Updated documentation

doc/conf.py

@@ -117,6 +117,7 @@
         ("Examples", "auto_examples/index"),
         ("GUI", "gui/index"),
         ("API", "api"),
+        ("Network File", "network_file_desc"),
         ("Glossary", "glossary"),
         ("Whats new", "whats_new"),
         ("GitHub", "https://github.com/jonescompneurolab/hnn-core", True)

doc/network_file_desc.rst

@@ -0,0 +1,196 @@
+:orphan:
+
+.. _network_file_content:
+
+====================
+Network File Content
+====================
+
+File Content Description
+------------------------
+
+    object_type : str
+        Type of object (Network) saved.
+    N_pyr_x : int
+        Nr of cells (x).
+    N_pyr_y : int
+        Nr of cells (y).
+    threshold : float
+        Firing threshold of all cells.
+    celsius : float
+        Temperature in degree celsius.
+    cell_types : dict of Cell Object
+        key : name of cell type.
+        value : Cell object.
+    gid_ranges : dict of dict
+        key : cell name or drive name.
+        value : dict.
+    pos_dict : dict
+        key : cell type name.
+        value : All co-ordintes of the cell types.
+    cell_response : Instance of Cell Response Object
+        The Cell Response object.
+    external_drives : dict of dict
+        key : external drive name.
+        value : dict.
+    external_biases : dict of dict
+        key : external bias name.
+        value : dict.
+    connectivity : list of dict
+        Contains connection info between cells and
+        cells and external drives.
+    rec_arrays : dict of Extracellular Arrays
+        key : extracellular array name.
+        value : Instance of Extracellular Array object.
+    delay : float
+        Synaptic delay in ms.
+
+Cell Type Description
+---------------------
+
+    cell_name : str
+        Name of the cell.
+    pos : tuple
+        The (x, y, z) coordinates.
+    sections : dict of Section
+        Dictionary with keys as section name.
+    synapses : dict of dict
+        Keys are name of synaptic mechanism. Each synaptic mechanism
+        has keys for parameters of the mechanism, e.g., 'e', 'tau1',
+        'tau2'.
+    cell_tree : dict of list
+        Stores the tree representation of a cell.
+    sect_loc : dict of list
+        Can have keys 'proximal' or 'distal' each containing
+        names of section locations that are proximal or distal.
+    gid : int
+        GID of the cell in a network (or None if not yet assigned).
+    dipole_pp : list of h.Dipole()
+        The Dipole objects (see dipole.mod).
+    vsec : dict
+        Recording of section specific voltage. Must be enabled
+        by running simulate_dipole(net, record_vsec=True) or
+        simulate_dipole(net, record_vsoma=True).
+    isec : dict
+        Contains recording of section specific currents indexed
+        by synapse type (keys can be soma_gabaa, soma_gabab etc.).
+        Must be enabled by running simulate_dipole(net, record_isec=True)
+        or simulate_dipole(net, record_isoma=True).
+    tonic_biases : list of h.IClamp
+        The current clamps inserted at each section of the cell
+        for tonic biasing inputs.
+
+Section Description
+-------------------
+
+    L : float
+        length of a section in microns.
+    diam : float
+        diameter of a section in microns.
+    cm : float
+        membrane capacitance in micro-Farads.
+    Ra : float
+        axial resistivity in ohm-cm.
+    end_pts : list of [x, y, z]
+        The start and stop points of the section.
+    syns : list of str
+        The synaptic mechanisms to add in this section.
+    mechs : dict
+        Mechanisms to insert in this section. The keys
+        are the names of the mechanisms and values
+        are the properties.
+
+Gid Range Description
+---------------------
+
+    start : int
+        Start of the gid_range.
+    stop : int
+        End of the gid_range.
+
+External Drive Description
+--------------------------
+
+    name : str
+        Unique name for the drive.
+    dynamics : dict
+        Parameters describing how the temporal dynamics of spike trains in the
+        drive. The keys are specific to the type of drive ('evoked', 'bursty',
+        etc.).
+    location : str
+        Target location of synapses.
+    cell_specific : bool
+        Whether each artifical drive cell has 1-to-1 (True, default) or
+        all-to-all (False) connection parameters.
+    weights_ampa : dict or None
+        Synaptic weights (in uS) of AMPA receptors on each targeted cell
+        type (dict keys).
+    weights_nmda : dict or None
+        Synaptic weights (in uS) of NMDA receptors on each targeted cell
+        type (dict keys).
+    probability : dict or float
+        Probability of connection between any src-target pair.
+    synaptic_delays : dict or float
+        Synaptic delay (in ms) at the column origin, dispersed laterally as
+        a function of the space_constant. If float, applies to all target
+        cell types.
+    event_seed : int
+        Optional initial seed for random number generator.
+    conn_seed : int
+        Optional initial seed for random number generator.
+    n_drive_cells : int | 'n_cells'
+        The number of drive cells that each contribute an independently
+        sampled synaptic spike to the network according to the Gaussian
+        time distribution (mu, sigma).
+    events : list
+        Contains the spike times of exogeneous inputs.
+
+External Bias Description
+-------------------------
+
+    cell_type : str
+        The cell type whose cells will get the tonic input.
+    amplitude : float
+        The amplitude of the input.
+    t0 : float
+        The start time of tonic input (in ms).
+    tstop : float
+        The end time of tonic input (in ms).
+
+Connection Description
+----------------------
+
+    target_types : str
+        Cell type of target gids.
+    target_gids : list of int
+        Identifer for targets of source cells.
+    num_targets : int
+        Number of unique target gids.
+    src_type : str
+        Cell type of source gids.
+    src_gids : list of int
+        Identifier for source cells.
+    num_srcs : int
+        Number of unique source gids.
+    gid_pairs : dict
+        dict indexed by src gids.
+    loc : str
+        Target location of synapses.
+    receptor : str
+        Synaptic receptor of connection.
+    nc_dict : dict
+        Contains information about delay, weight, lamtha etc.
+    allow_autapses : bool
+        If True, allow connecting neuron to itself.
+    probability : float
+        Probability of connection between any src-target pair.
+
+Extracellular Array Description
+-------------------------------
+
+    positions : tuple | list of tuple
+        The (x, y, z) coordinates (in um) of the extracellular electrodes.
+    conductivity : float
+        Extracellular conductivity, in S/m.
+    method : str
+        Approximation to use.

hnn_core/cell.py

@@ -239,7 +239,7 @@ def __eq__(self, other):
         # Check end_pts
         for self_end_pt, other_end_pt in zip(self.end_pts, other.end_pts):
             if np.testing.assert_almost_equal(self_end_pt,
-                                              other_end_pt, 5) != None:
+                                              other_end_pt, 5) is not None:
                 return False
 
         # Check all other attributes

hnn_core/docs.py

@@ -170,16 +170,6 @@
     or simulate_dipole(net, record_isoma=True).
 """
 
-docdict[
-    "isec"
-] = """
-isec : dict
-    Contains recording of section specific currents indexed
-    by synapse type (keys can be soma_gabaa, soma_gabab etc.).
-    Must be enabled by running simulate_dipole(net, record_isec=True)
-    or simulate_dipole(net, record_isoma=True).
-"""
-
 docdict[
     "tonic_biases"
 ] = """