API docs: always show full path to function

docs/source/api.rst

@@ -13,87 +13,87 @@ Neurons
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_neuron
-    ~pymaid.delete_neuron
-    ~pymaid.find_neurons
-    ~pymaid.get_arbor
-    ~pymaid.get_neurons_in_volume
-    ~pymaid.get_neuron_list
-    ~pymaid.get_skids_by_annotation
-    ~pymaid.get_skids_by_name
-    ~pymaid.rename_neurons
-    ~pymaid.get_names
+    pymaid.get_neuron
+    pymaid.delete_neuron
+    pymaid.find_neurons
+    pymaid.get_arbor
+    pymaid.get_neurons_in_volume
+    pymaid.get_neuron_list
+    pymaid.get_skids_by_annotation
+    pymaid.get_skids_by_name
+    pymaid.rename_neurons
+    pymaid.get_names
 
 Annotations
 -----------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.add_annotations
-    ~pymaid.get_annotations
-    ~pymaid.get_annotation_details
-    ~pymaid.get_user_annotations
-    ~pymaid.remove_annotations
+    pymaid.add_annotations
+    pymaid.get_annotations
+    pymaid.get_annotation_details
+    pymaid.get_user_annotations
+    pymaid.remove_annotations
 
 Treenodes
 ----------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_treenode_table
-    ~pymaid.get_treenode_info
-    ~pymaid.get_treenodes_by_tag
-    ~pymaid.get_skid_from_treenode
-    ~pymaid.get_node_details
+    pymaid.get_treenode_table
+    pymaid.get_treenode_info
+    pymaid.get_treenodes_by_tag
+    pymaid.get_skid_from_treenode
+    pymaid.get_node_details
     pymaid.get_node_location
 
 Tags
 ----
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_label_list
-    ~pymaid.add_tags
-    ~pymaid.delete_tags
-    ~pymaid.get_node_tags
+    pymaid.get_label_list
+    pymaid.add_tags
+    pymaid.delete_tags
+    pymaid.get_node_tags
 
 Connectivity
 ------------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_connectors
-    ~pymaid.get_connector_details
-    ~pymaid.get_connectors_between
-    ~pymaid.get_connector_links
-    ~pymaid.get_edges
-    ~pymaid.get_partners
-    ~pymaid.get_partners_in_volume
-    ~pymaid.get_nth_partners
-    ~pymaid.get_paths
-    ~pymaid.adjacency_from_connectors
-    ~pymaid.cn_table_from_connectors
+    pymaid.get_connectors
+    pymaid.get_connector_details
+    pymaid.get_connectors_between
+    pymaid.get_connector_links
+    pymaid.get_edges
+    pymaid.get_partners
+    pymaid.get_partners_in_volume
+    pymaid.get_nth_partners
+    pymaid.get_paths
+    pymaid.adjacency_from_connectors
+    pymaid.cn_table_from_connectors
 
 User stats
 ----------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_user_list
-    ~pymaid.get_history
-    ~pymaid.get_time_invested
-    ~pymaid.get_user_contributions
-    ~pymaid.get_contributor_statistics
-    ~pymaid.get_logs
-    ~pymaid.get_transactions
-    ~pymaid.get_team_contributions
+    pymaid.get_user_list
+    pymaid.get_history
+    pymaid.get_time_invested
+    pymaid.get_user_contributions
+    pymaid.get_contributor_statistics
+    pymaid.get_logs
+    pymaid.get_transactions
+    pymaid.get_team_contributions
 
 Volumes
 -------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.get_volume
+    pymaid.get_volume
 
 .. _api_misc:
 
@@ -102,11 +102,11 @@ Misc
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.url_to_coordinates
-    ~pymaid.get_review
-    ~pymaid.get_review_details
-    ~pymaid.clear_cache
-    ~pymaid.has_soma
+    pymaid.url_to_coordinates
+    pymaid.get_review
+    pymaid.get_review_details
+    pymaid.clear_cache
+    pymaid.has_soma
 
 
 CatmaidInstance
@@ -133,8 +133,8 @@ CatmaidNeuron/List
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.CatmaidNeuron
-    ~pymaid.CatmaidNeuronList
+    pymaid.CatmaidNeuron
+    pymaid.CatmaidNeuronList
 
 CatmaidNeuron/List methods
 --------------------------
@@ -186,31 +186,31 @@ Plotting
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.plot3d
-    ~pymaid.plot2d
-    ~pymaid.plot1d
-    ~pymaid.plot_network
-    ~pymaid.clear3d
-    ~pymaid.close3d
-    ~pymaid.get_viewer
-    ~pymaid.screenshot
-    ~pymaid.Volume
+    pymaid.plot3d
+    pymaid.plot2d
+    pymaid.plot1d
+    pymaid.plot_network
+    pymaid.clear3d
+    pymaid.close3d
+    pymaid.get_viewer
+    pymaid.screenshot
+    pymaid.Volume
 
