Commit 9b01da33 authored by Tiago Peixoto's avatar Tiago Peixoto
Browse files

Fix docstrings

parent d6f1dcf7
Pipeline #944 failed with stage
in 69 minutes and 47 seconds
......@@ -173,7 +173,7 @@ htmlhelp_basename = 'graph-tooldoc'
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
'numpy': ('https://docs.scipy.org/doc/numpy', None),
'numpy': ('https://numpy.org/doc/stable/', None),
'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
'matplotlib': ('https://matplotlib.org', None),
'cairo': ('https://www.cairographics.org/documentation/pycairo/3', None),
......@@ -201,6 +201,8 @@ autodoc_default_options = {
}
autosummary_gerenerate = True
autosummary_imported_members = True
autosummary_ignore_module_all = False
numpydoc_show_class_members = False
autodoc_docstring_signature = False
autoclass_content = 'both'
......
.. automodule:: graph_tool.inference
:no-undoc-members:
:no-members:
:show-inheritance:
:inherited-members:
..
.. testcode:: inference_detailed
......@@ -111,3 +111,9 @@
:no-undoc-members:
:show-inheritance:
:inherited-members:
.. automodule:: graph_tool.inference.norm_cut
:no-undoc-members:
:show-inheritance:
:inherited-members:
......@@ -36,11 +36,13 @@ Nonparametric stochastic block model inference
High-level functions
====================
.. currentmodule:: graph_tool.inference
.. autosummary::
:nosignatures:
~graph_tool.inference.minimize.minimize_blockmodel_dl
~graph_tool.inference.minimize.minimize_nested_blockmodel_dl
minimize_blockmodel_dl
minimize_nested_blockmodel_dl
State classes
=============
......@@ -48,26 +50,27 @@ State classes
.. autosummary::
:nosignatures:
~graph_tool.inference.blockmodel.BlockState
~graph_tool.inference.overlap_blockmodel.OverlapBlockState
~graph_tool.inference.layered_blockmodel.LayeredBlockState
~graph_tool.inference.nested_blockmodel.NestedBlockState
~graph_tool.inference.planted_partition.PPBlockState
~graph_tool.inference.modularity.ModularityState
~graph_tool.inference.mcmc.TemperingState
~graph_tool.inference.clique_decomposition.CliqueState
BlockState
OverlapBlockState
LayeredBlockState
NestedBlockState
PPBlockState
ModularityState
NormCutState
TemperingState
CliqueState
Abstract base classes
=====================
.. autosummary::
:nosignatures:
~graph_tool.inference.base_states.MCMCState
~graph_tool.inference.base_states.MultiflipMCMCState
~graph_tool.inference.base_states.MultilevelMCMCState
~graph_tool.inference.base_states.GibbsMCMCState
~graph_tool.inference.base_states.MulticanonicalMCMCState
~graph_tool.inference.base_states.ExhaustiveSweepState
MCMCState
MultiflipMCMCState
MultilevelMCMCState
GibbsMCMCState
MulticanonicalMCMCState
ExhaustiveSweepState
Sampling and minimization
=========================
......@@ -75,10 +78,10 @@ Sampling and minimization
.. autosummary::
:nosignatures:
~graph_tool.inference.mcmc.mcmc_equilibrate
~graph_tool.inference.mcmc.mcmc_anneal
~graph_tool.inference.mcmc.multicanonical_equilibrate
~graph_tool.inference.mcmc.MulticanonicalState
mcmc_equilibrate
mcmc_anneal
multicanonical_equilibrate
MulticanonicalState
Comparing and manipulating partitions
=====================================
......@@ -86,25 +89,25 @@ Comparing and manipulating partitions
.. autosummary::
:nosignatures:
~graph_tool.inference.partition_modes.PartitionModeState
~graph_tool.inference.partition_modes.ModeClusterState
~graph_tool.inference.partition_centroid.PartitionCentroidState
~graph_tool.inference.partition_modes.partition_overlap
~graph_tool.inference.partition_modes.nested_partition_overlap
~graph_tool.inference.partition_centroid.variation_information
~graph_tool.inference.partition_centroid.mutual_information
~graph_tool.inference.partition_centroid.reduced_mutual_information
~graph_tool.inference.partition_modes.contingency_graph
~graph_tool.inference.partition_modes.shuffle_partition_labels
~graph_tool.inference.partition_modes.order_partition_labels
~graph_tool.inference.partition_modes.order_nested_partition_labels
~graph_tool.inference.partition_modes.align_partition_labels
~graph_tool.inference.partition_modes.align_nested_partition_labels
