IsoCor 2.2.2__tar.gz → 2.2.3__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (37) hide show
  1. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/PKG-INFO +5 -3
  2. {IsoCor-2.2.2 → isocor-2.2.3}/PKG-INFO +5 -3
  3. {IsoCor-2.2.2 → isocor-2.2.3}/README.md +2 -1
  4. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/__init__.py +1 -1
  5. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/mscorrectors.py +4 -3
  6. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_process_HighRes.py +7 -0
  7. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_process_LowRes.py +6 -0
  8. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocorcli.py +5 -5
  9. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/SOURCES.txt +0 -0
  10. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/dependency_links.txt +0 -0
  11. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/entry_points.txt +0 -0
  12. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/requires.txt +0 -0
  13. {IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/top_level.txt +0 -0
  14. {IsoCor-2.2.2 → isocor-2.2.3}/LICENSE.md +0 -0
  15. {IsoCor-2.2.2 → isocor-2.2.3}/MANIFEST.in +0 -0
  16. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/__main__.py +0 -0
  17. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/base.py +0 -0
  18. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/data/Data_example.tsv +0 -0
  19. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/data/Derivatives.dat +0 -0
  20. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/data/Isotopes.dat +0 -0
  21. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/data/Metabolites.dat +0 -0
  22. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/__init__.py +0 -0
  23. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/conftest.py +0 -0
  24. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_all_cases.py +0 -0
  25. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_matrix_HighRes_resolved.py +0 -0
  26. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_matrix_HighRes_unresolved.py +0 -0
  27. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_matrix_LowRes.py +0 -0
  28. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_factory.py +0 -0
  29. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_isotopic_cluster_HighRes.py +0 -0
  30. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_isotopic_cluster_LowRes.py +0 -0
  31. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_m_min_constant.py +0 -0
  32. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_m_min_orbitrap.py +0 -0
  33. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/__init__.py +0 -0
  34. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocordb.py +0 -0
  35. {IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocorgui.py +0 -0
  36. {IsoCor-2.2.2 → isocor-2.2.3}/pyproject.toml +0 -0
  37. {IsoCor-2.2.2 → isocor-2.2.3}/setup.cfg +0 -0
{IsoCor-2.2.2 → isocor-2.2.3}/IsoCor.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: IsoCor
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- Version: 2.2.2
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+ Version: 2.2.3
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  Summary: IsoCor: Isotope Correction for mass spectrometry labeling experiments
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  Home-page: https://github.com/MetaSys-LISBP/IsoCor/
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  Author: Pierre Millard, Baudoin Délépine, Matthieu Guionnet
@@ -23,13 +23,15 @@ Requires-Dist: scipy>=0.12.1
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  Provides-Extra: testing
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  Requires-Dist: pytest>=7.1.2; extra == "testing"
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  Requires-Dist: tox>=3.25.0; extra == "testing"
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+ Dynamic: license-file
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  # IsoCor - **Iso**tope **Cor**rection for mass spectrometry labeling experiments
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  [![PyPI version](https://badge.fury.io/py/IsoCor.svg)](https://badge.fury.io/py/IsoCor)
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  [![PyPI pyversions](https://img.shields.io/pypi/pyversions/isocor.svg)](https://pypi.python.org/pypi/isocor/)
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- [![Build Status](https://travis-ci.com/MetaSys-LISBP/IsoCor.svg?branch=master)](https://travis-ci.com/MetaSys-LISBP/IsoCor)
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  [![Documentation Status](https://readthedocs.org/projects/isocor/badge/?version=latest)](http://isocor.readthedocs.io/?badge=latest)
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+ [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/isocor/README.html)
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+
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  [![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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{IsoCor-2.2.2 → isocor-2.2.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.4
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  Name: IsoCor
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- Version: 2.2.2
3
+ Version: 2.2.3
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  Summary: IsoCor: Isotope Correction for mass spectrometry labeling experiments
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  Home-page: https://github.com/MetaSys-LISBP/IsoCor/
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  Author: Pierre Millard, Baudoin Délépine, Matthieu Guionnet
@@ -23,13 +23,15 @@ Requires-Dist: scipy>=0.12.1
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23
  Provides-Extra: testing
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  Requires-Dist: pytest>=7.1.2; extra == "testing"
25
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  Requires-Dist: tox>=3.25.0; extra == "testing"
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+ Dynamic: license-file
26
27
 
27
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  # IsoCor - **Iso**tope **Cor**rection for mass spectrometry labeling experiments
28
29
 
29
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  [![PyPI version](https://badge.fury.io/py/IsoCor.svg)](https://badge.fury.io/py/IsoCor)
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  [![PyPI pyversions](https://img.shields.io/pypi/pyversions/isocor.svg)](https://pypi.python.org/pypi/isocor/)
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- [![Build Status](https://travis-ci.com/MetaSys-LISBP/IsoCor.svg?branch=master)](https://travis-ci.com/MetaSys-LISBP/IsoCor)
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  [![Documentation Status](https://readthedocs.org/projects/isocor/badge/?version=latest)](http://isocor.readthedocs.io/?badge=latest)
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+ [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/isocor/README.html)
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+
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  [![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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{IsoCor-2.2.2 → isocor-2.2.3}/README.md RENAMED
@@ -2,8 +2,9 @@
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  [![PyPI version](https://badge.fury.io/py/IsoCor.svg)](https://badge.fury.io/py/IsoCor)
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  [![PyPI pyversions](https://img.shields.io/pypi/pyversions/isocor.svg)](https://pypi.python.org/pypi/isocor/)
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- [![Build Status](https://travis-ci.com/MetaSys-LISBP/IsoCor.svg?branch=master)](https://travis-ci.com/MetaSys-LISBP/IsoCor)
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  [![Documentation Status](https://readthedocs.org/projects/isocor/badge/?version=latest)](http://isocor.readthedocs.io/?badge=latest)
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+ [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/isocor/README.html)
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+
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  [![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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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/__init__.py RENAMED
@@ -5,7 +5,7 @@ for conveniance.
