Fixed Link error

doc/api.rst

@@ -94,14 +94,6 @@ Parallel backends (:py:mod:`hnn_core.parallel_backends`):
    MPIBackend
    JoblibBackend
 
-Batch Simulation (:py:mod:`hnn_core.batch_simulate`):
----------------------------------------------------------
-.. currentmodule:: hnn_core.batch_simulate
-
-.. autosummary::
-   :toctree: generated/
-
-   BatchSimulate
 
 Input and Output:
 -----------------

examples/howto/plot_batch_simulate.py

@@ -1,6 +1,6 @@
 """
 ====================
-06. Batch Simulation
+07. Batch Simulation
 ====================
 
 This example shows how to do batch simulations in HNN-core, allowing users to
@@ -13,17 +13,17 @@
 #          Ryan Thorpe <[email protected]>
 #          Mainak Jas <[email protected]>
 
-#############################################################################
-# Let us import hnn_core.
+###############################################################################
+# Let us import ``hnn_core``.
 
 import hnn_core
 import numpy as np
-from hnn_core import BatchSimulate
+from hnn_core.batch_simulate import BatchSimulate
 from hnn_core import jones_2009_model
 
 # The number of cores may need modifying depending on your current machine.
 n_jobs = 10
-###########################################################################
+###############################################################################
 
 
 def set_params(param_values, net=None):
@@ -57,7 +57,8 @@ def set_params(param_values, net=None):
                          weights_ampa=weights_ampa,
                          synaptic_delays=synaptic_delays)
 
-###########################################################################
+###############################################################################
+# Define a parameter grid for the batch simulation.
 
 
 param_grid = {
@@ -67,6 +68,9 @@ def set_params(param_values, net=None):
     'sigma': np.linspace(1, 20, 5)
 }
 
+###############################################################################
+# Run the batch simulation and collect the results.
+
 batch_simulation = BatchSimulate(set_params=set_params)
 simulation_results = batch_simulation.run(param_grid,
                                           n_jobs=n_jobs,

hnn_core/__init__.py

@@ -6,6 +6,5 @@
 from .cell_response import CellResponse, read_spikes
 from .cells_default import pyramidal, basket
 from .parallel_backends import MPIBackend, JoblibBackend
-from .batch_simulate import BatchSimulate
 
 __version__ = '0.4.dev0'

hnn_core/batch_simulate.py

@@ -1,4 +1,4 @@
-"""Batch simulation."""
+"""Batch Simulation."""
 
 # Authors: Abdul Samad Siddiqui <[email protected]>
 #          Nick Tolley <[email protected]>
@@ -8,21 +8,24 @@
 from joblib import Parallel, delayed
 from .dipole import simulate_dipole
 from .network_models import (jones_2009_model,
-                                     calcium_model, law_2021_model)
+                             calcium_model, law_2021_model)
 
 
 class BatchSimulate:
     def __init__(self, set_params, net_name='jones', tstop=170,
                  dt=0.025, n_trials=1, record_vsec=False,
                  record_isec=False, postproc=False):
-        """
-        Initialize the BatchSimulate class.
+        """Initialize the BatchSimulate class.
 
         Parameters
         ----------
         set_params : func
             User-defined function that sets parameters in network drives.
-            `set_params(net, params) -> None`
+
+                ``set_params(net, params) -> None``
+
+            where ``net`` is a Network object and ``params`` is a dictionary
+            of the parameters that will be set inside the function.
         net_name : str
             The name of the network model to use. Default is `jones`.
         tstop : float, optional
@@ -59,8 +62,7 @@ def __init__(self, set_params, net_name='jones', tstop=170,
         self.postproc = postproc
 
     def run(self, param_grid, return_output=True, combinations=True, n_jobs=1):
-        """
-        Run batch simulations.
+        """Run batch simulations.
 
         Parameters
         ----------
@@ -88,8 +90,7 @@ def run(self, param_grid, return_output=True, combinations=True, n_jobs=1):
             return results
 
     def simulate_batch(self, param_combinations, n_jobs=1):
-        """
-        Simulate a batch of parameter sets in parallel.
+        """Simulate a batch of parameter sets in parallel.
 
         Parameters
         ----------
@@ -113,8 +114,7 @@ def simulate_batch(self, param_combinations, n_jobs=1):
         return res
 
     def _run_single_sim(self, param_values):
-        """
-        Run a single simulation.
+        """Run a single simulation.
 
         Parameters
         ----------
@@ -154,8 +154,7 @@ def _run_single_sim(self, param_values):
         return {'net': net, 'dpl': dpl, 'param_values': param_values}
 
     def _generate_param_combinations(self, param_grid, combinations=True):
-        """
-        Generate combinations of parameters from the grid.
+        """Generate combinations of parameters from the grid.
 
         Parameters
         ----------

hnn_core/tests/test_batch_simulate.py

@@ -6,7 +6,7 @@
 import pytest
 import numpy as np
 
-from hnn_core import BatchSimulate
+from hnn_core.batch_simulate import BatchSimulate
 
 
 @pytest.fixture