~graph_tool.inference.partition_modes.partition_overlap_center
~graph_tool.inference.partition_modes.nested_partition_overlap_center
~graph_tool.inference.partition_modes.nested_partition_clear_null
~graph_tool.inference.util.contiguous_map
~graph_tool.inference.util.nested_contiguous_map
PartitionModeState
ModeClusterState
PartitionCentroidState
partition_overlap
nested_partition_overlap
variation_information
mutual_information
reduced_mutual_information
contingency_graph
shuffle_partition_labels
order_partition_labels
order_nested_partition_labels
align_partition_labels
align_nested_partition_labels
partition_overlap_center
nested_partition_overlap_center
nested_partition_clear_null
contiguous_map
nested_contiguous_map
Auxiliary functions
===================
......@@ -112,12 +115,12 @@ Auxiliary functions
.. autosummary::
:nosignatures:
~graph_tool.inference.blockmodel.mf_entropy
~graph_tool.inference.blockmodel.bethe_entropy
~graph_tool.inference.blockmodel.microstate_entropy
~graph_tool.inference.uncertain_blockmodel.marginal_multigraph_entropy
~graph_tool.inference.overlap_blockmodel.half_edge_graph
~graph_tool.inference.overlap_blockmodel.get_block_edge_gradient
mf_entropy
bethe_entropy
microstate_entropy
marginal_multigraph_entropy
half_edge_graph
get_block_edge_gradient
Auxiliary classes
=================
......@@ -125,8 +128,8 @@ Auxiliary classes
.. autosummary::
:nosignatures:
~graph_tool.inference.blockmodel.PartitionHist
~graph_tool.inference.blockmodel.BlockPairHist
PartitionHist
BlockPairHist
Nonparametric network reconstruction
++++++++++++++++++++++++++++++++++++
......@@ -137,20 +140,20 @@ State classes
.. autosummary::
:nosignatures:
~graph_tool.inference.uncertain_blockmodel.LatentMultigraphBlockState
~graph_tool.inference.latent_layers.LatentClosureBlockState
~graph_tool.inference.uncertain_blockmodel.MeasuredBlockState
~graph_tool.inference.latent_layers.MeasuredClosureBlockState
~graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState
~graph_tool.inference.uncertain_blockmodel.UncertainBlockState
~graph_tool.inference.uncertain_blockmodel.UncertainBaseState
~graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase
~graph_tool.inference.uncertain_blockmodel.EpidemicsBlockState
~graph_tool.inference.uncertain_blockmodel.IsingBaseBlockState
~graph_tool.inference.uncertain_blockmodel.IsingGlauberBlockState
~graph_tool.inference.uncertain_blockmodel.CIsingGlauberBlockState
~graph_tool.inference.uncertain_blockmodel.PseudoIsingBlockState
~graph_tool.inference.uncertain_blockmodel.PseudoCIsingBlockState
LatentMultigraphBlockState
LatentClosureBlockState
MeasuredBlockState
MeasuredClosureBlockState
MixedMeasuredBlockState
UncertainBlockState
UncertainBaseState
DynamicsBlockStateBase
EpidemicsBlockState
IsingBaseBlockState
IsingGlauberBlockState
CIsingGlauberBlockState
PseudoIsingBlockState
PseudoCIsingBlockState
Expectation-maximization Inference
==================================
......@@ -158,7 +161,7 @@ Expectation-maximization Inference
.. autosummary::
:nosignatures:
~graph_tool.inference.latent_multigraph.latent_multigraph
latent_multigraph
Semiparametric stochastic block model inference
+++++++++++++++++++++++++++++++++++++++++++++++
......@@ -169,7 +172,7 @@ State classes
.. autosummary::
:nosignatures:
~graph_tool.inference.blockmodel_em.EMBlockState
EMBlockState
Expectation-maximization Inference
==================================
......@@ -177,7 +180,7 @@ Expectation-maximization Inference
.. autosummary::
:nosignatures:
~graph_tool.inference.blockmodel_em.em_infer
em_infer
Large-scale descriptors
+++++++++++++++++++++++
......@@ -185,7 +188,7 @@ Large-scale descriptors
.. autosummary::
:nosignatures:
~graph_tool.inference.modularity.modularity
modularity
Contents
++++++++
......@@ -209,7 +212,9 @@ __all__ = ["minimize_blockmodel_dl",
"MeasuredBlockState",
"UncertainBaseState",
"MixedMeasuredBlockState",
"DynamicsBlockStateBase",
"EpidemicsBlockState",
"IsingBaseBlockState",
"IsingGlauberBlockState",
"PseudoIsingBlockState",
"CIsingGlauberBlockState",
......
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