Changelog

Source: NEWS.md

aedes 0.4

This version includes substantial improvements to the functions for handling flytable metadata (especially aedes_add_neurons()), which should now provide an efficient approach to add newrows including automatic definition of key points on the neuron, soma location, side of brain etc.

• coconatfly adapter (cf_meta()/cf_partners()): ungrouped neurons now reach coconatfly as an integer64 NA group, so cf_cosine_plot(group="group") drops them instead of collapsing every ungrouped partner into one spurious shared feature column. (An NA group already came out of aedes_meta(), but coconatfly re-runs fafbseg::flywire_ids() on the group column, which preserves an integer64 NA yet maps a numeric/character NA to "0".)
• New aedes_set_meta() bulk-updates existing flytable rows. (#10)
• New aedes_set_group() sets group to lowest serial_id (but maintains selected serial number if joining an existing group in the table). (#10)
• aedes_add_neurons() enrichment: auto-fill soma_xyz/nucleus_id/side/point_xyz and require superclass/status/initials on new rows; also adds annotator/proofreader multi-select handling. (#10)
• aedes_meta() gains a translate_ids argument to ensure incoming ids match the requested materialisation state so that rows are reliably selected. (#10)
• aedes_add_neurons() accepts a data.frame ids carrying a root_id column plus per-row metadata (one value per id, vs. the recycled scalars of ...); a data.frame column naming an auto-fill field overrides the auto-fill and skips the corresponding soma/side service call. (#17)
• aedes_meta() / aedes_ids() default expiry = 0 and document expiry/refresh, so metadata reads are fresh by default. Requires fafbseg (>= 0.15.17). (#16)
• aedes_add_neurons(): robust handling of ids that collapse to one neuron after pinning — recycled scalars drop the duplicate with a warning, per-id values are a hard error. (#15)
• New aedes_partner_summary(), an Aedes-aware wrapper around fafbseg::flywire_partner_summary() (one row per synaptic partner). (#14)
• aedes_key_point() delegates to fafbseg::flywire_key_point() / key_point_from_neuron(), becoming a thin with_aedes() wrapper. (#13)
• aedes_flytable_update(): don’t flag NA root_ids as duplicated. (#12)
• aedes_flytable_update(): only write columns that can change, treat NA root_duplicated as FALSE, and return the changed-rows data frame. (#11)
• New aedes_soma_side() / aedes_point_side(); predict the side of a point or soma. (#9)

Committed directly to main:

• aedes_xyz2id() now defaults to mip = 1 (the LMB transform service dropped scale 0). (fbdbc71)
• Docs: clarify the three aedes_main editing functions (c25ff33); add a citation and Zenodo badge (d768f1c).

Full diff: https://github.com/flyconnectome/aedes/compare/v0.3...v0.4

aedes v0.3

• New aedes_add_neurons() for upserting rows in the FlyTable aedes_main table. Pins a single materialisation timestamp on both the supplied ids and a fresh aedes_meta(expiry=0) read so the join-by-root_id is reliable, and computes point_xyz for new rows via aedes_key_point(). Avoids the heavy aedes_flytable_update() pass. (#8)
• New aedes_key_point() returns a “good” annotation point on a neuron: the principal branch point of its L2 skeleton, with the neuron optionally rerooted onto its furthest endpoint first. (#8)
• aedes_sequential_update() gains version and timestamp arguments so callers can pin all downstream service calls (aedes_xyz2id(), fafbseg::flywire_updateids()) to the same materialisation. Defaults to timestamp = 'now' when neither is supplied. (#8)
• read_aedes_neurons() wraps fafbseg::read_l2skel() and reroots each neuron via a per-neuron cascade: FlyTable soma_xyz → flywire_nuclei() → the packaged neuropil mesh (signed-distance fallback). Provenance recorded in a soma_source column. (#6)
• New aedes_soma_position() returns one-row-per-id soma positions, matching strictly by root_id; private helper silently collapses bookkeeping duplicates in the nucleus table and warns only when a root_id has genuinely distinct nuclei. (#6)
• New aedes_neuropil_mesh dataset: mesh3d of the Aedes brain neuropil (nm coordinates), shipped via LazyData. (#6)
• New aedes_mirror() and related transforms for mirroring points and objects through the Aedes brain. (#5)
• aedes_chunkedgraph_edits() fixes data-frame assembly for chunked responses that include empty batches or missing names, and adds incremental on-disk caching for operation fetches (Arrow plus a missing-op sidecar). (#4)
• aedes_sequential_update() no longer loses work when individual supervoxel lookups fail. (#3)

aedes v0.2

• Fast supervoxel lookups via the MRC LMB transform service (aedes_xyz2id() with method="auto"), > 100x faster than cloudvolume for bulk queries.
• also features chunked requests with progress reporting and automatic retry at reduced chunk size on failure.
• aedes_sequential_update() now uses the fast transform service for supervoxel lookups.
• aedes_meta() now wraps fafbseg::cam_meta() for metadata queries, with improved documentation of version/timestamp handling.
• Refactored aedes_cfmeta() column renaming for robustness.
• Package hygiene: removed unused imports, added glue, httr, nat.utils, pbapply to Imports, pinned fafbseg (>= 0.15.5).

aedes v0.1

• Initial version on github with basic functions from 2025aedes aedes-dataset-funs.R
• also has docs at https://flyconnectome.github.io/aedes