[BBPBGLIB-1175] Handle deleted sections correctly (#182)

## Context
User reported an error when creating synapse points on deleted sections.
This kind of synapses should have been skipped by
`Connection::add_synapses()`. This PR handles deleted sections correctly
so that they are skipped.

## Scope
In `target_manager.py` and `connection.py`, deleted sections are added
to TPointList as `None` type, and skipped by
`Connection::add_synapses()`.

## Testing
n/a

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [ ] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation

neurodamus/connection.py

@@ -271,7 +271,7 @@ def add_synapses(self, target_manager, synapses_params, base_id=0):
             syn_params['location'] = syn_point.x[0]
             section = syn_point.sclst[0]
 
-            if not section.exists():
+            if section is None or not section.exists():
                 target_point_str = "({0.isec:.0f} {0.ipt:.0f} {0.offset:.4f})".format(syn_params)
                 logging.warning("SKIPPED Synapse %s on gid %d. Src gid: %d. Deleted TPoint %s",
                                 base_id + i, self.tgid, self.sgid, target_point_str)

neurodamus/target_manager.py

@@ -649,7 +649,7 @@ def append(self, *args):
             # Called with a section and a point
             section, point = args
             self.x.append(point)
-            self.sclst.append(Nd.SectionRef(section.sec))  # Create and append a SectionRef
+            self.sclst.append(section)  # Create and append a SectionRef
         else:
             raise ValueError("append() takes 1 or 2 arguments ({} given)".format(len(args)))