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  """
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  # Version number MUST be maintained here (x.y.z format)
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- __version__ = '2.2.2'
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+ __version__ = '2.2.3'
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  from isocor.mscorrectors import MetaboliteCorrectorFactory
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  from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector
{IsoCor-2.2.2 → isocor-2.2.3}/isocor/mscorrectors.py RENAMED
@@ -240,13 +240,13 @@ class LowResMetaboliteCorrector(LabelledChemical, InterfaceMSCorrector):
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  enrichment = math.fsum(
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  p*i for i, p in enumerate(isotopologue_fraction))/self.formula[self._tracer_el]
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  else:
243
- isotopologue_fraction = [np.NaN for p in corrected_area]
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- enrichment = np.NaN
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+ isotopologue_fraction = [np.nan for p in corrected_area]
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+ enrichment = np.nan
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  sum_m = math.fsum(measurement)
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  if sum_m != 0:
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  residuum = [v/sum_m for v in resi]
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  else:
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- residuum = [np.NaN for v in resi]
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+ residuum = [np.nan for v in resi]
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  return corrected_area, isotopologue_fraction, residuum, enrichment
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  def get_mass_distribution_vector(self):
@@ -671,3 +671,4 @@ class HighResMetaboliteCorrector(LowResMetaboliteCorrector):
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  else:
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  correction_matrix = self._correctionmatrix_combination()
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  return correction_matrix
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+
{IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_process_HighRes.py RENAMED
@@ -14,6 +14,13 @@ import isocor as hrcor
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  @pytest.mark.parametrize("data", [{"formula": "C2H2",
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+ "resolution_at_400": 1e3,
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+ "tracer": "13C",
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+ "v_expected": "[np.nan, np.nan, np.nan]",
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+ "v_measured": "[0, 0, 0]",
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+ "correct_NA_tracer": False,
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+ "tracer_purity": [0.0, 1.0]},
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+ {"formula": "C2H2",
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  "resolution_at_400": 1e3,
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  "tracer": "13C",
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  "v_expected": "[1., 0., 0.]",
{IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/test_correction_process_LowRes.py RENAMED
@@ -13,6 +13,12 @@ import isocor as hrcor
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  # Tests the entire correction process at low resolution
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  # (here pXY represents natural abundance of isotope X of element Y)
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  @pytest.mark.parametrize("data", [{"formula": "C2H2",
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+ "tracer": "13C",
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+ "v_expected": "[np.nan, np.nan, np.nan]",
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+ "v_measured": "[0, 0, 0]",
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+ "correct_NA_tracer": False,
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+ "tracer_purity": [0.0, 1.0]},
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+ {"formula": "C2H2",
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  "tracer": "13C",
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  "v_expected": "[1., 0., 0.]",
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  "v_measured": "[p1H * p1H, p1H * p2H * 2, p2H * p2H]",
{IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocorcli.py RENAMED
@@ -2,6 +2,7 @@ import argparse
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  import isocor as hr
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  import isocor.ui.isocordb
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  import pandas as pd
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+ import numpy as np
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  import io
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  import logging
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  from pathlib import Path
@@ -148,7 +149,6 @@ def process(args):
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  dictMetabolites[label] = None
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  errors['labels'] = errors['labels'] + [label]
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  logger.error("cannot construct {}: {}".format(label, err))
151
- sys.exit(2)
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  logger.info('------------------------------------------------')
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  logger.info('Correcting raw MS data...')
@@ -170,15 +170,15 @@ def process(args):
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  logger.info("{} - {}: processed".format(serie[0], label))
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  except Exception as err:
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  isotopic_inchi = ['']*len(serie[1])
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- valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan]
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- * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan)
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+ valuesCorrected = ([np.nan]*len(serie[1]), [np.nan]
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+ * len(serie[1]), [np.nan]*len(serie[1]), np.nan)
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  logger.error("{} - {}: {}".format(serie[0], label, err))
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  errors['measurements'] = errors['measurements'] + \
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  ["{} - {}".format(serie[0], label)]
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  else:
179
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  isotopic_inchi = ['']*len(serie[1])
180
- valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan]
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- * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan)
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+ valuesCorrected = ([np.nan]*len(serie[1]), [np.nan]
181
+ * len(serie[1]), [np.nan]*len(serie[1]), np.nan)
182
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  errors['measurements'] = errors['measurements'] + \
183
183
  ["{} - {}".format(serie[0], label)]
184
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  logger.error(
{IsoCor-2.2.2 → isocor-2.2.3}/LICENSE.md RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/MANIFEST.in RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/__main__.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/base.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/data/Isotopes.dat RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/__init__.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/tests/conftest.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/__init__.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocordb.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/isocor/ui/isocorgui.py RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/pyproject.toml RENAMED
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{IsoCor-2.2.2 → isocor-2.2.3}/setup.cfg RENAMED
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