BioProv - A provenance library for bioinformatics workflows - Release v0.1.24

• [x] State requirements more clearly
• [x] Improve error handling when getting Program attributes
• [x] Add __doc__ variable to modules to build documentation
• [x] Fix File.size property
• [x] Add File.raw_size property

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.23a

• Patch PresetProgram SeqFile addition feature [x]
• Fix SeqFile deserializer [x]
• Add importrecords arg to `bp.loadproject()` [x]
• Improve reserved aminoacid characters [x]
• Add SeqFile.max_seq and .min_seq properties [x]
• Patch Project deserializer to improve BioProvDocument creation [x]
• Make shorter Environment hashes [x]
• Improve Project __repr__ [x]

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.23

• Patch PresetProgram SeqFile addition feature [x]
• Fix SeqFile deserializer [x]
• Add importrecords arg to `bp.loadproject()` [x]
• Improve reserved aminoacid characters [x]
• Add SeqFile.max_seq and .min_seq properties [x]
• Patch Project deserializer to improve BioProvDocument creation [x]
• Make shorter Environment hashes [x]
• Improve Project __repr__ [x]

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.22

Changes in this Release - First Change - Second Change

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.21

v0.1.21

• Add config argument to bp.loadproject() (this is a temporary fix) [x]
• Add db property to Config class (prevents bug when setting DB path) [x]
• Improve a few docstrings [x]
• Refactor sha1 as sha256 [x]
• Add add and radd dunder methods for Directory and File [x]
• Package workflows in single module [x]
• Add FastTree PresetProgram [x]

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.20

• Changes in this Release
• Debug graphical DOT output
• Add Muscle PresetProgram
• Add MAFFT PresetProgram
• Add Kallisto PresetProgram
• Add extra_flags attribute to PresetProgram
• Refactor EnvProv class as Environment
• Allow creation of users and envs to be optional
• Create environments only when there's an associated activity
• Create Sample dunder enter and dunder exit methods
• Fixing wasDerivedFrom bug when sample and file have same names
• Fix extra Environments bug

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.19

v0.1.19

• Debug API endpoint (#23) [x]
• Implement logging [x]
  • Implement Workflow logging [x]
• Debug Workflow Steps [x]
• Remove workflow main methods [x]
  • Workflows must now be called only from the CLI [x]
• Implement post-workflow actions [x]
  • Update db [x]
  • Upload to ProvStore [x]
  • Write PROVN [x]
  • Write PDF [x]
• Add Sample.autoupdatedb() methods [x]
• Remove logger call when updating Project in database [x]

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.18a

Changes in this Release - First Change - Second Change

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

BioProv - A provenance library for bioinformatics workflows - Release v0.1.18

• Add support for ProvStore API (#23) [x]
• Add subparsers for CLI commands [x]
• Add Directories class to Files module [x]
  • Support globbing Directory outputs [x]
• Increase test coverage [x]
• Added more example data [x]
• Make config.threads an integer to support operations [x]

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago