qiime2/provenance-lib

Issues

• BUG: reproducibility-supplement renders temp filepaths in scripts

  #100 opened 2 years ago by ChrisKeefe
  3

• update README and forum tutorial in preparation for inclusion of provenance-lib in the QIIME 2 2023.5

  #108 opened a year ago by gregcaporaso
  0

• Report plugin dependencies missing from the environment

  #54 opened 3 years ago by ChrisKeefe
  3

• q2_citation.bib for found in /conda/envs/qiime2-2022.2/lib/python3.8/site-packages/provenance_lib/

  #103 opened 2 years ago by cherman2
  5

• Improve replay from captured metadata files

  #63 opened 2 years ago by ChrisKeefe
  1

• Allow user to pass output folder for recorded metadata dumps

  #57 opened 2 years ago by ChrisKeefe
  0

• REFAC: write_citations should handle dags or filepaths

  #101 opened 2 years ago by ChrisKeefe
  0

• Don't dump captured metadata multiple times

  #99 opened 2 years ago by ChrisKeefe
  0

• Touchless replay

  #98 opened 2 years ago by ChrisKeefe
  0

• Metadata .tsvs lost in replay with multiple metadata inputs

  #97 opened 2 years ago by ChrisKeefe
  1

• Simplify sample_metadata loading

  #44 opened 3 years ago by ChrisKeefe
  1

• Scripts should include target version information

  #91 opened 2 years ago by ChrisKeefe
  1

• Allow command aliasing

  #95 opened 2 years ago by ChrisKeefe
  0

• Replay Does not Accept Symlink Files

  #94 opened 2 years ago by cherman2
  0

• FileNotFoundError: [Errno 2]. No 'copyright_note.txt'

  #92 opened 2 years ago by cherman2
  0

• OSX may break replay

  #70 opened 3 years ago by ChrisKeefe
  1

• Package for Conda

  #90 opened 2 years ago by ChrisKeefe
  0

• Improve support for replay in upstream Usage driver code

  #40 opened 3 years ago by ChrisKeefe
  1

• CI: MYPY and coverage checks

  #50 opened 3 years ago by ChrisKeefe
  0

• Simple checksum validation tool for CLI?

  #68 opened 3 years ago by ChrisKeefe
  0

• citation for provenance replay paper

  #55 opened 3 years ago by ChrisKeefe
  1

• Broad analysis metadata reporting

  #76 opened 3 years ago by ChrisKeefe
  0

• Compute environment reporting

  #77 opened 3 years ago by ChrisKeefe
  0

• ENH: early stopping in replay scripts

  #82 opened 2 years ago by nbokulich
  1

• DOC: TODO notes -> FIX ME ?

  #83 opened 2 years ago by ChrisKeefe
  1

• Acknowledge original analyst's IP

  #87 opened 2 years ago by ChrisKeefe
  0

• Support data integrity bug identification

  #86 opened 2 years ago by ChrisKeefe
  1

• Add instructions for replay to replay scripts

  #81 opened 2 years ago by ChrisKeefe
  0

• Replay produces a methods manifest

  #75 opened 3 years ago by ChrisKeefe
  2

• Additional target interfaces

  #65 opened 3 years ago by ChrisKeefe
  0

• Annotate transitions into/out of QIIME 2 analysis

  #80 opened 3 years ago by ChrisKeefe
  0

• Additional user interfaces

  #79 opened 3 years ago by ChrisKeefe
  0

• Automate computing environment management

  #78 opened 3 years ago by ChrisKeefe
  0

• Inner view of nested provenance

  #74 opened 3 years ago by ChrisKeefe
  0

• ReplayPythonUsage should optionally capture all results from each action

  #69 opened 3 years ago by ChrisKeefe
  0

• DirectoryParser's recursive behavior should be optional.

  #58 opened 3 years ago by ChrisKeefe
  0

• ReplayCLIUsage: Support lumping outputs into output_dir

  #66 opened 3 years ago by ChrisKeefe
  0

• Better error message for non-file-like objects passed to ArtifactParser

  #37 opened 3 years ago by ChrisKeefe
  0

• Mandatory replay features

  #43 opened 3 years ago by ChrisKeefe
  1

• Thoughts: Replay UI Options

  #45 opened 3 years ago by ChrisKeefe
  1

• Memoize topological sort, and related questions

  #60 opened 3 years ago by ChrisKeefe
  0

• OPT: Memoize dag.collapsed_view

  #62 opened 3 years ago by ChrisKeefe
  0

• Insert abstract Metaclass for ReplayUsage drivers

  #67 opened 3 years ago by ChrisKeefe
  0

• Add DOIs to citations for common methods.

  #59 opened 3 years ago by ChrisKeefe
  1

• Consider supporting a minimal ProvNode definition

  #61 opened 3 years ago by ChrisKeefe
  0

• Use ExecutionUsage to test validity of written usage examples

  #52 opened 3 years ago by ChrisKeefe
  0

• efficient replay for multiple interfaces

  #42 opened 3 years ago by ChrisKeefe
  0

• Improve input sanitization

  #41 opened 3 years ago by ChrisKeefe
  0

• ProvDAG should check its own "guaranteed" properties

  #38 opened 3 years ago by ChrisKeefe
  0

• Think about ProvDAG equality criteria

  #36 opened 3 years ago by ChrisKeefe
  0