fix rebase conflicts

hnn_core/cell.py

@@ -760,11 +760,15 @@ def record(self, record_vsec=False, record_isec=False, record_ca=False):
             Option to record voltages from all sections ('all'), or just
             the soma ('soma'). Default: False.
         record_ca : 'all' | 'soma' | False
+<<<<<<< HEAD
 <<<<<<< HEAD
             Option to record calcium concentration from all sections ('all'),
 =======
             Option to record calcium concentration from all sections ('all'), 
 >>>>>>> d3105f90 (record calcium concentration in L5pyr)
+=======
+            Option to record calcium concentration from all sections ('all'),
+>>>>>>> a1d230e27c4585f7612290bf90cf572c5102dfaf
             or just the soma ('soma'). Default: False.
         """
 
@@ -825,6 +829,19 @@ def record(self, record_vsec=False, record_isec=False, record_ca=False):
                     self.ca[sec_name].record(
                         self._nrn_sections[sec_name](0.5)._ref_cai)
 
+        # calcium concentration
+        if record_ca == 'soma':
+            self.ca = dict.fromkeys(['soma'])
+        elif record_ca == 'all':
+            self.ca = dict.fromkeys(section_names)
+
+        if record_ca:
+            for sec_name in self.ca:
+                if hasattr(self._nrn_sections[sec_name](0.5), '_ref_cai'):
+                    self.ca[sec_name] = h.Vector()
+                    self.ca[sec_name].record(
+                        self._nrn_sections[sec_name](0.5)._ref_cai)
+
     def syn_create(self, secloc, e, tau1, tau2):
         """Create an h.Exp2Syn synapse.
 

hnn_core/cell_response.py

@@ -242,6 +242,10 @@ def ca(self):
     def ca(self):
         return self._ca
 
+    @property
+    def ca(self):
+        return self._ca
+
     @property
     def times(self):
         return self._times

hnn_core/network_builder.py

@@ -114,6 +114,13 @@ def simulation_time():
             if ca is not None:
                 ca_py[gid][sec_name] = ca.to_python()
 
+    ca_py = dict()
+    for gid, ca_dict in neuron_net._ca.items():
+        ca_py[gid] = dict()
+        for sec_name, ca in ca_dict.items():
+            if ca is not None:
+                ca_py[gid][sec_name] = ca.to_python()
+
     dpl_data = np.c_[
         neuron_net._nrn_dipoles['L2_pyramidal'].as_numpy() +
         neuron_net._nrn_dipoles['L5_pyramidal'].as_numpy(),

hnn_core/tests/conftest.py

@@ -77,7 +77,7 @@ def _run_hnn_core_fixture(backend=None, n_procs=None, n_jobs=1,
                               reduced=False, record_vsec=False,
                               record_isec=False, record_ca=False,
                               postproc=False, electrode_array=None):
-
+        
         hnn_core_root = op.dirname(hnn_core.__file__)
 
         # default params

hnn_core/tests/test_dipole.py

@@ -235,7 +235,7 @@ def test_cell_response_backends(run_hnn_core_fixture):
                trial_idx][gid]['soma']['soma_gabaa']) == n_times 
 
     assert len(joblib_net.cell_response.ca[
-               trial_idx][gid]['soma']) == n_times
+               trial_idx][gid]['soma']['soma_gabaa']) == n_times
     assert len(mpi_net.cell_response.vsec) == n_trials
     assert len(mpi_net.cell_response.isec) == n_trials
     assert len(mpi_net.cell_response.vsec[trial_idx][gid]) == 8  # num sec