Merge pull request #5 from molssi-seamm/cleanup/description

Cleanup/description

packmol_step/__init__.py

@@ -1,15 +1,23 @@
 # -*- coding: utf-8 -*-
 
-"""Top-level package for packmol step."""
-
-__author__ = """Paul Saxe"""
-__email__ = '[email protected]'
-__version__ = '0.1.0'
+"""
+packmol_step
+A step for building fluid boxes using Packmol
+"""
 
 # Bring up the classes so that they appear to be directly in
 # the packmol_step package.
 
-from packmol_step.packmol import PACKMOL  # noqa: F401
-from packmol_step.packmol_parameters import PACKMOL_Parameters  # noqa: F401
-from packmol_step.packmol_step import PACKMOLStep  # noqa: F401
-from packmol_step.tk_packmol import TkPACKMOL  # noqa: F401
+from packmol_step.packmol import Packmol  # noqa: F401
+from packmol_step.packmol_parameters import PackmolParameters  # noqa: F401
+from packmol_step.packmol_step import PackmolStep  # noqa: F401
+from packmol_step.tk_packmol import TkPackmol  # noqa: F401
+
+# Handle versioneer
+from ._version import get_versions
+__author__ = """Paul Saxe"""
+__email__ = '[email protected]'
+versions = get_versions()
+__version__ = versions['version']
+__git_revision__ = versions['full-revisionid']
+del get_versions, versions

packmol_step/packmol.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""A node or step for PACKMOL in a seamm"""
+"""A node or step for Packmol in a seamm"""
 
 import logging
 import mendeleev
@@ -18,24 +18,47 @@
 printer = printing.getPrinter('packmol')
 
 
-class PACKMOL(seamm.Node):
+class Packmol(seamm.Node):
 
     def __init__(self, flowchart=None, extension=None):
-        '''Setup the main PACKMOL step
+        '''Setup the main Packmol step
 
         Keyword arguments:
         '''
-        logger.debug('Creating PACKMOL {}'.format(self))
+        logger.debug('Creating Packmol {}'.format(self))
 
         super().__init__(
-            flowchart=flowchart, title='PACKMOL', extension=extension
+            flowchart=flowchart, title='Packmol', extension=extension
         )
 
-        self.parameters = packmol_step.PACKMOL_Parameters()
+        self.parameters = packmol_step.PackmolParameters()
 
-    def description(self, P):
-        """Prepare information about what this node will do
+    @property
+    def version(self):
+        """The semantic version of this module.
         """
+        return packmol_step.__version__
+
+    @property
+    def git_revision(self):
+        """The git version of this module.
+        """
+        return packmol_step.__git_revision__
+
+    def description_text(self, P=None):
+        """Return a short description of this step.
+
+        Return a nicely formatted string describing what this step will
+        do.
+
+        Keyword arguments:
+            P: a dictionary of parameter values, which may be variables
+                or final values. If None, then the parameters values will
+                be used as is.
+        """
+
+        if not P:
+            P = self.parameters.values_to_dict()
 
         text = 'Creating a cubic supercell '
         if P['method'][0] == '$':
@@ -72,26 +95,10 @@ def description(self, P):
                 "Don't recognize the submethod {}".format(P['submethod'])
             )
 
-        return text
-
-    def describe(self, indent='', json_dict=None):
-        """Write out information about what this node will do
-        If json_dict is passed in, add information to that dictionary
-        so that it can be written out by the controller as appropriate.
-        """
-
-        next_node = super().describe(indent, json_dict)
-
-        P = self.parameters.values_to_dict()
-
-        text = self.description(P)
-
-        job.job(__(text, **P, indent=self.indent + '    '))
-
-        return next_node
+        return self.header + '\n' + __(text, **P, indent=4*' ').__str__()
 
     def run(self):
-        """Run a PACKMOL building step
+        """Run a Packmol building step
         """
 
         next_node = super().run(printer)
@@ -104,8 +111,7 @@ def run(self):
         logger.info('submethod = {}'.format(P['submethod']))
 
         # Print what we are doing
-        text = self.description(P)
-        printer.important(__(text, **P, indent='    '))
+        printer.important(__(self.description_text(P), indent=self.indent))
 
         size = None
         volume = None
@@ -197,7 +203,7 @@ def run(self):
         n_atoms = len(atoms['elements'])
         if n_atoms_per_molecule * n_molecules != n_atoms:
             raise RuntimeError(
-                'Serious problem in PACKMOL with the number of atoms'
+                'Serious problem in Packmol with the number of atoms'
                 ' {} != {}'.format(
                     n_atoms, n_atoms_per_molecule * n_molecules
                 )
@@ -237,9 +243,10 @@ def run(self):
         string += ' for a total of {n_atoms} atoms in the cell'
         string += ' and a density of {density:.5~P}.'
         printer.important(__(string, indent='    ', **tmp))
+        printer.important('')
 
         logger.log(
-            0, 'Structure created by PACKMOL:\n\n' +
+            0, 'Structure created by Packmol:\n\n' +
             pprint.pformat(data.structure)
         )
 
