Save particle state in a dict (Issue #3916)

[mili1247]

#3916

Add functions:
ParticleHandle.to_dict()
ParticleSlice.to_dict()

Description of changes:
Returns the particles attributes as a dictionary, such that it can be used to save the particle data and recover it by using

p = system.part.add(...)
particle_dict = p.to_dict()
system.part.add(particle_dict)

Codes are mainly written by @RiccardoFrenner

[espresso-ci]

Your pull request does not meet our code formatting rules. Specifically, I suggest you make the following changes:

diff --git a/src/python/espressomd/particle_data.pyx b/src/python/espressomd/particle_data.pyx
index 281a2d5ed..d6afb6b02 100644
--- a/src/python/espressomd/particle_data.pyx
+++ b/src/python/espressomd/particle_data.pyx
@@ -55,9 +55,8 @@ cdef class ParticleHandle:
 
     cdef int update_particle_data(self) except -1:
         self.particle_data = &get_particle_data(self._id)
-        
-    def to_dict(self):
 
+    def to_dict(self):
         """
         Returns the particle's attributes as a dictionary.
         It includes the content of \`\`particle_attributes\`\`, minus a few exceptions:
@@ -179,7 +178,7 @@ cdef class ParticleHandle:
 
         def __get__(self):
             self.update_particle_data()
-            return make_array_locked(unfolded_position(< Vector3d > self.particle_data.r.p, < Vector3i > self.particle_data.l.i, box_geo.length()))
+            return make_array_locked(unfolded_position( < Vector3d > self.particle_data.r.p, < Vector3i > self.particle_data.l.i, box_geo.length()))
 
     property pos_folded:
         """
@@ -1701,17 +1700,16 @@ class ParticleSlice(_ParticleSliceImpl):
             raise AttributeError(
                 f"ParticleHandle does not have the attribute {name}.")
         super().__setattr__(name, value)
-        
-    def to_dict(self):
 
+    def to_dict(self):
         """
         Returns the particles attributes as a dictionary, such that it can
         be used to save the particle data and recover it easily using
-        
+
         >>> p = system.part.add(...)
         >>> particle_dict = p.to_dict()
         >>> system.part.add(particle_dict)
-        
+
         It includes the content of \`\`particle_attributes\`\`, minus a few exceptions:
 
         - :attr:\`~ParticleHandle.dip\`, :attr:\`~ParticleHandle.director\`:
@@ -1723,7 +1721,7 @@ class ParticleSlice(_ParticleSliceImpl):
 
         odict = {}
         key_list = [p.id for p in self]
-        
+
         for particle_number in key_list:
             pdict = ParticleHandle(particle_number).to_dict()
             for p_key, p_value in pdict.items():
@@ -1768,7 +1766,7 @@ cdef class ParticleList:
         - :attr:\`~ParticleHandle.image_box\`, :attr:\`~ParticleHandle.node\`
 
         """
-        
+
         odict = {}
         for p in self:
             pdict = p.to_dict()
diff --git a/testsuite/python/particle_to_dict.py b/testsuite/python/particle_to_dict.py
index ce45cdc82..1a4b60e07 100644
--- a/testsuite/python/particle_to_dict.py
+++ b/testsuite/python/particle_to_dict.py
@@ -3,17 +3,22 @@ import unittest_decorators as utx
 import numpy as np
 import espressomd
 
+
 class ParticleDictionaryTest(ut.TestCase):
     box_l = 30.
-    system = espressomd.System(box_l = 3 * [box_l])
+    system = espressomd.System(box_l=3 * [box_l])
 
     def test(self):
-        p = self.system.part.add(pos = np.random.uniform(size = (10,3)) * self.box_l)
+        p = self.system.part.add(
+            pos=np.random.uniform(
+                size=(
+                    10, 3)) * self.box_l)
         pp = str(p)
         pdict = p.to_dict()
         p.remove()
         self.system.part.add(pdict)
         self.assertEqual(str(self.system.part.select()), pp)
 
+
 if __name__ == "__main__":
     ut.main()

To apply these changes, please do one of the following:

• You can download a patch with my suggested changes here, inspect it and make changes manually.
• You can directly apply it to your repository by running curl https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/jobs/265985/artifacts/raw/style.patch | git apply -.
• You can run maintainer/CI/fix_style.sh to automatically fix your coding style. This is the same command that I have executed to generate the patch above, but it requires certain tools to be installed on your computer.

You can run gitlab-runner exec docker style afterwards to check if your changes worked out properly.

Please note that there are often multiple ways to correctly format code. As I am just a robot, I sometimes fail to identify the most aesthetically pleasing way. So please look over my suggested changes and adapt them where the style does not make sense.

[espresso-ci]

Your pull request does not meet our code style rules. Pylint summary:

************* Module particle_to_dict
testsuite/python/particle_to_dict.py:2:0: W0611: Unused unittest_decorators imported as utx (unused-import)

You can generate these warnings with maintainer/CI/fix_style.sh. This is the same command that I have executed to generate the log above.