Changelog

Source: NEWS.md

malevnc (development version)

malevnc 0.4.0

Breaking change to manc_annotate_body() defaults:

• test now defaults to FALSE (was TRUE). Calls without an explicit test argument now hit the production Clio store rather than the (retired) test server.
• New dry_run argument with default TRUE. Calls without an explicit dry_run argument now return a preview tibble of the POST body that would be sent, instead of writing annotations. Pass dry_run=FALSE to actually write.

Together these defaults make the function safe-by-default while actually offering an opportunity for end users to check the annotations to be uploaded. Since test=FALSE essentially always generated an error at the moment, it was not very useful. Existing scripts intended to write to Clio will need to add dry_run=FALSE; scripts that intentionally relied on the test server will need to add test=TRUE.

Other changes in this release:

• New dry_run argument on manc_annotate_body() preview the POST body that would be sent to Clio, without writing.
• Fix latent bug in compute_clio_delta() that stripped the fetched status column, causing redundant writes of unchanged status values.
• Clio schema type checks in manc_annotate_body() based on check_types, coerce_integerish which default to TRUE.

Full Changelog: https://github.com/natverse/malevnc/compare/v0.3.3…v0.4.0

malevnc 0.3.3

• switch to manc:v1.2.3 as default public dataset
• manc_connection_table: check if desired fields exist
• cache manc_ids, manc_neuprint_meta for static data

Full Changelog: https://github.com/natverse/malevnc/compare/v0.3.2…v0.3.3

malevnc 0.3.2

• Update to cope with malecns clio config by @jefferis in https://github.com/natverse/malevnc/pull/77
• support clio configs that refer to any DVID node by @jefferis in https://github.com/natverse/malevnc/pull/76
• Add clio new fields annotation check by @jefferis in https://github.com/natverse/malevnc/pull/75
• Support for yakuba by @jefferis in https://github.com/natverse/malevnc/pull/74

Full Changelog: https://github.com/natverse/malevnc/compare/v0.3.1…v0.3.2

malevnc 0.3.1

• make manc:v1.2.1 the public default
• fix bug in reading meshes for id=100000
• Feature/flexible url shortening by @jefferis in https://github.com/natverse/malevnc/pull/70
• doc polishing by @jefferis in https://github.com/natverse/malevnc/pull/71

Full Changelog: https://github.com/natverse/malevnc/compare/v0.3…v0.3.1

malevnc 0.3

Version 0.3 provides stable access to the public manc data release.

• support annotating with alternative clio user by @jefferis in https://github.com/natverse/malevnc/pull/68
• support for 64 bit ids in manc_annotate_body by @jefferis in https://github.com/natverse/malevnc/pull/69
• Update MANC.nerves to 35 meshes and update cols / docs for nerve meshes
• Respect show.extra even for long id lists (d25fdfd6e9e8a4d7032a4ab964eee8ec30181687)
• support for meshes with public manc release
• Respect show.extra even for long id lists (d25fdfd6e9e8a4d7032a4ab964eee8ec30181687)

Full Changelog: https://github.com/natverse/malevnc/compare/v0.2.9…v0.3

malevnc 0.2.9

This is a major release providing support for the publication of the [MANC connectome] (https://www.janelia.org/project-team/flyem/manc-connectome). We expect to bump to v0.3 when all changes have stabilised.

• Feature/neuron units by @jefferis in https://github.com/natverse/malevnc/pull/60
• Feature/manc 1.0 by @jefferis in https://github.com/natverse/malevnc/pull/65
• improved support for JRC xforms by @jefferis in https://github.com/natverse/malevnc/pull/66
• Test/actionsv3 by @jefferis in https://github.com/natverse/malevnc/pull/67

malevnc 0.2.8

• switch repo to natverse org preparing for public data release
• Add show.extra to manc_body_annotations
• more options to exclude neuprint fields driven by the (temporary) addition of hundreds of new columns to the visual system for the male cns dataset. https://github.com/flyconnectome/malevnc/commit/0cb652aade1835d33f290e2a4a1bc7c3b9e1c2df
• Switch @dokato to author

malevnc 0.2.7

What’s Changed

• Add flyem_shorten_url(), flyem_expand_url() by @jefferis in https://github.com/flyconnectome/malevnc/pull/54

• manc_connection_table() defaults to selected neuprint metadata

• MANC.tracts meshes object added by @dokato in https://github.com/flyconnectome/malevnc/pull/59

• Added download_manc_registrations() to download bridging registrations MANC <> JRC2018VNCU/M/F by @dokato in https://github.com/flyconnectome/malevnc/pull/58

• Add colour_leg_muscles() by @jefferis in https://github.com/flyconnectome/malevnc/pull/62

• New Clio query parsing (for manc_annotate_body) parametrized by @dokato in https://github.com/flyconnectome/malevnc/pull/55 Also provides support for malecns annotation

• read options(malevnc.dataset) in clio_version (mostly for malecns)

• Critical fix to clio_set_token() by @dokato in https://github.com/flyconnectome/malevnc/pull/56

• fix bug in manc_meta() due to retired instance field by @jefferis in e6035ad31e7b3d75d7395079c6821d62a8933922

• Retire manc_set_lrgroup() We will now just set the group column directly via the clio interface. No need to use DVID / set instance values / sides etc.

