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RELEASE_NOTES.txt
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OVERVIEW
-----------------------------------------
This KBase service provides helper methods for performing data access, manipulation, analysis,
and visualization of multiple sequence alignments (MSAs) and phylogenetic trees.
VERSION: 1.1.0 (Released 12/5/2014)
------------------------------------------
This minor release fixes several small bugs, and improves support for working
with GenomeSet and FeatureSet objects.
NEW FEATURES:
- added the "build_genome_set_from_tree" helper method
- GenomeSet reference accepted as input to construct_species_tree
- FeatureSet reference accepted as input to construct_multiple_alignment
VERSION: 1.0.0 (Released 7/24/2014)
------------------------------------------
This is a major refactor of the Tree service, which has now migrated to a more
stable Java-based server. Old methods are either ported to the new Java code
or are relayed to the original perl functionality. We anticipate that all
methods will eventually be ported into the Java-based server. The module name
has also changed to KBaseTrees (to reflect the format of KBase module names in
the Workspace). Thus old deployments that use the old Tree clients will no
longer work. You should migrate to the new KBaseTrees set of clients.
The original service specification file (Tree.spec) is also now deprecated and
no new functions or changes will be added. The replacement API specification
file is named KBaseTrees.spec. The CLI has not changed.
NEW FEATURES:
- added method for constructing species trees with user genomes
- added method for rerooting tree
VERSION: 0.91 (never released to production)
------------------------------------------
NEW FEATURES:
- none
UPDATED FEATURES / MAJOR BUG FIXES:
-trivial update to conform to API standards
-deprecated script tree-url (because users should no longer change the url, and
it doesn't work in IRIS)
-migrated to COMMANDS.json format for deploy
-allow deploying commands on make to dev_container/bin
VERSION: 0.9 (Released 8/5/2013)
------------------------------------------
NEW FEATURES:
- none
UPDATED FEATURES / MAJOR BUG FIXES:
-general backend code cleanup, improvement
-trivial API changes to conform to new API standards (note, may break old Java clients)
-removed dependency on kb_seed
-improved test coverage
VERSION: 0.04 (Released 4/4/2013)
------------------------------------------
NEW FEATURES:
-abundance profile workflow operates on tables of data (grouping by sample) rather than
requiring iteration over each sample.
-get_tree method supports options to replace node names with a feature id or genome id
even when there is no canonical feature per leaf
-added api method to merge leaves that have zero distance; this method is exposed through
the tree-remove-nodes script.
UPDATED FEATURES / MAJOR BUG FIXES:
-fixed scripts so that end-to-end abundance profiling workflow can operate in IRIS.
VERSION: 0.03 (Released 2/4/2013)
------------------------------------------
NEW FEATURES:
-added command line scripts that wrap client methods for fetching trees/alignments and
relabeling nodes in trees; command line scripts are wrapped for IRIS deployment/testing
UPDATED FEATURES / MAJOR BUG FIXES:
-none.
ANTICIPATED FUTURE DEVELOPMENTS:
-ability to associate nodes with data (e.g. descriptions, abundance values) by mapping node
ids to data in tab-delimited tables
-additional options for tree visualization
VERSION: 0.02 (Released 11/20/2012)
------------------------------------------
NEW FEATURES:
-This is the first public release of the Phylogenetic Tree Service.
-added query methods for tree/alignment retrieval by tree ID, feature ID, protein MD5
-added basic tree label/structure manipulation methods
-added basic tree introspection methods which accept tree structures and returns computed or extracted
properties of the tree structure or select tree nodes
-added basic html visualization method (draw_html_tree)
UPDATED FEATURES / MAJOR BUG FIXES:
-none.
ANTICIPATED FUTURE DEVELOPMENTS:
-command line scripts that wrap every client library method and are available through IRIS
-richer set of query methods for retrieiving trees
-ability to associate nodes with data (e.g. descriptions, abundance values) by mapping node
ids to data in tab-delimited tables
-additional options for tree visualization
VERSION: 0.01 (Released 8/16/2012)
------------------------------------------
NEW FEATURES:
-This is the first internal release of the Phylogenetic Tree Service, all methods are new.
UPDATED FEATURES / MAJOR BUG FIXES:
-none.
ANTICIPATED FUTURE DEVELOPMENTS:
-public release of the service