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Merged
pierremillard merged 3 commits into from
Apr 25, 2025
Merged

Dev to 2.2.3 #46

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d51530c
fix: np.NaN to np.nan in mscorrectors.py
pierremillard Apr 25, 2025
c03609b
remove travis badge and add bioconda badge in readme.md
pierremillard Apr 25, 2025
357008a
remove new class for future version
pierremillard Apr 25, 2025
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3 changes: 2 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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/)

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2 changes: 1 addition & 1 deletion isocor/__init__.py
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Expand Up @@ -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
7 changes: 4 additions & 3 deletions isocor/mscorrectors.py
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Expand Up @@ -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):
Expand Down Expand Up @@ -671,3 +671,4 @@ def compute_correction_matrix(self):
else:
correction_matrix = self._correctionmatrix_combination()
return correction_matrix

7 changes: 7 additions & 0 deletions isocor/tests/test_correction_process_HighRes.py
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Expand Up @@ -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.]",
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6 changes: 6 additions & 0 deletions isocor/tests/test_correction_process_LowRes.py
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Expand Up @@ -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]",
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