Merge pull request #5 from MetaSys-LISBP/dev

v2.0.5 to fix #4

doc/conf.py

@@ -57,7 +57,7 @@
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
 # Do not forget to update PyPi (setup.py) version
-release = '2.0.4'
+release = '2.0.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

isocor/__init__.py

@@ -4,7 +4,7 @@
 for conveniance.
 """
 
-__version__ = '2.0.4'
+__version__ = '2.0.5'
 
 from isocor.mscorrectors import MetaboliteCorrectorFactory
 from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector

isocor/ui/isocordb.py

@@ -60,7 +60,7 @@ def registerIsopotes(self, isotopesfile=Path("Isotopes.dat")):
         if not isotopesfile.is_file():
             raise ValueError(
                 "Isotopes database not found in:\n'{}'.".format(isotopesfile))
-        with open(isotopesfile, 'r') as fp:
+        with open(str(isotopesfile), 'r') as fp:  # str for compatibility with Python3.5
             self.dfIsotopes = pd.read_csv(fp)
         for i in ['element', 'mass', 'abundance']:
             if i not in self.dfIsotopes.columns:
@@ -79,7 +79,7 @@ def registerIsopotes(self, isotopesfile=Path("Isotopes.dat")):
             except:
                 raise ValueError("Error in 'Isotopes.dat' at line {}:\nabundance={!r}".format(i+2, item))
         # reload file
-        with open(isotopesfile, 'r') as fp:
+        with open(str(isotopesfile), 'r') as fp:
             self.dfIsotopes = pd.read_csv(
                  fp, converters={'mass': Decimal, 'abundance': np.float64})
         self._stripColNames(self.dfIsotopes)
@@ -93,7 +93,7 @@ def registerDerivativesDB(self, derivativesfile=Path("Derivatives.dat")):
         if not derivativesfile.is_file():
             raise ValueError(
                 "Derivatives database not found in:\n'{}'.".format(derivativesfile))
-        with open(derivativesfile, 'r') as fp:
+        with open(str(derivativesfile), 'r') as fp:
             self.dfDerivatives = pd.read_csv(fp, delimiter='\t')
         for i in ['name', 'formula']:
             if i not in self.dfDerivatives.columns:
@@ -105,7 +105,7 @@ def registerMetabolitesDB(self, metabolitesfile=Path("Metabolites.dat")):
         if not metabolitesfile.is_file():
             raise ValueError(
                 "Metabolites database not found in:\n'{}'.".format(metabolitesfile))
-        with open(metabolitesfile, 'r') as fp:
+        with open(str(metabolitesfile), 'r') as fp:
             self.dfMetabolites = pd.read_csv(fp, delimiter='\t')
         for i in ['name', 'formula']:
             if i not in self.dfMetabolites.columns:
@@ -116,7 +116,7 @@ def registerMetabolitesDB(self, metabolitesfile=Path("Metabolites.dat")):
     def registerDatafile(self, datafile=Path("mydata.tsv")):
         if not Path(datafile).is_file():
             raise ValueError("No data file selected.")
-        with open(datafile, 'r') as fp:
+        with open(str(datafile), 'r') as fp:
             self.dfDatafile = pd.read_csv(fp, delimiter='\t')
         for i in ['sample', 'metabolite', 'derivative', 'area', 'isotopologue']:
             if i not in self.dfDatafile.columns:

isocor/ui/isocorgui.py

@@ -174,7 +174,7 @@ def process(self):
         formatter = logging.Formatter(
             '%(asctime)s - %(name)s - %(levelname)s - %(message)s', "%Y-%m-%d %H:%M:%S")
         log_file = Path(self.varOutputPath.get()).joinpath(fin_base + '.log')
-        file_handler = logging.FileHandler(log_file, mode='w+')
+        file_handler = logging.FileHandler(str(log_file), mode='w+')
         file_handler.setLevel(self.log_level)
         file_handler.setFormatter(formatter)
         self.logger.addHandler(file_handler)

setup.py

@@ -7,7 +7,7 @@
 
 setuptools.setup(
     name="IsoCor",
-    version="2.0.4",
+    version="2.0.5",
     author="Pierre Millard, Baudoin Delépine, Matthieu Guionnet",
     author_email="[email protected]",
     description="IsoCor: Isotope Correction for mass spectrometry labeling experiments",