None:
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has_space = string.find(" ")
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has_underscore = string.find("_")
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has_dot = string.find(".")
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if has_space != -1:
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my_sep = " "
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elif has_underscore != -1:
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my_sep = "_"
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elif has_dot != -1:
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my_sep = "."
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else:
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# no separator found, does string consist of only one element?
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if num == -1 or num == 1:
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my_sep = None
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else:
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raise ValueError(
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"No separator (' ', '_', or '.') found in string"
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+ f" '{string}', cannot split"
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)
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else:
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if not string.find(sep):
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raise ValueError(
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f"No separator '{sep}' found in string '{string}' cannot split"
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)
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my_sep = sep
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res = string.split(my_sep)
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if num != -1 and num != len(res) and stop:
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raise ValueError(
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f"String '{len(res)}' has length {num}, required is {num}"
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)
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return res
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def read_param_script(params_in_path, params_def, verbose=False):
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"""Read Params Scritpt.
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Reads a python parameter script, or prompts user for input if file does not
175+
exist.
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Returns updated parameters.
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Parameters
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----------
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params_in_path : str
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input file path
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params : dict
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default parameters
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verbose : bool, optional
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verbose output if ``True``; default is ``False``
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Returns
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-------
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dict :
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updated parameters
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"""
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params_in = {}
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params_out = {}
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for key in params_def:
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params_out[key] = params_def[key]
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if os.path.exists(params_in_path):
199+
if verbose:
200+
print(f"Reading parameter script {params_in_path}")
201+
with open(params_in_path) as f:
202+
exec(f.read())
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# Set instance parameters, copy from above
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for key in params_in:
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params_out[key] = params_in[key]
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else:
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print(
208+
f"Configuration script {params_in_path} not found, asking for user input"
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)
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for key in params_def:
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msg = f"{key}? [{params_def[key]}] "
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val_user = input(msg)
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if val_user != "":
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params_out[key] = val_user
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return params_out

‎cs_util/cfis.py‎

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Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@
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"""
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import re
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import numpy as np
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from astropy import units

‎cs_util/logging.py‎

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@@ -7,7 +7,6 @@
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"""
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10-
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import os
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import sys
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‎cs_util/plots.py‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@
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99
"""
1010

11-
1211
import matplotlib.pylab as plt
1312
import numpy as np
1413

@@ -207,7 +206,7 @@ def plot_data_1d(
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markers=None,
208207
xlim=None,
209208
ylim=None,
210-
shift_x=True,
209+
shift_x=False,
211210
close_fig=True,
212211
):
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"""Plot Data 1D.

‎cs_util/tests/test_args.py‎

Lines changed: 130 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,130 @@
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"""UNIT TESTS FOR ARGS SUBPACKAGE.
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This module contains unit tests for the args subpackage.
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"""
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import os
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import numpy as np
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from numpy import testing as npt
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import optparse
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import pytest
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from unittest import TestCase
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from unittest.mock import patch
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from cs_util import args
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class ArgsTestCase(TestCase):
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"""Test case for the ``args`` module."""
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def setUp(self):
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"""Set test parameter values."""
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self._params_def = {
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"p_int": 1,
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"p_float": 0.612,
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"p_str": "some_string",
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"p_bool": -1,
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"p_Bool": -1,
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"p_str_def": "second_string",
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"p_none": "",
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}
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self._types = {
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"p_int": "int",
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"p_float": "float",
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"p_bool": "bool",
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"p_Bool": "bool",
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"p_str": "str",
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}
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self._short_options = {
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"p_int": "-i",
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"p_float": "-f",
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"p_bool": "-b",
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"p_Bool": "-B",
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"p_str": "-s",
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}
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self._help_strings = {
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"p_int": "integer option, default={}",
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"p_float": "float option, default={}",
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"p_bool": "bool option, set to True if given",
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"p_Bool": "bool option, set to True if given",
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"p_str": "string option, default={}",
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}
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self._string0 = None
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self._string1 = "abc"
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self._string3 = "a b c"
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def tearDown(self):
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"""Unset test parameter values."""
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self._params_def = None
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self._types = None
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self._short_options = None
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self._help_strings = None
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self._string1 = None
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def test_parse_options(self):
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"""Test `cs_util.args.parse_options` method."""
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self._options = args.parse_options(
70+
self._params_def,
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self._short_options,
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self._types,
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self._help_strings,
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args=["-i", "2", "-s", "test", "-b"],
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)
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# Test updated options
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npt.assert_equal(self._options["p_int"], 2)
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npt.assert_equal(self._options["p_str"], "test")
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npt.assert_equal(self._options["p_bool"], True)
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# Test unchanged (default) options
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npt.assert_equal(self._options["p_float"], 0.612)
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npt.assert_equal(self._options["p_Bool"], False)
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npt.assert_equal(self._options["p_str_def"], "second_string")
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# Test default args array
88+
test_argv = [None, "-i", "2"]
89+
with patch("sys.argv", test_argv):
90+
self._options = args.parse_options(
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self._params_def,
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self._short_options,
93+
self._types,
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self._help_strings,
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args=None,
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)
97+
npt.assert_equal(self._options["p_int"], 2)
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def test_my_string_split(self):
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"""Test `cs_util.args.my_string_split` method."""
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# Test string=None
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results = args.my_string_split(self._string0)
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self.assertIsNone(results)
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# Test string without separator
107+
results = args.my_string_split(self._string1)
108+
npt.assert_equal(len(results), 1)
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npt.assert_equal(results[0], self._string1)
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# Test string with separators
112+
results = args.my_string_split(self._string3)
113+
npt.assert_equal(len(results), 3)
114+
for idx in (0, 1, 2):
115+
npt.assert_equal(results[idx], self._string3[idx * 2])
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# Test different separator
118+
results = args.my_string_split(self._string3, sep="_")
119+
npt.assert_equal(len(results), 1)
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npt.assert_equal(results[0], self._string3)
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# Test mismatching number of substrings
123+
# Exception for stop=True
124+
with self.assertRaises(ValueError):
125+
args.my_string_split(self._string3, num=2, stop=True)
126+
# Return value when stop is False
127+
results = args.my_string_split(self._string3, num=2, stop=False)
128+
npt.assert_equal(len(results), 3)
129+
for idx in (0, 1, 2):
130+
npt.assert_equal(results[idx], self._string3[idx * 2])

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