Merge pull request #46 from MetaSys-LISBP/dev

Dev to 2.2.3

Author: pierremillard

README.md

@@ -2,8 +2,9 @@
 
 [![PyPI version](https://badge.fury.io/py/IsoCor.svg)](https://badge.fury.io/py/IsoCor)
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/isocor.svg)](https://pypi.python.org/pypi/isocor/)
-[![Build Status](https://travis-ci.com/MetaSys-LISBP/IsoCor.svg?branch=master)](https://travis-ci.com/MetaSys-LISBP/IsoCor)
 [![Documentation Status](https://readthedocs.org/projects/isocor/badge/?version=latest)](http://isocor.readthedocs.io/?badge=latest)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/isocor/README.html)
+
 
 [![IsoCor graphical user interface](https://raw.githubusercontent.com/MetaSys-LISBP/IsoCor/master/doc/_static/isocor_GUI.png)](https://isocor.readthedocs.io/en/latest/)
 

isocor/__init__.py

@@ -5,7 +5,7 @@
 """
 
 # Version number MUST be maintained here (x.y.z format)
-__version__ = '2.2.2'
+__version__ = '2.2.3'
 
 from isocor.mscorrectors import MetaboliteCorrectorFactory
 from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector

isocor/mscorrectors.py

@@ -240,13 +240,13 @@ def _correct_with_bfgs(self, measurement):
             enrichment = math.fsum(
                 p*i for i, p in enumerate(isotopologue_fraction))/self.formula[self._tracer_el]
         else:
-            isotopologue_fraction = [np.NaN for p in corrected_area]
-            enrichment = np.NaN
+            isotopologue_fraction = [np.nan for p in corrected_area]
+            enrichment = np.nan
         sum_m = math.fsum(measurement)
         if sum_m != 0:
             residuum = [v/sum_m for v in resi]
         else:
-            residuum = [np.NaN for v in resi]
+            residuum = [np.nan for v in resi]
         return corrected_area, isotopologue_fraction, residuum, enrichment
 
     def get_mass_distribution_vector(self):
@@ -671,3 +671,4 @@ def compute_correction_matrix(self):
         else:
             correction_matrix = self._correctionmatrix_combination()
         return correction_matrix
+

isocor/tests/test_correction_process_HighRes.py

@@ -14,6 +14,13 @@
 
 
 @pytest.mark.parametrize("data", [{"formula": "C2H2",
+                                   "resolution_at_400": 1e3,
+                                   "tracer": "13C",
+                                   "v_expected": "[np.nan, np.nan, np.nan]",
+                                   "v_measured": "[0, 0, 0]",
+                                   "correct_NA_tracer": False,
+                                   "tracer_purity": [0.0, 1.0]},
+                                  {"formula": "C2H2",
                                    "resolution_at_400": 1e3,
                                    "tracer": "13C",
                                    "v_expected": "[1., 0., 0.]",

isocor/tests/test_correction_process_LowRes.py

@@ -13,6 +13,12 @@
 # Tests the entire correction process at low resolution
 # (here pXY represents natural abundance of isotope X of element Y)
 @pytest.mark.parametrize("data", [{"formula": "C2H2",
+                                   "tracer": "13C",
+                                   "v_expected": "[np.nan, np.nan, np.nan]",
+                                   "v_measured": "[0, 0, 0]",
+                                   "correct_NA_tracer": False,
+                                   "tracer_purity": [0.0, 1.0]},
+                                  {"formula": "C2H2",
                                    "tracer": "13C",
                                    "v_expected": "[1., 0., 0.]",
                                    "v_measured": "[p1H * p1H, p1H * p2H * 2, p2H * p2H]",