pyEQL 0.5.2__py3-none-any.whl → 1.1.0__py3-none-any.whl

pyEQL/logging_system.py

@@ -1,53 +0,0 @@
-# logging system
-""" Create a logging system using Python's built-in module. 
-
-Each module within pyEQL has its own logger, with a StreamHandler attached to it that
-directs formatted messages to standard output. This is intended to facilitate the use
-of pyEQL as an interactive console program, at the expense of some flexibility when
-using it as a true library in another application.
-
-The default logging levels are mapped to pyEQL events as follows:
- 
-DEBUG       -   detailed messages about function execution including methods used, data sources,
-                temperature adjustments, etc.
-INFO        -   Messages indicating calculation steps, function calls, etc.
-WARNING     -   assumptions or limitations of module output
-ERROR       -   Module could not complete a task due to invalid input or other problem
-CRITICAL    -   not used
-
-:copyright: 2013-2020 by Ryan S. Kingsbury
-:license: LGPL, see LICENSE for more details.
-
-"""
-import logging
-
-# define a log filter to emit only unique log messages
-
-
-class Unique(logging.Filter):
-    """Messages are allowed through just once.
-    The 'message' includes substitutions, but is not formatted by the 
-    handler. If it were, then practically all messages would be unique!
-    """
-
-    def __init__(self, name=""):
-        logging.Filter.__init__(self, name)
-        self.reset()
-
-    def reset(self):
-        """Act as if nothing has happened."""
-        self.__logged = {}
-
-    def filter(self, rec):
-        """logging.Filter.filter performs an extra filter on the name."""
-        return logging.Filter.filter(self, rec) and self.__is_first_time(rec)
-
-    def __is_first_time(self, rec):
-        """Emit a message only once."""
-        msg = rec.msg % (rec.args)
-        if msg in self.__logged:
-            self.__logged[msg] += 1
-            return False
-        else:
-            self.__logged[msg] = 1
-            return True

pyEQL/parameter.py

@@ -1,435 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-This module implements the Parameter() class, which is used to store
-values, units, uncertainties, and reference data for various quantities
-used throughout pyEQL.
-
-:copyright: 2013-2020 by Ryan S. Kingsbury
-:license: LGPL, see LICENSE for more details.
-
-"""
-
-# logging system
-import logging
-import os
-
-# per the pint documentation, it's important that pint and its associated Unit
-# Registry are only imported once.
-from pint import UnitRegistry
-
-# add a filter to emit only unique log messages to the handler
-from pyEQL.logging_system import Unique
-
-logger = logging.getLogger(__name__)
-unique = Unique()
-logger.addFilter(unique)
-
-# add a handler for console output, since pyEQL is meant to be used interactively
-ch = logging.StreamHandler()
-
-# create formatter for the log
-formatter = logging.Formatter("(%(name)s) - %(levelname)s - %(message)s")
-
-# add formatter to the handler
-ch.setFormatter(formatter)
-logger.addHandler(ch)
-
-# Units handling
-
-# here we assign the identifier 'unit' to the UnitRegistry
-unit = UnitRegistry()
-
-# use this to enable legacy handling of offset units
-# TODO fix this to handle offsets the way pint wants us to since 0.7
-unit.autoconvert_offset_to_baseunit = True
-
-# append custom unit definitions and contexts
-directory = os.path.dirname(__file__)
-unit.load_definitions(directory + "/pint_custom_units.txt")
-# activate the "chemistry" context globally
-unit.enable_contexts("chem")
-# set the default string formatting for pint quantities
-unit.default_format = "P~"
-
-
-def testfunc(val):
-    list = []
-    try:
-        list.append(float(val) * unit(""))
-        return list
-    except ValueError:
-        print("Value Error")
-        return None
-
-
-class Parameter:
-    """
-    Class for storing and retrieving measured parameter values together with their
-    units, context, and reference information.
-
-    Some pyEQL functions search for specific parameter names, such as:
-    diffusion_coefficient
-
-
-
-    """
-
-    def __init__(self, name, magnitude, units="", **kwargs):
-        """
-        Parameters
-        ----------
-        name : str
-                    A short name (akin to a variable name) for the parameter
-
-        magnitude : float, int, str, tuple or list of floats, ints, or strs
-                    The value of the parameter. In most cases this will only be a single numerical value.
