Fix broken Sphinx formatting

Inconsistent indentation can cause issues in recent Sphinx versions
(2.4.0+), e.g. `"""Line1\n  Line2"""` (with 2 leading spaces) can
cause an `Unexpected section title` error; correct formats are
`"""Line1\nLine2"""` and `"""\nLine1\nLine2"""` (numpydoc).

Bullet lists must have the same level of indentation as the
preceding paragraph. Adding one extra indentation on a bullet
list causes it to be wrapped inside a <blockquote> HTML tag.

src/python/espressomd/cluster_analysis.py

@@ -136,16 +136,16 @@ class Clusters:
 
     """Access to the clusters in the cluster structure.
 
-       Access is as follows:
+    Access is as follows:
 
-       * Number of clusters: len(clusters)
-       * Access a cluster via its id: clusters[id]
-       * Iterate over clusters::
+    * Number of clusters: len(clusters)
+    * Access a cluster via its id: clusters[id]
+    * Iterate over clusters::
 
-            for c in clusters:
+          for c in clusters:
 
-         where c will be a tuple containing the cluster id and the cluster object
-     """
+      where c will be a tuple containing the cluster id and the cluster object
+    """
 
     def __init__(self, cluster_structure):
         self.cluster_structure = cluster_structure

src/python/espressomd/io/mpiio.py

@@ -38,14 +38,14 @@ def write(self, prefix=None, positions=False, velocities=False,
         Outputs binary data using MPI-IO to several files starting with prefix.
         Suffixes are:
 
-            - head: Information about fields that are dumped,
-            - pref: Information about processes: 1 int per process,
-            - id: Particle ids: 1 int per particle,
-            - pos: Position information (if dumped): 3 doubles per particle,
-            - vel: Velocity information (if dumped): 3 doubles per particle,
-            - typ: Type information (if dumped): 1 int per particle,
-            - bond: Bond information (if dumped): variable amount of data,
-            - boff: Bond offset information (if bonds are dumped): 1 int per particle.
+        - head: Information about fields that are dumped,
+        - pref: Information about processes: 1 int per process,
+        - id: Particle ids: 1 int per particle,
+        - pos: Position information (if dumped): 3 doubles per particle,
+        - vel: Velocity information (if dumped): 3 doubles per particle,
+        - typ: Type information (if dumped): 1 int per particle,
+        - bond: Bond information (if dumped): variable amount of data,
+        - boff: Bond offset information (if bonds are dumped): 1 int per particle.
 
         .. note::
             Do not read the files on a machine with a different architecture!

src/python/espressomd/pair_criteria.py

@@ -46,13 +46,13 @@ def decide(self, p1, p2):
 class DistanceCriterion(_PairCriterion):
 
     """Pair criterion returning true, if particles are closer than a cutoff.
-       Periodic boundaries are treated via minimum image convention.
+    Periodic boundaries are treated via minimum image convention.
 
-       The following parameters can be passed to the constructor, changed via set_params()
-       and retrieved via get_params()
+    The following parameters can be passed to the constructor, changed via set_params()
+    and retrieved via get_params()
 
-       cut_off : :obj:`float`
-           distance cut off for the criterion
+    cut_off : :obj:`float`
+        distance cut off for the criterion
     """
     _so_name = "PairCriteria::DistanceCriterion"
     _so_creation_policy = "LOCAL"
@@ -63,14 +63,14 @@ class EnergyCriterion(_PairCriterion):
 
     """Pair criterion returning true, if the short range energy between the particles is >= the cutoff
 
-       Be aware that the short range energy contains the short range part of dipolar and electrostatic interactions,
-       but not the long range part.
+    Be aware that the short range energy contains the short range part of dipolar and electrostatic interactions,
+    but not the long range part.
 
-       The following parameters can be passed to the constructor, changed via set_params()
-       and retrieved via get_params()
+    The following parameters can be passed to the constructor, changed via set_params()
+    and retrieved via get_params()
 
-       cut_off : :obj:`float`
-           energy cut off for the criterion
+    cut_off : :obj:`float`
+        energy cut off for the criterion
     """
     _so_name = "PairCriteria::EnergyCriterion"
     _so_creation_policy = "LOCAL"
@@ -81,11 +81,11 @@ class BondCriterion(_PairCriterion):
 
     """Pair criterion returning true, if a pair bond of given type exists between them
 
-       The following parameters can be passed to the constructor, changed via set_params()
-       and retrieved via get_params()
+    The following parameters can be passed to the constructor, changed via set_params()
+    and retrieved via get_params()
 
-       bond_type : :obj:`int`
-           numeric type of the bond
+    bond_type : :obj:`int`
+        numeric type of the bond
     """
     _so_name = "PairCriteria::BondCriterion"
     _so_creation_policy = "LOCAL"

src/python/espressomd/particle_data.pyx

@@ -1315,11 +1315,11 @@ cdef class ParticleHandle:
         """
         Checks the validity of the given bond:
 
-            - If the bondtype is given as an object or a numerical id
-            - If all partners are of type :obj:`int`
-            - If the number of partners satisfies the bond
-            - If the bond type used exists (is lower than ``n_bonded_ia``)
-            - If the number of bond partners fits the bond type
+        - If the bondtype is given as an object or a numerical id
+        - If all partners are of type :obj:`int`
+        - If the number of partners satisfies the bond
+        - If the bond type used exists (is lower than ``n_bonded_ia``)
+        - If the number of bond partners fits the bond type
 
         Throws an exception if any of these are not met.