catmaid v0.9.9

• catmaid_query_connected() now returns stats for all connections but
  also allows a confidence threshold to be set. The default threshold of 1
  is a new more permissive behaviour (#113).
  Thanks to Sebastian Cachero / @schlegelp for the bug report.
• Fix bug in catmaid_connection_getenv() and friends in getting environment
  variables on some OSes. It turns out that we should switch to recommending
  variables of the form catmaid_* (#110).
  Thanks to @SridharJagannathan for detective work and a PR with a fix.

catmaid v0.9.8

• Fix bug in catmaid_get_connectors_between() when getting neuron names.
  There was an off by one error for the postsynaptic partner name (#109).
  Thanks to @mmc46 for the bug report.

catmaid v0.9.7

• New catmaid_userids() function converts user login names to ids.
• catmaid_connection() gets a new config argument to allow curl options to
  be set (#108).
• Return format and documentation fix: tree node ids in
  catmaid_get_connector_table() always refer to the query skeleton and not
  the partner neuron (#107)

catmaid 0.9.6

• Give read.neurons.catmaid() an optional fetch.annotations argument that
  adds a second metadata data.frame as an attribute to the resultant
  neuronlist() object (#18).
• Fix handling of CATMAID version string (#103)

catmaid R package v0.9.5

catmaid 0.9.5

• Stop catmaid_get_connector_table() returning duplicate rows when there are
  multiple connections between the same partner neurons at a given connector.
  Thanks to Shanice Bailey and Istvan Taisz for the bug report (#106).
• Pass on pid in catmaid_skids(), thereby fixing an issue with
  read.neurons.catmaid() with annotation queries when project id is not 1.
  Thanks to Marta Costa for the bug report (#105)

catmaid 0.9.4

• write_catmaid_selection() accepts annotations/name specs

catmaid 0.9.3

• workaround for bug in catmaid_version() (#103). Still waiting on changes in CATMAID
  for more permanent fix.
• fix import error with jsonlite version >=1.6

catmaid 0.9.2

• Teach catmaid_get_volumelist() about new API return format (#102)
• Sync catmaid_get_treenode_table() with API (#101)
• make catmaid_query_by_name() treat query as regex (#100)
• Fix bug in metadata for read_catmaid_selection (#99)
• Sort tags for neurons so that they are always returned in the same order (#98)
• Add catmaid_get_node_count() to get the number of nodes per skeleton
• Teach catmaid_get_treenodes_detail() to search by labels - can use this e.g.
  to find all nodes (regardless of neuron) with a certain tag e.g. soma.
• Fix bug in nsoma() for duplicate skids; also speed-up
• Make catmaid_login() explain why passing server directly doesn't work
• Add name|nodes to results of catmaid_get_connector_table()
• Speed-up in catmaid_get_compact_skeleton()/read.neuron.catmaid()
• Teach catmaid_get_node_count() to handle NAs/dupes

catmaid R package v0.9.1

• Add catmaid_get_labels, catmaid_set_labels, catmaid_remove_labels to
  manipulate labels (aka tags) on treenodes and connectors (#95)
• Add catmaid_get_all_labels
• Add nsoma function to return number of somata (#96)
• Add catmaid_get_treenodes_detail to get location and other information for
  many nodes at once (#94)
• Teach catmaid_get_connectors_between to find names for pre/post skids
  (optional, #93)
• Teach catmaid_get_neuronnames to handle duplicate requests efficiently (#92)
• Teach catmaid_login to accept arguments in a list (#91)

catmaid R package v0.9

This version is synced with the upcoming release of nat v1.9.0 which streamlines
some functionality but has some breaking changes in behaviour. It must be used
with nat >=1.8.12.900 from github.

• switch to Ops.catmaidneuron to match nat 1.9.0 in prep (and add version
  requirement)
• Simple search for skids with exact annotation match (#89)
  Now you can do: catmaid_skids("ORN") or read.neurons.catmaid("ORN")
• Fix bug in catmaid_skids error message when looking for one skid (#90)

catmaid R package v0.8.1

• Add function to get volumes from catmaid (#82)
• Add functions to read/write catmaid json selection files
• make catmaid_neuronnames returns NA for NA skids

catmaid R package v0.8

This is a major version update because of the new support (and recommendation)
to use environment variables for login (.Rprofile is still supported).

• support fetching login informaion from environment variables (#80)
• catmaid_get_compact_skeleton now returns list of vectors (#79)
  (used to be a list of lists, but this was less convenient and not helpful)
• fix query_by_neuron_or_annotation adding empty annotations attribute

catmaid R package v0.7.2

• Add catmaid_get_label_stats (use it to find neurons with soma)
• Add copy_tags_connectors (bring over tags/connector info)
• improve summary.catmaidneuron (#78)
• plot3d bugfix when there are NA points (and soma=T) (#77)