 Vispy 3D viewer
 
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.Viewer
-    ~pymaid.Viewer.add
-    ~pymaid.Viewer.clear
-    ~pymaid.Viewer.close
-    ~pymaid.Viewer.colorize
-    ~pymaid.Viewer.set_colors
-    ~pymaid.Viewer.hide_neurons
-    ~pymaid.Viewer.unhide_neurons
-    ~pymaid.Viewer.screenshot
-    ~pymaid.Viewer.show
+    pymaid.Viewer
+    pymaid.Viewer.add
+    pymaid.Viewer.clear
+    pymaid.Viewer.close
+    pymaid.Viewer.colorize
+    pymaid.Viewer.set_colors
+    pymaid.Viewer.hide_neurons
+    pymaid.Viewer.unhide_neurons
+    pymaid.Viewer.screenshot
+    pymaid.Viewer.show
 
 
 .. _api_morph:
@@ -223,53 +223,53 @@ Manipulation
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.cut_neuron
-    ~pymaid.reroot_neuron
-    ~pymaid.stitch_neurons
-    ~pymaid.split_axon_dendrite
-    ~pymaid.split_into_fragments
-    ~pymaid.longest_neurite
-    ~pymaid.prune_by_strahler
-    ~pymaid.subset_neuron
-    ~pymaid.average_neurons
-    ~pymaid.remove_tagged_branches
-    ~pymaid.despike_neuron
-    ~pymaid.smooth_neuron
-    ~pymaid.guess_radius
-    ~pymaid.time_machine
-    ~pymaid.tortuosity
+    pymaid.cut_neuron
+    pymaid.reroot_neuron
+    pymaid.stitch_neurons
+    pymaid.split_axon_dendrite
+    pymaid.split_into_fragments
+    pymaid.longest_neurite
+    pymaid.prune_by_strahler
+    pymaid.subset_neuron
+    pymaid.average_neurons
+    pymaid.remove_tagged_branches
+    pymaid.despike_neuron
+    pymaid.smooth_neuron
+    pymaid.guess_radius
+    pymaid.time_machine
+    pymaid.tortuosity
 
 Resampling
 ----------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.resample_neuron
-    ~pymaid.downsample_neuron
+    pymaid.resample_neuron
+    pymaid.downsample_neuron
 
 Analysis
 --------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.arbor_confidence
-    ~pymaid.bending_flow
-    ~pymaid.calc_cable
-    ~pymaid.classify_nodes
-    ~pymaid.find_main_branchpoint
-    ~pymaid.flow_centrality
-    ~pymaid.segregation_index
-    ~pymaid.strahler_index
+    pymaid.arbor_confidence
+    pymaid.bending_flow
+    pymaid.calc_cable
+    pymaid.classify_nodes
+    pymaid.find_main_branchpoint
+    pymaid.flow_centrality
+    pymaid.segregation_index
+    pymaid.strahler_index
 
 Distances
 ---------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.cable_overlap
-    ~pymaid.geodesic_matrix
-    ~pymaid.distal_to
-    ~pymaid.dist_between
+    pymaid.cable_overlap
+    pymaid.geodesic_matrix
+    pymaid.distal_to
+    pymaid.dist_between
 
 Intersection
 ------------
@@ -289,50 +289,50 @@ Graphs
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.neuron2nx
-    ~pymaid.neuron2igraph
-    ~pymaid.neuron2KDTree
-    ~pymaid.network2nx
-    ~pymaid.network2igraph
+    pymaid.neuron2nx
+    pymaid.neuron2igraph
+    pymaid.neuron2KDTree
+    pymaid.network2nx
+    pymaid.network2igraph
 
 Predicting connectivity
 -----------------------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.predict_connectivity
-    ~pymaid.connection_density
+    pymaid.predict_connectivity
+    pymaid.connection_density
 
 Adjacency matrices
 ------------------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.adjacency_matrix
-    ~pymaid.group_matrix
+    pymaid.adjacency_matrix
+    pymaid.group_matrix
 
 Connectivity clustering
 -----------------------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.cluster_by_connectivity
-    ~pymaid.cluster_by_synapse_placement
-    ~pymaid.ClustResults
+    pymaid.cluster_by_connectivity
+    pymaid.cluster_by_synapse_placement
+    pymaid.ClustResults
 
 Plotting network
 ----------------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.plot_network
+    pymaid.plot_network
 
 Filtering
 ---------
 .. autosummary::
     :toctree: generated/
 
-    ~pymaid.filter_connectivity
+    pymaid.filter_connectivity
 
 Import/Export
 +++++++++++++
@@ -445,6 +445,7 @@ R interface (rMAID)
     pymaid.rmaid.dotprops2py
     pymaid.rmaid.neuron2r
     pymaid.rmaid.NBLASTresults
+    pymaid.rmaid.get_neuropil
 
 Utility
 +++++++