Add functionality for specifying the format string when exporting data, bump version number to 0.8.4.1

Author: exe0cdc

psctb/analyse/_ratechar.py

@@ -206,7 +206,7 @@ def save_session(self, file_name=None):
         numpy.savez(file_name, **to_save)
 
 
-    def save_results(self, folder=None, separator=',', ):
+    def save_results(self, folder=None, separator=',',format='%f'):
         base_folder = folder
         for species in self.mod.species:
             if folder:
@@ -424,7 +424,7 @@ def _make_prc_summary(self):
 
         self._prc_summary = prcs
 
-    def save_summary(self, file_name=None, separator=','):
+    def save_summary(self, file_name=None, separator=',',fmt='%f'):
         file_name = modeltools.get_file_path(working_dir=self._working_dir,
                                              internal_filename='mca_summary',
                                              fmt='csv',
@@ -440,11 +440,12 @@ def save_summary(self, file_name=None, separator=','):
                        names=keys,
                        header=['Value'],
                        fname=file_name,
-                       sep=separator)
+                       sep=separator,
+                       format=fmt)
         except IOError as e:
             print e.strerror
 
-    def save_flux_results(self, file_name=None, separator=','):
+    def save_flux_results(self, file_name=None, separator=',',fmt='%f'):
         file_name = modeltools.get_file_path(working_dir=self._working_dir,
                                              internal_filename='flux_results',
                                              fmt='csv',
@@ -462,15 +463,17 @@ def save_flux_results(self, file_name=None, separator=','):
                        names=None,
                        header=column_names,
                        fname=file_name,
-                       sep=separator)
+                       sep=separator,
+                       format=fmt)
         except IOError as e:
             print e.strerror
 
     def save_coefficient_results(self,
                                  coefficient,
                                  file_name=None,
                                  separator=',',
-                                 folder=None):
+                                 folder=None,
+                                 fmt='%f'):
         assert_message = 'coefficient must be one of "ec", "rc" or "prc"'
 
         assert coefficient in ['rc', 'ec', 'prc'], assert_message
@@ -493,32 +496,34 @@ def save_coefficient_results(self,
                        names=None,
                        header=new_names,
                        fname=file_name,
-                       sep=separator)
+                       sep=separator,
+                       format=fmt)
         except IOError as e:
             print e.strerror
 
     # TODO fix this method so that folder is a parameter only her
-    def save_all_results(self, folder=None, separator=','):
+    def save_all_results(self, folder=None, separator=',',fmt='%f'):
         if not folder:
             folder = self._working_dir
 
         file_name = modeltools.get_file_path(working_dir=folder,
                                              internal_filename='flux_results',
                                              fmt='csv')
-        self.save_flux_results(separator=separator, file_name=file_name)
+        self.save_flux_results(separator=separator, file_name=file_name,fmt=fmt)
 
         file_name = modeltools.get_file_path(working_dir=folder,
                                              internal_filename='mca_summary',
                                              fmt='csv')
-        self.save_summary(separator=separator, file_name=file_name)
+        self.save_summary(separator=separator, file_name=file_name, fmt=fmt)
         for each in ['ec', 'rc', 'prc']:
             base_name = each + '_results'
             file_name = modeltools.get_file_path(working_dir=folder,
                                                  internal_filename=base_name,
                                                  fmt='csv')
             self.save_coefficient_results(coefficient=each,
                                           separator=separator,
-                                          file_name=file_name)
+                                          file_name=file_name,
+                                          fmt=fmt)
 
     def _min_max_setup(self):
         # Negative minimum linear values mean nothing

psctb/analyse/_symca/_symca.py

@@ -288,7 +288,7 @@ def load_session(self, file_name=None):
         for key, value in cc_containers.iteritems():
             setattr(self, key, value)
 
-    def save_results(self, file_name=None, separator=','):
+    def save_results(self, file_name=None, separator=',',fmt='%.9f'):
         file_name = get_file_path(working_dir=self._working_dir,
                                   internal_filename='cc_summary',
                                   fmt='csv',
@@ -348,9 +348,9 @@ def save_results(self, file_name=None, separator=','):
         try:
             savetxt(fname=file_name,
                     X=X,
-                    header=','.join(head),
+                    header=separator.join(head),
                     delimiter=separator,
-                    fmt=['%s', '%.9f', '%s', '%s'],)
+                    fmt=['%s', fmt, '%s', '%s'],)
 
         except IOError as e:
             print e.strerror

psctb/analyse/_thermokin.py

@@ -166,7 +166,7 @@ def _populate_ec_results(self):
         for rate_eqn in self.reaction_results.itervalues():
             self.ec_results.update(rate_eqn.ec_results)
 
-    def save_results(self, file_name=None, separator=','):
+    def save_results(self, file_name=None, separator=',',fmt='%.9f'):
         file_name = get_file_path(working_dir=self._working_dir,
                                   internal_filename='tk_summary',
                                   fmt='csv',
@@ -208,9 +208,9 @@ def save_results(self, file_name=None, separator=','):
         try:
             savetxt(fname=file_name,
                     X=X,
-                    header=','.join(head),
+                    header=separator.join(head),
                     delimiter=separator,
-                    fmt=['%s', '%.9f', '%s', '%s'], )
+                    fmt=['%s', fmt, '%s', '%s'], )
 
         except IOError as e:
             print e.strerror

psctb/utils/plotting/_plotting.py

@@ -515,7 +515,7 @@ def plot(self):
 
         return scan_fig
 
-    def save_results(self, file_name=None, separator=','):
+    def save_results(self, file_name=None, separator=',',fmt='%f'):
         """
         Saves data stores in current instance of ``Data2D`` as a comma
         separated file.
@@ -530,12 +530,8 @@ def save_results(self, file_name=None, separator=','):
         separator : str, Optional (Default : ',')
             The symbol which should be used to separate values in the output
             file.
-        folder : str, Optional (Default : None)
-            The folder under which the file should be saved. Only comes into
-            consideration if file_name is None. If None the file will be saved
-            under the the folder specified in the ``self._working_dir`` field,
-            which itself is determined by the ``analysis_method`` parameter of
-            __init__.
+        format : str, Optional (Default : '%f')
+            Format for the data.
         """
         file_name = modeltools.get_file_path(working_dir=self._working_dir,
                                              internal_filename=self._fname,
@@ -551,7 +547,8 @@ def save_results(self, file_name=None, separator=','):
                        names=None,
                        header=column_names,
                        fname=file_name,
-                       sep=separator)
+                       sep=separator,
+                       format=fmt)
         except IOError as e:
             print e.strerror
 

setup.py

@@ -4,7 +4,7 @@
 
 setup(
     name='PyscesToolbox',
-    version='0.8.4',
+    version='0.8.4.1',
     packages=packages,
     url='https://github.com/PySCeS/PyscesToolbox',
     license='',