GitHub repository: phyloref/klados

Issues:
issue_326: state: open
title: Backend reasoning is currently down because of some sort of SSL issue on phyloref.org
user: gaurav
issue_325: state: open
title: Add link to phylogeny display explanation in lieu of a phylogeny legend
user: gaurav
issue_324: state: open
title: Do we support annotations in Newick?
user: gaurav
issue_322: state: open
title: Improve display of phyloref resolution on phylogeny
user: gaurav
issue_321: state: open
title: Documentation and Summary page improvements
user: gaurav
issue_320: state: open
title: Add UUIDs to specimen specifiers
user: gaurav
labels: difficulty: easy: Should be easy to do (1-2 days)
issue_319: state: open
title: Add support for adding a Phyx file to an existing Phyx file
user: gaurav
issue_318: state: open
title: Bump vite from 3.2.7 to 3.2.8
user: dependabot[bot]
labels: dependencies: Pull requests that update a dependency file
issue_315: state: open
title: Display multiple phylogenies
user: gaurav
issue_314: state: open
title: Prevent phylorefs from being modified by being opened by the Specifier component
user: gaurav
issue_313: state: open
title: Add an option to export phylogenies in Nexus
user: gaurav
issue_302: state: open
title: Improve the apomorphy description in apomorphy-based phylorefs
user: gaurav
issue_300: state: open
title: Improve the Phyx summary page
user: gaurav
labels: user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
difficulty: easy: Should be easy to do (1-2 days)
issue_298: state: open
title: External specifier incorrectly displayed as an internal specifier in Fisher et al, 2007 phyoref Leucophanes
user: gaurav
issue_292: state: open
title: Integrate Whelk into Klados to break the dependency on JPhyloRef
user: gaurav
issue_290: state: open
title: Display multiple resolved phylorefs on a single phylogeny
user: gaurav
labels: difficulty: moderate: Should take 3-5 days to close
issue_287: state: open
title: Test Phyx files
user: gaurav
issue_280: state: open
title: Add support for setting curators for each phyloref separately
user: gaurav
issue_277: state: open
title: Make sure example files are compliant with Phyx format
user: gaurav
issue_263: state: open
title: Simply opening a phyloreference marks it as modified
user: hlapp
labels: testing: Issues relating to improving automated tested of the Curation Tool
user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
issue_257: state: open
title: Document CSV export format
user: gaurav
issue_249: state: open
title: Add testing
user: gaurav
issue_242: state: open
title: Add per-phyloreference curator information to Phyx and Klados
user: gaurav
issue_241: state: open
title: Add "Simplify phylogeny" button to simplify trees (especially Open Tree of Life induced subtree)
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
issue_231: state: open
title: Remove baseIRI from n-Quads generation
user: gaurav
issue_227: state: open
title: Tutorial for Klados
user: gaurav
labels: difficulty: moderate: Should take 3-5 days to close
issue_226: state: open
title: Add support for exporting annotated phylogenies as Newick
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_224: state: open
title: Add automated tests for common use cases
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: hard: Will take a while to close (>5 days)
issue_223: state: open
title: Test for some common invalid phyloreferences
user: gaurav
labels: user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
programming only: No discussion necessary; just pure programming needed
difficulty: easy: Should be easy to do (1-2 days)
issue_191: state: open
title: Add autocomplete for specifiers
user: gaurav
issue_182: state: open
title: Determine how to automatically compress AJAX requests to the server
user: gaurav
issue_176: state: open
title: Improve user-facing error messages
user: gaurav
labels: user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
difficulty: easy: Should be easy to do (1-2 days)
issue_169: state: open
title: Add UI for specifiers that include both a specimen identifier and a scientific name
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_168: state: open
title: Add support for documenting qualifiers in clade definitions
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_162: state: open
title: Fix display of error messages from reasoning
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
issue_157: state: open
title: Replace UI selection using state with Vue Router
user: gaurav
issue_152: state: open
title: Create a teaching kit for Phyloref
user: gaurav
issue_146: state: open
title: Add tests for Citation.vue
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
issue_145: state: open
title: Split author/editor/series editor names into firstname-lastname
user: gaurav
issue_141: state: open
title: Bug: modifying phylogenies should reset reasoning results
user: gaurav
