fixed smaller formatting issues in mesa_pd

python/mesa_pd/Module.py

@@ -2,7 +2,6 @@
 
 from pathlib import Path
 import shutil
-import os
 
 
 class Module:
@@ -32,14 +31,14 @@ class Module:
     def rename(self):
         for filename in (f for f in self.context['module_path'].glob('**/*') if f.is_file()):
             filedata = None
-            #print(f'renaming module name: {filename}')
+            # print(f'renaming module name: {filename}')
             with open(filename, encoding="utf-8") as fin:
-               filedata = fin.read()
+                filedata = fin.read()
 
             filedata = filedata.replace('mesa_pd', self.context['name'])
 
             with open(filename, 'w', encoding="utf-8") as fout:
-               fout.write(filedata)
+                fout.write(filedata)
 
     def generate(self, folder_check=True):
         print(f"This operation will overwrite the content of: {self.context['module_path']}")

python/mesa_pd/__init__.py

 from .Module import Module
 
-__all__ = ['Module']
+__all__ = ['Module']
\ No newline at end of file

python/mesa_pd/data/ContactHistory.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import TerminalColor, find, generate_file
 
 
@@ -25,7 +24,7 @@ class ContactHistory():
 
     def add_property(self, name, type, defValue=""):
         prop = find(lambda x: x['name'] == name, self.context['properties'])
-        if (prop == None):
+        if (prop is None):
             # print(f"{TerminalColor.GREEN} creating property: {name} {TerminalColor.DEFAULT}")
             self.context['properties'].append(create_contact_history_property(name, type, defValue=defValue))
         else:
@@ -54,8 +53,7 @@ class ContactHistory():
         print("=" * 90)
 
     def generate(self, module):
-        ctx = {}
-        ctx['module'] = module
+        ctx = {'module': module}
         ctx.update(self.context)
 
         generate_file(module['module_path'], 'data/ContactHistory.templ.h', ctx, filename='data/ContactHistory.h')

python/mesa_pd/data/ContactStorage.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import TerminalColor, find, generate_file
 
 
@@ -26,7 +25,7 @@ class ContactStorage():
 
     def add_property(self, name, type, defValue=""):
         prop = find(lambda x: x['name'] == name, self.context['properties'])
-        if (prop == None):
+        if (prop is None):
             # print(f"{TerminalColor.GREEN} creating property: {name} {TerminalColor.DEFAULT}")
             self.context['properties'].append(create_contact_storage_property(name, type, defValue=defValue))
         else:
@@ -55,8 +54,7 @@ class ContactStorage():
         print("=" * 90)
 
     def generate(self, module):
-        ctx = {}
-        ctx['module'] = module
+        ctx = {'module': module}
         ctx.update(self.context)
 
         generate_file(module['module_path'], 'data/ContactStorage.templ.h', ctx, filename='data/ContactStorage.h')

python/mesa_pd/data/LinkedCells.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import generate_file
 
 

python/mesa_pd/data/ParticleStorage.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import find, TerminalColor, generate_file
 
 
@@ -27,8 +26,8 @@ def create_particle_property(name, type, access="grs", defValue="", syncMode="AL
     """
 
     if (type == 'bool'):
-        raise RuntimeError(f"Due to flaws in the implementation of std::vector<bool>, bool is not supported as a "
-                           f"property type! Please use char instead.")
+        raise RuntimeError("Due to flaws in the implementation of std::vector<bool>, bool is not supported as a "
+                           "property type! Please use char instead.")
 
     # sort access specifier and remove duplicates
     foo = "".join(sorted(access))
@@ -65,7 +64,7 @@ class ParticleStorage():
 
     def add_property(self, name, type, access="grs", defValue="", syncMode="ALWAYS"):
         prop = find(lambda x: x['name'] == name, self.context['properties'])
-        if (prop == None):
+        if (prop is None):
             # print(f"{TerminalColor.GREEN} creating particle property: {name} {TerminalColor.DEFAULT}")
             self.context['properties'].append(
                 create_particle_property(name, type, access=access, defValue=defValue, syncMode=syncMode))

python/mesa_pd/data/ShapeStorage.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import generate_file
 
 

python/mesa_pd/data/SparseLinkedCells.py

 # -*- coding: utf-8 -*-
 
-import numpy as np
 from ..utility import generate_file
 
 

python/mesa_pd/data/__init__.py

@@ -11,4 +11,5 @@ __all__ = ['ContactHistory',
            'ContactStorage',
            'LinkedCells',
            'ParticleStorage',
+           'ShapeStorage',
            'SparseLinkedCells']

python/mesa_pd/kernel/VelocityVerlet.py

@@ -5,7 +5,7 @@ from mesa_pd.utility import generate_file
 
 
 class VelocityVerlet:
-    def __init__(self, integrate_rotation = True):
+    def __init__(self, integrate_rotation=True):
         self.context = {'bIntegrateRotation': integrate_rotation, 'interface': []}
         self.context['interface'].append(create_access("position", "walberla::mesa_pd::Vec3", access="gs"))
         self.context['interface'].append(create_access("linearVelocity", "walberla::mesa_pd::Vec3", access="gs"))

python/mesa_pd/mpi/Notifications.py

@@ -2,19 +2,20 @@
 
 from ..utility import generate_file
 
+
 class Notifications:
-   def __init__(self, particle_storage):
-      self.ps = particle_storage
+    def __init__(self, particle_storage):
+        self.ps = particle_storage
 
-   def generate(self, module):
-      ctx = {'module': module, 'particle' : self.ps.get_context()}
+    def generate(self, module):
+        ctx = {'module': module, 'particle': self.ps.get_context()}
 
-      generate_file(module['module_path'], 'mpi/notifications/ParseMessage.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleCopyNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleGhostCopyNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/NewGhostParticleNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleMigrationNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleRemoteMigrationNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleRemovalInformationNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleRemovalNotification.templ.h', ctx)
-      generate_file(module['module_path'], 'mpi/notifications/ParticleUpdateNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParseMessage.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleCopyNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleGhostCopyNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/NewGhostParticleNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleMigrationNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleRemoteMigrationNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleRemovalInformationNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleRemovalNotification.templ.h', ctx)
+        generate_file(module['module_path'], 'mpi/notifications/ParticleUpdateNotification.templ.h', ctx)

python/mesa_pd/mpi/PropertyNotification.py

@@ -9,7 +9,7 @@ class PropertyNotification:
 
     def add_property(self, name, type, reset_value):
         prop = find(lambda x: x['name'] == name, self.context['properties'])
-        if (prop == None):
+        if (prop is None):
             self.context['properties'].append({'name': name, 'type': type, 'resetValue': reset_value})
         else:
             if not (prop['type'] == type and prop['name'] == name and prop['resetValue'] == reset_value):

python/mesa_pd/mpi/__init__.py

@@ -15,6 +15,7 @@ from .SyncNextNeighborsNoGhosts import SyncNextNeighborsNoGhosts
 __all__ = ['BroadcastProperty',
            'ClearGhostOwnerSync',
            'ClearNextNeighborSync',
+           'Notifications',
            'PropertyNotification',
            'ReduceContactHistory',
            'ReduceProperty',

python/mesa_pd/utility.py

@@ -31,7 +31,7 @@ def get_jinja_environment():
 
 
 def generate_file(path, template, context={}, filename=None):
-    if filename == None:
+    if filename is None:
         filename = template.replace(".templ", "")
     env = get_jinja_environment()
     print(f"generating: {(path / filename)}")