Merge branch 'development'

README.md

@@ -21,6 +21,11 @@ One-line install using [pip](https://pypi.python.org/pypi/pip):
 
     pip install ionize
 
+Alternatively, if you're installing from source:
+- Clone the repository, and `cd` into the `ionize` directory.
+- Install the dependencies with `pip3 install -r requirements.txt`
+- Install `ionize` using `python3 setup.py install`
+
 Tutorial
 --------
 Want to use **ionize**? Read the [tutorial][tutorial].

docs/source/conf.py

@@ -17,7 +17,7 @@
 
 import sys
 import os
-import mock
+import unittest.mock as mock
 MOCK_MODULES = ['numpy', 'scipy', 'scipy.optimize', 'numpy.linalg', 'Bio',
                 'Bio.SeqUtils', 'Bio.SeqUtils.IsoelectricPoint',
                 'Bio.SeqUtils.ProtParam']

ionize/Ion/__init__.py

@@ -1,13 +1,9 @@
 """Module containing the Ion class."""
 from __future__ import division
-import warnings
-from math import copysign
-import json
 import numpy as np
 
 from .BaseIon import BaseIon
-from ..constants import reference_temperature, boltzmann, kelvin, \
-                        elementary_charge
+from ..constants import reference_temperature
 from .fixed_state import fixed_state
 
 

ionize/Solution/titrate.py

@@ -5,6 +5,7 @@
 import warnings
 from copy import deepcopy
 
+from ..Ion.BaseIon import BaseIon
 from ..Ion import Ion
 from ..Database import Database
 from ..constants import atmospheric_CO2
@@ -45,25 +46,46 @@ def titrate(self, titrant, target, titration_property='pH'):
     To titrate to a target property other than pH, simply set the property
     to a property of the Solution class.
     """
+    from . import Solution
     if isinstance(titrant, str):
         titrant = database.load(titrant)
 
-    att = getattr(self, titration_property)
-    if isinstance(att, numbers.Number):
-        def min_func(c):
-            return getattr(self + (titrant, c), titration_property)-target
+    if isinstance(titrant, BaseIon):
+        att = getattr(self, titration_property)
+        if isinstance(att, numbers.Number):
+            def min_func(c):
+                return getattr(self + (titrant, c), titration_property)-target
+        else:
+            def min_func(c):
+                return getattr(self + (titrant, c), titration_property)()-target
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            c, r = brentq(min_func, 0, 55, full_output=True)
+
+        if r.converged:
+            return (self + (titrant, c))
+        else:
+            raise RuntimeError('Solver did not converge.')
+    elif isinstance(titrant, Solution):
+        att = getattr(self, titration_property)
+        if isinstance(att, numbers.Number):
+            def min_func(c):
+                return getattr((self*(1-c) + titrant*c), titration_property)-target
+        else:
+            def min_func(c):
+                return getattr((self*(1-c) + titrant*c), titration_property)()-target
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            c, r = brentq(min_func, 0, 1, full_output=True)
+
+        if r.converged:
+            return (self*(1-c)+titrant*c)
+        else:
+            raise RuntimeError('Solver did not converge.')
     else:
-        def min_func(c):
-            return getattr(self + (titrant, c), titration_property)()-target
-
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        c, r = brentq(min_func, 0, 55, full_output=True)
-
-    if r.converged:
-        return (self + (titrant, c))
-    else:
-        raise RuntimeError('Solver did not converge.')
+        raise TypeError('Titrant must be an Ion, an ion name string, or a Solution.')
 
 
 def equilibrate_CO2(self, partial_pressure=atmospheric_CO2):

ionize/__version__.py

@@ -1 +1 @@
-__version__ = '1.2.0'
+__version__ = '1.3.0'

ionize/tests.py

@@ -274,6 +274,13 @@ def test_titrate(self):
             self.assertAlmostEqual(base.titrate('hydrochloric acid', pH).pH,
                                    pH)
 
+    def test_solution_titrate(self):
+        """Test titration with a solution."""
+        base = Solution(['tris'], [0.1])
+        titrant = Solution('hydrochloric acid', 0.2)
+        for pH in (1, 3, 5, 7):
+            self.assertAlmostEqual(base.titrate(titrant, pH).pH, pH)
+
     def test_solution_properties(self):
         for buf in self.solutions:
             buf.conductivity()

requirements.txt

@@ -0,0 +1,7 @@
+pandas>=1.0.1
+pypandoc>=1.4
+numpy>=1.18.1
+scipy>=1.4.1
+Click>=7.0
+biopython>=0.0.6
+simplejson>=3.17.2