-                    However, in some cases it may be desirable to store a group of parameters (such as coefficients
-                    for an equation) together in a tuple or list.
-
-                    Numeric values can be input as strings (or lists of strings) and they will be converted to
-                    floats.
-
-                    Non-numeric values are permissible as well. When specifying non-numeric values, the units
-                    argument must either be 'dimensionless' or left blank.
-
-                    Lists of non-numeric strings are not permitted.
-
-        units : str, optional
-                    A string representing the units of measure for the parameter value
-                    given in 'magnitude.' See the pint documentation for proper syntax. In general
-                    common abbreviations or unit names can be used, but pythonic math syntax
-                    must be followed. e.g. 'meters ** 2 / second' and 'm **2 /s' are valid but
-                    'm2/s' is not.
-
-                    If a parameter has no units, leave blank or enter 'dimensionless'
-
-                    Note that if a parameter DOES have units but they are not specified, all
-                    calculations involving this parameter will return incorrect units.
-
-        Optional Keyword Arguments
-        --------------------------
-        reference : str, optional
-                    A string containing reference information documenting the source of
-                    the parameter.
-        uncertainty : tuple of floats or ints, optional
-                    The uncertainty of the parameter value as a percentage (0-100). If only one value is supplied in 
-                    the tuple,
-                    the same uncertainty will be used for positive and negative. If two values are supplied, the first
-                    is the positive uncertainty and the second is the negative.
-        uncertainty_type: str, optional
-                    A string specifying different ways of measuring uncertainty.
-        temperature : str, optional
-                    The temperature at which 'magnitude' was measured in degrees Celsius.
-                    Specify the temperature as a string containing the magnitude and
-                    a unit, e.g. '25 degC', '32 degF', '298 kelvin', and '500 degR'
-        pressure : str, optional
-                    The pressure at which 'magnitude' was measured in Pascals
-                    Specify the pressure as a string containing the magnitude and a
-                    unit. e.g. '101 kPa'.
-                    Typical valid units are 'Pa', 'atm', or 'torr'.
-        ionic_strength : str, optional
-                    The ionic strength of the solution in which 'magnitude' was measured. Specify
-                    the ionic strength as a string containing the magnitude and a unit. e.g. '2 mol/kg'
-        description : str, optional
-                    A string contiaining a longer name describing the paramter. For example
-                    'Diffusion Coefficient' or 'Hydrated Ionic Radius'
-        comments : str, optional
-                    A string containing additional notes pertaining to the context,
-                    conditions, or assumptions that may restrict the use of 'value'
-
-        Notes
-        -----
-        In general, parameter values are assumed to be entered in fundamental
-        SI units (m, kg, s, etc.). The 'units' field is required to call attention
-        to this fact and provide a levelof error-checking in calculations involving
-        the parameter.
-
-        Examples
-        --------
-        # TODO fix this example
-        >>> sodium_diffusion = Parameter('diffusion coefficient',(1.334e-9,),'m2/s','CRC Handbook of Chemistry and
-            Physics, 92nd Ed., pp. 5-77 to 5-79',(),25,101325,0)
-        >>> print(sodium_diffusion)
-        Parameter diffusion coefficient
-        <BLANKLINE>
-        -------------------------------------------
-        Value: (1.334e-09,) m2/s at 25 degrees C.
