NEWS.md
Full Changelog: https://github.com/natverse/neuprintr/compare/v1.3.1…v1.3.2
add neuprint_cosine_plot() and neuprint_cosine_matrix() to support cosine similarity clustering by @jefferis in https://github.com/natverse/neuprintr/pull/167
Fix when dataset for connection not passed on by @jefferis in https://github.com/natverse/neuprintr/pull/162
WIP: improved error messages by @jefferis in https://github.com/natverse/neuprintr/pull/161
Fix adjacency matrix names by @jefferis in https://github.com/natverse/neuprintr/pull/163
fix bug (noticed w malecns) when correct rois not fetched by @jefferis in https://github.com/natverse/neuprintr/pull/165
Fix bug when only presynapse is inside ROI by @jefferis in https://github.com/natverse/neuprintr/pull/166
neuprint_get_adjacency_matrix() by @jefferis includes chunking and an optional threshold (#147)Full Changelog: https://github.com/natverse/neuprintr/compare/v1.2…v1.3
neuprint_connection_table() returns error when no connections found (#135)neuprint_connection_table(): pass on details argument when using progress bug (#133)neuprint_connection_table() (#132)neuprint_login() should choose the newest dataset as default (#124, #125)neuprint_get_roiInfo() and neuprint_get_meta() (#113)neuprint_ROI_hierarchy() (#110)neuprint_get_meta() has more efficient handling of duplicates (#92)neuprint_read_skeletons() fails to pass on heal.threshold for >1 skeleton bug (#121)neuprint_login() more robust to variations in server specification (#118)This release bumps neuprintr to v1.0. There have been a huge number of fixes and improvements since the last release. Furthermore we would now consider it a mature package; we are currently using it for analysis in a number of late stage papers and would be happy for others to do the same. You can see the full list of closed issues on GitHub.
New and Improved Functionality for End Users: * Chunking for large neuprint_get_roiInfo() and neuprint_get_meta queries() (#100) * Chunk connection table (#99) * Better paths function #98 * Speed up neuprint_get_synapses() (#94, #96) * Flexible fields for roiInfo (#95) * Add “upstream” and “downstream” fields in extract_connectivity_df (#93) * Use (escaped) double quotes in neuprint_search() string to support e.g. neuron names with prime characters (#86) * Add an option to make fixed searches #80 * More flexible bodyid specification (#83) * Improved healing function for skeletons (thanks also to @SridharJagannathan) #76, #32 * Add statusLabel to neuprint_get_meta() (#73) * neuprint_get_neuron_names() should always return as many outputs as inputs #65 * Teach neuprint_get_adjacency_matrix() to accepts inputs/outputs #64, #62 * Option for neuprint_ROIs() to get only superLevelROIs #55 (thanks to @mmc46 for suggestion) * return bodyids as characters, not factors #30, #27 * Teach neuprint_search() to query type as well instance/name #28 * Adding depth to path functions #37 * Return link order in paths functions #36
Lower Level: * More informative errors for neuprint_fetch_custom() #38, #44 * Harmonise approach to dataset specification #29, #26, #25 * Use neuprint_datasets() to define a default dataset #68
Fixes: * Fix breaking change in tibble v3.0 (#108, #109) * Add an argument to bypass roi checks (#103) * Get synapses fix (#102) * Make returned bodyids in neuprint_get_roiInfo() characters (#101) * Connector IDs are only for presynapses (#97) * Make neuprint_read_neurons() show more errors (#84, #91) * Fix bug in neuprint_get_synapses() when progress=T (#90) * Fix neuprint_ROI_connectivity() (#87, #88) * Bug in neuprint_read_neurons() when connectors=FALSE (#85) * Character vectors specifying ids > max big int should trigger errors (#82) * Fix duplicate columns in output of neuprint_find_neurons() #81 * Fix neuprint_bodies_in_ROI() #78, #79 * Define a default dataset based on current neuPrint connection #77 * Path queries always return the total weight #72 * Fix fetching and plotting some bodyids fails in neuprintr #71 (thanks to @lisa-marin for report) * Fix neuprint_connection_table() does not pass on by.roi when progress=T #70 * Fix by.roi argument in neuprint_connection_table() (#69) (thanks to @markuspleijzier for report) * Fix neuprint_simple_connectivity() #61, #59 * Fix neuprint_read_neurons() #54 (thank to @mmc46 for report) * Fix neuprint_ROI_mesh() encoding warning #49 * prefer character vectors over factors for result dataframes #48, #47 * Adding basic examples for path functions #46 * Flow centrality #45 * add cellBodyFiber() and soma to neuprint_get_meta() #43 * Fix handling of unique bodyids #42, #39 * Fix neuprint_read_neurons() fails because of id2bit64() #41 * Make neuprint_connection_table return same results with progress=T/F #40
Docs/Build: * Add slideshare to readme #35 * Add code coverage #33 * Travis build docs #31
This release includes a large number of changes targeted at the public release of the hemibrain dataset. Much of this work was contributed by Romain Franconville, who is now a core author of the package.
neuprint_get_meta() (#24)neuprint_get_paths(), neuprint_get_shortest_paths() functions to find connection paths between neurons (#15, #17, #23)neuprint_read_neuron_simple (#12)neuprint_get_synapses() (#10)neuprint_connection_table() (#8)extract_connectivity_df*() (#7)neuprint_get_roiInfo() function to access the roiInfo field (#5 by @romainFr)neuprint_connection_table() and neuprint_get_synapses() for ROIs with parentheses (#4 by @romainFr)grepl for ROIs (#3 by @romainFr)neuprint_connection() for explicit server / token arguments.neuprint_fetch() when server ends in a /neuprint_login() or your .Renviron
NEWS.md file to track changes to the package.