Merge branch 'development' into nosimplejson

.travis.yml

@@ -1,26 +1,16 @@
 sudo: false
 language: python
 python:
-- '2.7'
-- '3.5'
+- '3.7'
+- '3.8'
 notifications:
   email: false
 install:
-- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  -O miniconda.sh; fi
-- bash miniconda.sh -b -p $HOME/miniconda
-- export PATH="$HOME/miniconda/bin:$PATH"
-- hash -r
-- conda config --set always_yes yes --set changeps1 no
-- conda update -q conda
-- conda info -a
-- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy nose
-  coverage biopython click
-- source activate test-environment
-- pip install coveralls
+  - pip install coverage coveralls
+  - pip install -r requirements.txt
 script:
-- coverage run --source=ionize setup.py test
+  - coverage run --source=ionize setup.py test
+
 after_success: coveralls
 deploy:
   provider: pypi

ionize/PolyIon/Peptide.py

@@ -68,9 +68,7 @@ def charge(self, pH=None, ionic_strength=None, temperature=None,
             neg_pKs['Cterm'] = pKcterminal[cterm]
 
         charge = IsoelectricPoint(self.sequence,
-                                  amino_acid_count)._chargeR(pH,
-                                                             pos_pKs,
-                                                             neg_pKs)
+                                  amino_acid_count).charge_at_pH(pH)
         return charge**moment
 
     def isoelectric_point(self, ionic_strength=None, temperature=None):

ionize/Solution/equilibrium.py

@@ -64,9 +64,9 @@ def _calculate_pH(self, ionic_strength):
                np.array(concentrations)[:, np.newaxis], 0)
     # Construct polynomial. Change the shapes as needed, then reverse the order
     if len(P) < len(Q):
-        P.resize(Q.shape)
+        P = np.resize(P, Q.shape)
     elif len(P) > len(Q):
-        Q.resize(P.shape)
+        Q = np.resize(Q, P.shape)
     poly = (P+Q)[::-1]
 
     # Solve Polynomial for concentration

requirements.txt

@@ -1,6 +1,6 @@
-pandas>=1.0.1
+pandas>=1.0.0
 pypandoc>=1.4
-numpy>=1.18.1
-scipy>=1.4.1
+numpy>=1.16.0
+scipy>=1.4.0
 Click>=7.0
 biopython>=0.0.6