-        Notes:
-        Reference: CRC Handbook of Chemistry and Physics, 92nd Ed., pp. 5-77 to 5-79
-        <BLANKLINE>
-        """
-        self.name = name
-        use_units = ""
-        # turn numeric parameters into quantities with associated units
-        # if units were specified as 'None', convert into something pint will understand
-        if (
-            units == "None"
-            or units == "none"
-            or units == ""
-            or units == "dimensionless"
-        ):
-            use_units = "dimensionless"
-        else:
-            use_units = units
-
-        # see if the input value is a list or tuple. If so, create a list of
-        # quantities (including units), and convert the list to a tuple
-        if isinstance(magnitude, (tuple, list)):
-            # check whether each element is a number
-            temp_list = []
-            for item in magnitude:
-                try:
-                    temp_list.append(float(item) * unit(use_units))
-                except ValueError:
-                    print("Value Error on %s" % item)
-                    # Throw an error if units are assigned to a non-numeric parameter
-                    if not (use_units == "dimensionless"):
-                        logger.error(
-                            "A non-numeric parameter cannot have units, but units of %s were specified"
-                            % units
-                        )
-                    temp_list.append(item)
-
-            # convert the resulting list into a tuple
-            self.value = tuple(temp_list)
-
-        # if the input is a single item, try to convert it to a number. If that
-        # doesn't work, it must be a str and will be passed on as-is
-        else:
-            try:
-                self.value = float(magnitude) * unit(use_units)
-            except ValueError:
-                # Throw an error if units are assigned to a non-numeric parameter
-                if not (use_units == "dimensionless"):
-                    logger.error(
-                        "A non-numeric parameter cannot have units, but units of %s were specified"
-                        % units
-                    )
-
-                self.value = magnitude
-
-        # process optional keyword arguments - reference conditions
-        self.base_temperature = "Not specified"
-        self.base_pressure = "Not specified"
-        self.base_ionic_strength = "Not specified"
-
-        if "temperature" in kwargs and kwargs["temperature"] != "":
-            self.temperature_set = True
-            self.base_temperature = unit(kwargs["temperature"])
-        if "pressure" in kwargs and kwargs["pressure"] != "":
-            self.pressure_set = True
-            self.base_pressure = unit(kwargs["pressure"])
-        if "ionic_strength" in kwargs and kwargs["ionic_strength"] != "":
-            self.ionic_strength_set = True
-            self.base_ionic_strength = unit(kwargs["ionic_strength"])
-
-        # process optional keyword arguments - descriptive and reference
-        self.reference = "Not specified"
-        self.description = ""
-        self.comment = ""
-
-        if "reference" in kwargs:
-            self.reference = kwargs["reference"]
-        if "description" in kwargs:
-            self.description = kwargs["description"]
-        if "comment" in kwargs:
-            self.comment = kwargs["comment"]
-
-        # process optional keyword arguments - uncertanty
-        # TODO - uncertainty functions / parameters
-
-        # process optional keyword arguments  - temperature adjustment
-        # TODO - temperature adjustment functions / parameters
-
-    def get_name(self):
-        """
-        Return the name of the parameter.
-
-        Parameters
-        ----------
-        None
-
-        Returns
-        -------
-        str
-            The name of the parameter
-        """
-        return self.name
-
-    def get_value(self, temperature=None, pressure=None, ionic_strength=None):
-        """
-        Return the value of a parameter at the specified conditions.
-
-        Parameters
-        ----------
-        temperature : str, optional
-                    The temperature at which 'magnitude' was measured in degrees Celsius.
-                    Specify the temperature as a string containing the magnitude and
-                    a unit, e.g. '25 degC', '32 degF', '298 kelvin', and '500 degR'
-        pressure : str, optional
-                    The pressure at which 'magnitude' was measured in Pascals
-                    Specify the pressure as a string containing the magnitude and a
-                    unit. e.g. '101 kPa'.
-                    Typical valid units are 'Pa', 'atm', or 'torr'.
-        ionic_strength : str, optional
-                    The ionic strength of the solution in which 'magnitude' was measured. Specify
-                    the ionic strength as a string containing the magnitude and a unit. e.g. '2 mol/kg'
-
-        Returns
-        -------
-        Quantity
-            The value of the parameter at the specified conditions.
-
-        """
-        # if the user does not specify conditions, return the value at base_temperature,
-        # base_pressure, and/or base_ionic_strength
-        if temperature is None:
-            temperature = self.base_temperature
-            logger.info(
-                "Temperature not specified for "
-                + str(self.name)
-                + ". Returning value at "
-                + str(temperature)
-                + "."
-            )
-        else:
-            temperature = unit(temperature)
-        if pressure is None:
-            pressure = self.base_pressure
-            logger.info(
-                "Pressure not specified for "
-                + str(self.name)
-                + ". Returning value at "
-                + str(pressure)
-                + "."
-            )
-        else:
-            pressure = unit(pressure)
-        if ionic_strength is None:
-            ionic_strength = self.base_ionic_strength
-            logger.info(
-                "Ionic Strength not specified for "
-                + str(self.name)
-                + ". Returning value at "
-                + str(ionic_strength)
-                + "."
