caporaso-lab/developing-with-qiime2

Issues

• when to raise an error versus when to `warnings.warn`

  #108 opened 24 days ago
  1

• DRY: figure out how to not duplicate code between the q2-dwq2 plugin and the plugin tutorial

  #103 opened 2 months ago
  0

• create plugin actions that wrap functionality written in R

  #98 opened 2 months ago
  0

• add help text and usage examples for all artifact classes and formats in `q2-types`

  #97 opened 2 months ago
  0

• logo background color is slightly off in dark mode - fix to match background

  #95 opened 2 months ago
  0

• link to the q2-dwq2 repo at the beginning of the plugin development tutorial, so the reader can/try see the final product

  #93 opened 2 months ago
  0

• review all API reference sections to confirm that the APIs that we want in each are referenced

  #91 opened 2 months ago
  0

• clarify that "derivative works" of the template plugin are allowed, which is different than the license of the book itself

  #90 opened 2 months ago
  0

• add how-to on distributing a plugin

  #88 opened 2 months ago
  1

• stop hosting at https://cap-lab.bio/developing-with-qiime2

  #86 opened 2 months ago
  0

• configure external links to open in a new tab

  #76 opened 2 months ago
  0

• add funding acknowledgements

  #75 opened 2 months ago
  0

• address API doc build warnings

  #74 opened 2 months ago
  0

• conclusion document

  #72 opened 2 months ago
  1

• "documentation engine" interface tutorial

  #71 opened 2 months ago
  0

• add sequence database search Pipeline, with parallel support

  #70 opened 2 months ago
  0

• add multiple sequence alignment Pipeline, with parallel support

  #69 opened 2 months ago
  0

• add a first Pipeline which calls nw-align and summarize-alignment

  #68 opened 2 months ago
  0

• centralize q2-dwq2 commit links with myst substitutions

  #67 opened 2 months ago
  0

• plugin tutorial: add transformer for `DNA.skbio` to `SingleRecordDNAFASTAFormat`, and adapt usage example code to use it

  #64 opened 2 months ago
  1

• integrate nw-align imports as they are introduced in the code

  #63 opened 2 months ago
  0

• structure of a plugin package

  #62 opened 2 months ago
  1

• artifact classes

  #59 opened 3 months ago
  0

• how-to: identify a relevant artifact class

  #58 opened 3 months ago
  0

• add license

  #55 opened 2 months ago
  1

• complete ArtifactClass definition

  #43 opened 2 months ago
  1

• semantic validation

  #42 opened 3 months ago
  0

• add framework explanation on Pickling

  #41 opened 3 months ago
  0

• transformation API

  #40 opened 3 months ago
  0

• update API doc strings in framework for public-facing APIs

  #38 opened 3 months ago
  0

• translate plugins *Writing Usage Examples* how-to from rst to md

  #36 opened 3 months ago
  0

• translate rst in `framework/explanations/types` to markdown

  #34 opened 3 months ago
  0

• document Archive Version 6

  #32 opened 3 months ago
  0

• explanation: CI for plugin development

  #31 opened 4 months ago
  0

• move *Parallel configuration and usage in QIIME 2* to general-purpose user documentation

  #29 opened 4 months ago
  0

• how-to: avoid putting artifacts in your repo for testing purposes (and why)

  #28 opened 4 months ago
  1

• how-to: test plugins without putting `.qza` files in the repo

  #27 opened 4 months ago
  1

• port old developer docs

  #21 opened 2 months ago
  0

• update user docs build instructions to use tiny distribution for faster build times

  #13 opened 5 months ago
  0

• port quickstart from old dev docs

  #8 opened 5 months ago
  1

• plugin development how-to: return `ResultCollection` with named outputs

  #7 opened 5 months ago
  0

• migrate (or just remove) "developing a QIIME 2 plugin" content from user docs

  #5 opened a year ago
  1

• convert all .rst files to .md files

  #2 opened 4 months ago
  1