@@ -258,8 +265,8 @@ def calculate(
         """Work out the other variables given any two independent ones"""
 
         if data.structure is None:
-            logger.error('PACKMOL run(): there is no structure!')
-            raise RuntimeError('PACKMOL run(): there is no structure!')
+            logger.error('Packmol run(): there is no structure!')
+            raise RuntimeError('Packmol run(): there is no structure!')
 
         elements = data.structure['atoms']['elements']
         n_atoms_per_molecule = len(elements)

packmol_step/packmol_parameters.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Control parameters for PACKMOL, currently for packing fluids
+"""Control parameters for Packmol, currently for packing fluids
 """
 
 import logging
@@ -8,8 +8,8 @@
 logger = logging.getLogger(__name__)
 
 
-class PACKMOL_Parameters(seamm.Parameters):
-    """The control parameters for PACKMOL packing fluids
+class PackmolParameters(seamm.Parameters):
+    """The control parameters for Packmol packing fluids
     """
     methods = {
         'size of cubic cell': (
@@ -76,7 +76,7 @@ class PACKMOL_Parameters(seamm.Parameters):
             "description": "Gap around cell:",
             "help_text":
                 (
-                    "Since PACKMOL does not support periodic systems "
+                    "Since Packmol does not support periodic systems "
                     "we will build a box with this gap around the "
                     "atoms, then make it periodic. The gap ensures "
                     "that molecules at the boundary do not hit images"
@@ -138,6 +138,6 @@ def __init__(self, defaults={}, data=None):
         parameters given in the class"""
 
         super().__init__(
-            defaults={**PACKMOL_Parameters.parameters, **defaults},
+            defaults={**PackmolParameters.parameters, **defaults},
             data=data
         )

packmol_step/packmol_step.py

@@ -8,11 +8,11 @@
 import packmol_step
 
 
-class PACKMOLStep(object):
+class PackmolStep(object):
     my_description = {
-        'description': 'An interface for PACKMOL',
+        'description': 'An interface for Packmol',
         'group': 'Building',
-        'name': 'PACKMOL'
+        'name': 'Packmol'
     }
 
     def __init__(self, flowchart=None, gui=None):
@@ -25,12 +25,12 @@ def __init__(self, flowchart=None, gui=None):
     def description(self):
         """Return a description of what this extension does
         """
-        return PACKMOLStep.my_description
+        return PackmolStep.my_description
 
     def create_node(self, flowchart=None, **kwargs):
         """Return the new node object"""
-        return packmol_step.PACKMOL(flowchart=flowchart, **kwargs)
+        return packmol_step.Packmol(flowchart=flowchart, **kwargs)
 
     def create_tk_node(self, canvas=None, **kwargs):
         """Return the graphical Tk node object"""
-        return packmol_step.TkPACKMOL(canvas=canvas, **kwargs)
+        return packmol_step.TkPackmol(canvas=canvas, **kwargs)

packmol_step/tk_packmol.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""The graphical part of a PACKMOL step"""
+"""The graphical part of a Packmol step"""
 
 import logging
 import seamm
@@ -13,8 +13,8 @@
 logger = logging.getLogger(__name__)
 
 
-class TkPACKMOL(seamm.TkNode):
-    """Graphical interface for using PACKMOL for fluid boxes
+class TkPackmol(seamm.TkNode):
+    """Graphical interface for using Packmol for fluid boxes
     """
 
     def __init__(
@@ -50,7 +50,7 @@ def create_dialog(self):
             self.toplevel,
             buttons=('OK', 'Help', 'Cancel'),
             master=self.toplevel,
-            title='Edit PACKMOL step',
+            title='Edit Packmol step',
             command=self.handle_dialog
         )
         self.dialog.withdraw()
@@ -76,7 +76,7 @@ def create_dialog(self):
         self.reset_dialog()
 
     def reset_dialog(self, widget=None):
-        methods = packmol_step.PACKMOL_Parameters.methods
+        methods = packmol_step.Packmol_Parameters.methods
 
         method = self['method'].get()
         submethod = self['submethod'].get()
@@ -154,7 +154,7 @@ def right_click(self, event):
         self.popup_menu.tk_popup(event.x_root, event.y_root, 0)
 
     def edit(self):
-        """Present a dialog for editing the PACKMOL input
+        """Present a dialog for editing the Packmol input
         """
         if self.dialog is None:
             self.create_dialog()

setup.py

@@ -85,10 +85,10 @@
     ],
     entry_points={
         'org.molssi.seamm': [
-            'PACKMOL = packmol_step:PACKMOLStep',
+            'Packmol = packmol_step:PackmolStep',
         ],
         'org.molssi.seamm.tk': [
-            'PACKMOL = packmol_step:PACKMOLStep',
+            'Packmol = packmol_step:PackmolStep',
         ],
     }
 )