labels: discussion needed: Discussion is needed before this issue can be closed
programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_130: state: open
title: Update model for storing additional node properties on phylogeny nodes
user: gaurav
labels: difficulty: hard: Will take a while to close (>5 days)
issue_129: state: open
title: Add support for recording cited relationships between taxonomic units
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: hard: Will take a while to close (>5 days)
issue_126: state: open
title: Add button to collapse other lineages in a phylogeny
user: gaurav
issue_121: state: open
title: Switch to using the npm release of Phylotree.js
user: gaurav
labels: difficulty: hard: Will take a while to close (>5 days)
issue_112: state: open
title: Add a field for a verbatim qualifying clause
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: easy: Should be easy to do (1-2 days)
issue_93: state: open
title: Add support for a general-purpose OWL reasoning API
user: gaurav
issue_87: state: open
title: Add support for testing Javascript in HTML files
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
issue_85: state: open
title: Add test suite to test browser compatibility
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
programming only: No discussion necessary; just pure programming needed
difficulty: hard: Will take a while to close (>5 days)
issue_83: state: open
title: Figure out the best way to test JSON-LD exports
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
issue_81: state: open
title: Add a "Deprecated" checkbox to indicate deprecated phyloreferences
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: easy: Should be easy to do (1-2 days)
issue_80: state: open
title: Provide a side-scrolling view for clades in large phylogenies
user: gaurav
issue_76: state: open
title: Update package.json to indicate that we use some ES6 (i.e. Node 6.0+) features
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_75: state: open
title: Supplement test suite with behavior-based tests
user: gaurav
labels: testing: Issues relating to improving automated tested of the Curation Tool
issue_70: state: open
title: Make it clear that Reference Phylogeny information can be added to the Curator Notes field
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: easy: Should be easy to do (1-2 days)
issue_64: state: open
title: Provide a display for the OWL property restriction representation of a phyloreference
user: gaurav
issue_59: state: open
title: Add support for multiple curators to be recorded
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_49: state: open
title: Allow curators to annotate specifiers as unmatchable
user: gaurav
issue_45: state: open
title: Add the ability to match specifiers using genus names
user: gaurav
labels: difficulty: easy: Should be easy to do (1-2 days)
issue_44: state: open
title: Test support for matching specifiers using monomial names
user: gaurav
labels: should be complete: This issue should be done, but has either not been completely tested or a PR is being prepared.
issue_42: state: open
title: Add support for undo and redo operations
user: gaurav
issue_38: state: open
title: Support ladderizing phylogenies and rotating branches
user: gaurav
issue_37: state: open
title: Add support for rearranging phyloreferences and phylogenies
user: gaurav
issue_31: state: open
title: Add support for bootstrap values and branch lengths in phylogenies
user: gaurav
issue_29: state: open
title: Allow PHYX files to be directly uploaded to the Clade Ontology in Github
user: gaurav
issue_25: state: open
title: Add phyloreference state so we can see if they are incomplete, unvalidated or validated
user: gaurav
labels: user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
difficulty: moderate: Should take 3-5 days to close
issue_20: state: open
title: Allow taxonomic units to record additional information about specimens
user: gaurav
issue_19: state: open
title: Add support for muting specifiers
user: gaurav
labels: difficulty: moderate: Should take 3-5 days to close
issue_18: state: open
title: Attempt to parse specifiers directly from the clade definition
user: gaurav
issue_15: state: open
title: Add name resolution to improve corrections and add other identifiers
user: gaurav
labels: programming only: No discussion necessary; just pure programming needed
difficulty: moderate: Should take 3-5 days to close
issue_14: state: open
title: Add name parsing libraries for scientific name-based taxonomic units
user: gaurav
issue_12: state: open
title: Make selected UI elements more visible
user: gaurav
labels: user interface: Issues involving the user interface. Suggests that further iteration might be necessary.
difficulty: moderate: Should take 3-5 days to close
issue_9: state: open
title: Develop a comprehensive editor for additional properties of labeled nodes
user: gaurav