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neuprintr (development version)

neuprintr 1.3.2

What's Changed

  • Interactive heatmaps in cosine plots by @jefferis in #168
  • neuprint_cosine_plot can now return hclust object by @jefferis in #169

Full Changelog: https://github.com/natverse/neuprintr/compare/v1.3.1...v1.3.2

neuprintr 1.3.1

What's Changed

  • add neuprint_cosine_plot() and neuprint_cosine_matrix() to support cosine similarity clustering by @jefferis in #167

  • Fix when dataset for connection not passed on by @jefferis in #162

  • WIP: improved error messages by @jefferis in #161

  • Fix adjacency matrix names by @jefferis in #163

  • fix bug (noticed w malecns) when correct rois not fetched by @jefferis in #165

  • Fix bug when only presynapse is inside ROI by @jefferis in #166

https://github.com/natverse/neuprintr/compare/v1.3...v1.3.1

neuprintr 1.3

  • Fix problem with numeric bodyids by @jefferis in #142
  • Feature/meta more fields by @jefferis in #144
  • Fix: more metadata fields by @jefferis in #145
  • Improvements for large matrices in neuprint_get_adjacency_matrix() by @jefferis includes chunking and an optional threshold (#147)
  • Fix pre post docs (and add partners arg) by @jefferis in #148
  • fix for dplyr type error in neuprint_get_meta by @jefferis in #149
  • Give neuprint_connection_table a summary option by @jefferis in #150
  • Feature/connection table summary by @jefferis in #151
  • Feature/search numeric by @jefferis in #152
  • implement where searches for ids/meta by @jefferis in #153
  • Allow neuprint_login to update connections by @jefferis in #154
  • Standardise metadata column types by @jefferis in #155
  • Fix fields with brackets by @jefferis in #158

Full Changelog: https://github.com/natverse/neuprintr/compare/v1.2...v1.3

neuprintr 1.2

  • Fixed querying by name for non-hemibrain neurons (#139, #140 by @dokato)
  • Fix error with bad login details (#138)
  • Ignore case of environment variable with login details (#137)
  • neuprint_connection_table() returns error when no connections found (#135)
  • neuprint_connection_table(): pass on details argument when using progress bug (#133)
  • Add neuron name/type to neuprint_connection_table() (#132)
  • Use server URL returned at login (#130)
  • Basic implementation and test for connection threshold (#127, #128)
  • Pass through NA bodyids when fetching metadata (#126)
  • neuprint_login() should choose the newest dataset as default (#124, #125)
  • Adding the synonyms field in metadata (#123 @romainFr)

Full list of fixed issues

neuprintr 1.1

  • Can now specify default dataset for a connection (#115, #116)
  • Optimise neuprint_get_roiInfo() and neuprint_get_meta() (#113)
  • More features for neuprint_ROI_hierarchy() (#110)
  • break down queries that are too large (#89)
  • neuprint_get_meta() has more efficient handling of duplicates (#92)
  • Fix neuprint_read_skeletons() fails to pass on heal.threshold for >1 skeleton bug (#121)
  • Fix and test for incomplete server url (#119)
  • Make neuprint_login() more robust to variations in server specification (#118)
  • Safe field catch (#111)
  • Update test baselines for R 4.0 (#120)

neuprintr 1.0

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

neuprintr 0.4

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.

  • Add @romainFr as an author
  • Update README to mention hemibrain dataset
  • Return the cropped parameter in neuprint_get_meta() (#24)
  • Add neuprint_get_paths(), neuprint_get_shortest_paths() functions to find connection paths between neurons (#15, #17, #23)
  • Roi connectivity fixes (#21, #20)
  • Fix neuprint_find_neurons("EB") returns error (#18)
  • Fix common connectivity fix (#13, #16)
  • Small fix to avoid returning results from ROIs that start with the same letters (#14)
  • Fixes for reading neurons with new data model switch to neuprint_read_neuron_simple (#12)
  • More fixes for new hemibrain server (#11)
  • Fix neuprint_get_synapses() (#10)
  • Fix neuprint_connection_table() (#8)
  • Update/simplify extract_connectivity_df*() (#7)

neuprintr 0.3

  • Support for new data model being tested for hemibrain data release (#6)
  • Add neuprint_get_roiInfo() function to access the roiInfo field (#5 by @romainFr)
  • Correction to neuprint_connection_table() and neuprint_get_synapses() for ROIs with parentheses (#4 by @romainFr)
  • Fix grepl for ROIs (#3 by @romainFr)
  • A few changes in metadata pulling (#2 by @romainFr)
  • Fix bug in neuprint_connection() for explicit server / token arguments.
  • Fix bug in neuprint_fetch() when server ends in a /

neuprintr 0.2.1

  • switch repo to github natverse organisation

neuprintr 0.2.0

  • Support for advanced curl options via neuprint_login() or your .Renviron
  • Added a NEWS.md file to track changes to the package.

neuprintr 0.1.0

  • First functional version