Merge pull request #39 from CosmoStat/develop

v0.1.0

Author: martinkilbinger

cs_util/__init__.py

@@ -23,4 +23,4 @@
 
 from warnings import warn
 
-__version__ = "0.0.6"
+__version__ = "0.1.0"

cs_util/args.py

@@ -0,0 +1,216 @@
+"""ARGS.
+
+:Description: Handling of command line arguments.
+
+:Author: Martin Kilbinger <martin.kilbinger@cea.fr>
+
+
+"""
+
+import sys
+import os
+
+from optparse import OptionParser
+
+
+def parse_options(p_def, short_options, types, help_strings, args=None):
+    """Parse command line options.
+
+    Parameters
+    ----------
+    p_def : dict
+        default parameter values
+    short_options : dict
+        command line options short (one character) versions
+    types : dict
+        command line options types
+    help_strings : dict
+        command line options help strings
+    args : list, optional
+        list of arguments, default is None, in which case sys.args[1:]
+        is used
+
+    Returns
+    -------
+    options: tuple
+        Command line options
+
+    """
+    if args is None:
+        args = sys.argv[1:]
+
+    usage = "%prog [OPTIONS]"
+    parser = OptionParser(usage=usage)
+
+    # Loop over default parameter values
+    for key in p_def:
+        # Process if help string exists
+        if key in help_strings:
+            # Set short option
+            short = short_options[key] if key in short_options else ""
+
+            # Set type
+            typ = types[key] if key in types else "string"
+
+            # Special case: bool type
+            if typ == "bool":
+                parser.add_option(
+                    f"{short}",
+                    f"--{key}",
+                    dest=key,
+                    default=False,
+                    action="store_true",
+                    help=help_strings[key].format(p_def[key]),
+                )
+            else:
+                parser.add_option(
+                    short,
+                    f"--{key}",
+                    dest=key,
+                    type=typ,
+                    default=p_def[key],
+                    help=help_strings[key].format(p_def[key]),
+                )
+
+    # Add verbose option
+    parser.add_option(
+        "-v",
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help="verbose output",
+    )
+
+    options_values, my_args = parser.parse_args(args)
+
+    # Transform parameter values to dict
+    options = {
+        key: getattr(options_values, key) for key in vars(options_values)
+    }
+
+    # Add other default values which do not have argument option
+    for key in p_def:
+        if key not in options:
+            options[key] = p_def[key]
+
+    return options
+
+
+def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
+    """My String Split.
+
+    Split a *string* into a list of strings. Choose as separator
+    the first in the list [space, underscore] that occurs in the string.
+    (Thus, if both occur, use space.)
+
+    Parameters
+    ----------
+    string : str
+        Input string
+    num : int
+        Required length of output list of strings, -1 if no requirement.
+    verbose : bool
+        Verbose output
+    stop : bool
+        Stop programs with error if True, return None and continues otherwise
+    sep : bool
+        Separator, try ' ', '_', and '.' if None (default)
+
+    Raises
+    ------
+    ValueError
+        If number of elements in string and num are different, for stop=True
+        If no separator found in string
+
+    Returns
+    -------
+    list
+        List of string on success, and None if failed
+
+    """
+    if string is None:
+        return None
+
+    if sep is None:
+        has_space = string.find(" ")
+        has_underscore = string.find("_")
+        has_dot = string.find(".")
+
+        if has_space != -1:
+            my_sep = " "
+        elif has_underscore != -1:
+            my_sep = "_"
+        elif has_dot != -1:
+            my_sep = "."
+        else:
+            # no separator found, does string consist of only one element?
+            if num == -1 or num == 1:
+                my_sep = None
+            else:
+                raise ValueError(
+                    "No separator (' ', '_', or '.') found in string"
+                    + f" '{string}', cannot split"
+                )
+    else:
+        if not string.find(sep):
+            raise ValueError(
+                f"No separator '{sep}' found in string '{string}' cannot split"
+            )
+        my_sep = sep
+
+    res = string.split(my_sep)
+
+    if num != -1 and num != len(res) and stop:
+        raise ValueError(
+            f"String '{len(res)}' has length {num}, required is {num}"
+        )
+
+    return res
+
+
+def read_param_script(params_in_path, params_def, verbose=False):
+    """Read Params Scritpt.
+
+    Reads a python parameter script, or prompts user for input if file does not
+    exist.
+    Returns updated parameters.
+
+    Parameters
+    ----------
+    params_in_path : str
+        input file path
+    params : dict
+        default parameters
+    verbose : bool, optional
+        verbose output if ``True``; default is ``False``
+
+    Returns
+    -------
+    dict :
+        updated parameters
+
+    """
+    params_in = {}
+    params_out = {}
+    for key in params_def:
+        params_out[key] = params_def[key]
+
+    if os.path.exists(params_in_path):
+        if verbose:
+            print(f"Reading parameter script {params_in_path}")
+        with open(params_in_path) as f:
+            exec(f.read())
+        # Set instance parameters, copy from above
+        for key in params_in:
+            params_out[key] = params_in[key]
+    else:
+        print(
+            f"Configuration script {params_in_path} not found, asking for user input"
+        )
+        for key in params_def:
+            msg = f"{key}? [{params_def[key]}] "
+            val_user = input(msg)
+            if val_user != "":
+                params_out[key] = val_user
+
+    return params_out

cs_util/cfis.py

@@ -8,7 +8,6 @@
 
 """
 
-
 import re
 import numpy as np
 from astropy import units

cs_util/logging.py

@@ -7,7 +7,6 @@
 
 """
 
-
 import os
 import sys