v1.5.3

What's Changed

• Deploy to PyPi on tagged release by @scottgigante in #65
• Use scipy.sparse.csgraph.shortest_path by @scottgigante in #66

Full Changelog: v1.5.2...v1.5.3

graphtools v1.5.0

Changeset:

• added graphtools.estimator abstract class: allows inheritance of basic takes-data-builds-graph functionality.

graphtools v1.4.0

Changeset:

• added knn_max argument to kNNGraph
• increased test coverage
• restyled code with black

graphtools v1.3.0

Changeset:

• shortest_path now works for all graphs with data and affinity distance metrics
• added automatic n_pca detection (thanks @stanleyjs)
• changed default decay to 40
• renamed kernel_symm='theta' to kernel_symm='mnn'
• bugfixes

graphtools v1.1.0

Changeset:

• Changed default value of theta for kernel_symm='theta' to 1 (was 0.5)
• Added BaseGraph.to_pickle and graphtools.read_pickle functionality for saving and storing graphs
• Improved warning message for many duplicate entries
• various bug fixes

graphtools v1.0.0

Changeset:

• knn no longer includes self. Note that this change means that to reproduce a graph created with graphtools v0.*, you will need to reduce knn by 1.
• deprecated Python 2.7
• fixed some inefficient sparse matrix functions

graphtools v0.2.1

Changes:

• added anisotropic kernel (alpha parameter from Coifman and Lafon 2006)
• added to_igraph function
• allowed from_igraph to return weighted kernel
• documentation updates

graphtools v0.2.0

Changeset:

• significant changes to MNNGraph kernel creation: between batch connections are now downweighted relative to the sum of within-batch connections
• added fixed bandwidth kernel creation with bandwidth parameter
• exposed clusters attribute on LandmarkGraph
• added igraph->graphtools conversion function
• added graphtools->PyGSP conversion function
• MNNGraph parameter gamma renamed to theta

graphtools v0.1.10

Changes:

• Uses tasklogger for logging
• Allows duplicates in building the graph; connections evaluated at nan are set to 1 with a warning.
• Landmarking is now done on the symmetric diffusion affinity matrix for true spectral clustering
• LandmarkGraph now exposes the transition matrix from samples to landmarks.

graphtools v0.1.9

Graphtools 0.1.9.

Changes:

• graphtools.base.Data accepts anndata.AnnData input
• graphtools.base.Data.inverse_transform accepts column indices to return only a subset of ambient dimensions
• minor bugfixes and improvements to documentation