-            )
-        else:
-            ionic_strength = unit(ionic_strength)
-
-        # compare requested conditions with base conditions
-        if temperature != self.base_temperature:
-            # TODO- implement temperature correction
-            logger.warning(
-                "Requested temperature for "
-                + str(self.name)
-                + " ("
-                + str(temperature)
-                + ") differs from measurement conditions."
-                + "Returning value at "
-                + str(self.base_temperature)
-            )
-
-        if pressure != self.base_pressure:
-            # TODO - implement pressure correction
-            logger.warning(
-                "Requested pressure for "
-                + str(self.name)
-                + " ("
-                + str(pressure)
-                + ") differs from measurement conditions."
-                + "Returning value at "
-                + str(self.base_pressure)
-            )
-
-        if ionic_strength != self.base_ionic_strength:
-            logger.warning(
-                "Requested ionic strength for "
-                + str(self.name)
-                + " ("
-                + str(ionic_strength)
-                + ") differs from measurement conditions."
-                + "Returning value at "
-                + str(self.base_ionic_strength)
-            )
-
-        return self.value
-
-    def get_magnitude(self, temperature=None, pressure=None, ionic_strength=None):
-        """
-        Return the magnitude of a parameter at the specified conditions.
-
-        Parameters
-        ----------
-        temperature : str, optional
-                    The temperature at which 'magnitude' was measured in degrees Celsius.
-                    Specify the temperature as a string containing the magnitude and
-                    a unit, e.g. '25 degC', '32 degF', '298 kelvin', and '500 degR'
-        pressure : str, optional
-                    The pressure at which 'magnitude' was measured in Pascals
-                    Specify the pressure as a string containing the magnitude and a
-                    unit. e.g. '101 kPa'.
-                    Typical valid units are 'Pa', 'atm', or 'torr'.
-        ionic_strength : str, optional
-                    The ionic strength of the solution in which 'magnitude' was measured. Specify
-                    the ionic strength as a string containing the magnitude and a unit. e.g. '2 mol/kg'
-
-        Returns
-        -------
-        Number
-            The magnitude of the parameter at the specified conditions.
-
-        """
-        return self.get_value(temperature, pressure, ionic_strength).magnitude
-
-    def get_units(self):
-        """
-        Return the units of a parameter
-        """
-        return self.get_value().units
-
-    def get_dimensions(self):
-        """
-        Return the dimensions of the parameter.
-        """
-        return self.get_value().dimensionality
-
-    def __str__(self):
-        """
-        Set the output of the print() statement for a parameter value
-        """
-        return (
-            "\n"
-            + "----------------------------------------------------------------------------"
-            + "\n"
-            + "Parameter "
-            + str(self.name)
-            + "\n\n"
-            + str(self.description)
-            + "\n"
-            "Value: "
-            + str(self.get_value())
-            + "\n"
-            + "Conditions (T,P,Ionic Strength): "
-            + str(self.base_temperature)
-            + ", "
-            + str(self.base_pressure)
-            + ", "
-            + str(self.base_ionic_strength)
-            + "\n"
-            + "Notes: "
-            + str(self.comment)
-            + "\n"
-            + "Reference: "
-            + str(self.reference)
-            + "\n"
-            + "--------------------------------------------------------------------------------------"
-            + "\n"
-        )
-
-
-# TODO - turn doctest back on when the nosigint error is gone
-# Tests
-# if __name__ == "__main__":
-#   import doctest
-#  doctest.testmod()

pyEQL/tests/__init__.py

@@ -1,32 +0,0 @@
-import unittest
-import os
-import logging
-
-
-def testsuite():
-    """A testsuite that includes all the pyEQL tests.
-    """
-    # turn off log warning messages during tests
-    logging.disable(logging.WARNING)
-
-    # include all files in the directory of this script
-    suite = unittest.TestLoader().discover(os.path.dirname(__file__))
-
-    return suite
-
-
-def main():
-    """Runs the testsuite as command line application.
-    """
-    try:
-        unittest.main()
-    except Exception as e:
-        print("Error: %s" % e)
-
-
-def run():
-    """Run all tests.
-    :return: a :class:`unittest.TestResult` object
-    """
-    test_runner = unittest.TextTestRunner()
-    return test_runner.run(testsuite())