orto 1.7.1__tar.gz → 1.8.1__tar.gz

{orto-1.7.1 → orto-1.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.7.1
+Version: 1.8.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.8.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.8.1'

{orto-1.7.1 → orto-1.8.1}/orto/cli.py

@@ -820,8 +820,11 @@ def plot_abs_func(uargs, save_data_only=False):
 
     # Find unique name from multiple file names
     if len(uargs.output_file) > 1:
-        base_names = [of.stem for of in uargs.output_file]
-        unique_names = ut.find_unique_substring(base_names)
+        if uargs.unique_names:
+            base_names = [of.stem for of in uargs.output_file]
+            unique_names = ut.find_unique_substring(base_names)
+        else:
+            unique_names = [of.stem for of in uargs.output_file]
         legend = True
     else:
         legend = False
@@ -928,6 +931,10 @@ def plot_abs_func(uargs, save_data_only=False):
         else:
             x_max = uargs.xlim[1]
 
+        # Trim transitions to a specific number of states if requested
+        if uargs.trim_transitions is not None:
+            abs_data.trim_to_n(uargs.trim_transitions)
+
         # Generate spectrum
         abs_data.generate_spectrum(
             fwhm=uargs.linewidth,
@@ -2016,6 +2023,28 @@ def read_args(arg_list=None):
         )
     )
 
+    gen_abs.add_argument(
+        '--unique_names',
+        action='store_true',
+        default=False,
+        help=(
+            'Attempt to shorten file names in plot legend\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_abs.add_argument(
+        '--trim_transitions',
+        '-tt',
+        type=int,
+        default=None,
+        help=(
+            'Trim to first n transitions\n'
+            'where n is an integer\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_subprog = all_subparsers.add_parser(
         'plot',
         description='Plot data from orca file',
@@ -2159,6 +2188,28 @@ def read_args(arg_list=None):
         )
     )
 
+    plot_abs.add_argument(
+        '--unique_names',
+        action='store_true',
+        default=False,
+        help=(
+            'Attempt to shorten file names in plot legend\n'
+            'Default: %(default)s'
+        )
+    )
+
+    plot_abs.add_argument(
+        '--trim_transitions',
+        '-tt',
+        type=int,
+        default=None,
+        help=(
+            'Trim to first n transitions\n'
+            'where n is an integer\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_xes = plot_parser.add_parser(
         'xes',
         description='Plots XES from CI calculation output',

{orto-1.7.1 → orto-1.8.1}/orto/data.py

@@ -181,6 +181,27 @@ class AbsorptionData():
         self._spectrum = spectrum
         return
 
+    def trim_to_n(self, n_transitions: int) -> None:
+        '''
+        Trims data to given number of transitions
+
+        Parameters
+        ----------
+        n_transitions: int
+            Number of transitions to keep from the start of the data
+
+        Returns
+        -------
+        None
+        '''
+
+        self.energies = self.energies[:n_transitions]
+        self.osc_strengths = self.osc_strengths[:n_transitions]
+
+        self.spectrum = None
+
+        return
+
     @classmethod
     def from_extractor(cls, extractor: oe.AbsorptionExtractor,
                        remove_zero_osc: float = 1E-4) -> list['AbsorptionData']: # noqa

{orto-1.7.1 → orto-1.8.1}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.7.1
+Version: 1.8.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.7.1 → orto-1.8.1}/setup.py

@@ -8,7 +8,7 @@ Please see the `orto` documentation for more details.
 
 # DO NOT EDIT THIS NUMBER!
 # IT IS AUTOMATICALLY CHANGED BY python-semantic-release
-__version__ = '1.7.1'
+__version__ = '1.8.1'
 
 setuptools.setup(
     name='orto',

orto-1.7.1/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.7.1'