Full Changelog: https://github.com/flyconnectome/malevnc/compare/v0.2.6…v0.2.7

malevnc 0.2.6

What’s Changed

• New test store address by @dokato in https://github.com/flyconnectome/malevnc/pull/49
• More options added to manc scene by @dokato in https://github.com/flyconnectome/malevnc/pull/50
• ENH: force option added to clio_token by @dokato in https://github.com/flyconnectome/malevnc/pull/51
• Clio set token function added by @dokato in https://github.com/flyconnectome/malevnc/pull/52
• manc_get supports new Clio API by @dokato in https://github.com/flyconnectome/malevnc/pull/53

Full Changelog: https://github.com/flyconnectome/malevnc/compare/v0.2.3…v0.2.6 # malevnc 0.2.5

• Fix manc_set_dvid_instance() for >1 input ids

malevnc 0.2.4

• update manc_set_dvid_instance() to cope with synonyms

malevnc 0.2.3

• add manc_view3d() function with standard views based on symmetric MANC template.

malevnc 0.2.2

• Factor out and export low level manc_set_dvid_annotations() function.
• Export manc_set_dvid_instance() and teach it to set instance/type and corresponding users for one or more body ids.

malevnc 0.2.1

• Updated manc scene links by @dokato in https://github.com/flyconnectome/malevnc/pull/42
• Fix point annotation dataset (e.g. for use by malecns) by @jefferis in https://github.com/flyconnectome/malevnc/pull/44

Full Changelog: https://github.com/flyconnectome/malevnc/compare/v0.2.0…v0.2.1

malevnc 0.2.0

• WIP: simplified compute_clio_delta and remove NAs by @dokato in https://github.com/flyconnectome/malevnc/pull/30
• Add manc_leg_summary/manc_side_summary by @jefferis in https://github.com/flyconnectome/malevnc/pull/31
• Fix/dvid nodes by @jefferis in https://github.com/flyconnectome/malevnc/pull/32
• MANC nerve mesh added by @dokato in https://github.com/flyconnectome/malevnc/pull/25
• Quck fix manc meta by @dokato in https://github.com/flyconnectome/malevnc/pull/33
• Fix handling of clio int64 bodyids by @jefferis in https://github.com/flyconnectome/malevnc/pull/34
• Feature/prepare mcns by @jefferis in https://github.com/flyconnectome/malevnc/pull/35
• don’t update bodyids in manc meta by @jefferis in https://github.com/flyconnectome/malevnc/pull/39
• Use non-default oauth app when talking to google by @jefferis in https://github.com/flyconnectome/malevnc/pull/40

Full Changelog: https://github.com/flyconnectome/malevnc/compare/v0.1.2…v0.2.0

malevnc 0.1.2

• updatebodyids - backward compatibility by @dokato in https://github.com/flyconnectome/malevnc/pull/27

Full Changelog: https://github.com/flyconnectome/malevnc/compare/v0.1.1…v0.1.2

malevnc 0.1.1

What’s Changed

• Add support for reading clio store body annotations by @jefferis in https://github.com/flyconnectome/malevnc/pull/3
• ellipsis passed to mirror_brain in mirror_manc by @dokato in https://github.com/flyconnectome/malevnc/pull/5
• manc tissue surface added by @dokato in https://github.com/flyconnectome/malevnc/pull/6
• handling missing values by @dokato in https://github.com/flyconnectome/malevnc/pull/7
• Use long-lived clio token by default by @jefferis in https://github.com/flyconnectome/malevnc/pull/9
• Fix/manc read neurons missing by @jefferis in https://github.com/flyconnectome/malevnc/pull/10
• Feature/clio annotate bodies by @jefferis in https://github.com/flyconnectome/malevnc/pull/14
• symmetrized tissue surface added by @dokato in https://github.com/flyconnectome/malevnc/pull/15
• randomise the id used for body annotation tests by @jefferis in https://github.com/flyconnectome/malevnc/pull/17
• Feature/new soma info by @jefferis in https://github.com/flyconnectome/malevnc/pull/18
• Update manc annotate body by @dokato in https://github.com/flyconnectome/malevnc/pull/19
• manc_set_lrgroup accepts partial changes by @dokato in https://github.com/flyconnectome/malevnc/pull/22
• Fixed dvidtools and tests added by @dokato in https://github.com/flyconnectome/malevnc/pull/24
• fix in manc_meta when setting dvid_group by @dokato in https://github.com/flyconnectome/malevnc/pull/26
• Added a NEWS.md file to track changes to the package.

Full Changelog: https://github.com/flyconnectome/malevnc/commits/v0.1.1

malevnc 0.1

• first version