CHANGELOG.md

Changelog

To-do

• Fix documentation issues
  • Add subpackage docstrings
• Create methods for Sample and Pro
  • .describe
  • .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir()
  • .total_duration
• Add logger calls when saving to JSON and uploading to ProvStore

v0.1.24

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

v0.1.23

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

v0.1.22

• Simplify bp.load_project() function
• Fix user and env PROV relationships
• Add Run attributes as Program class properties (will consume from the last run)
• Add sequence dunder methods for Project class
• Improve run methods
• Allow specifying sequence format to PresetProgram outputs
• Update env file to Py 3.9

v0.1.21

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

v0.1.20

• 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

v0.1.19

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

v0.1.18a

• Patch file deserializer bug

v0.1.18

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

v0.1.17

• Add more database methods
• Improver error handling for JSON methods
• Add Project.run_programs method
• Create ProvEntity and ProvActivity for Project.files and .programs
  • Create Project Bundle for .files and .programs

v0.1.16

• Update README
• Add Project.add_files() and add_programs() method
• Improve Project deserializer
• Add Project steps to Workflow class

v0.1.15

• Improve Sample.to_series() and Project.to_csv() methods
• Add Project.to_csv() calls to tests
• Add database commands to CLI options
• Remodel environment as Agent rather than Entity
• Improve output PROVN documents
• Add Diamond preset and tests

v0.1.14

• Add blastdb example data
• Add BLASTn preset and workflow and respective tests
• Improve BioProvDB tests
• Improve Project.auto_update and Project.sha1 behaviour and tests
• Improve Workflow behaviour for custom Workflow arguments

v0.1.13

• Add BioProvDB class
• Add database methods to Project class
• Add BioProvDB tests
• Add dot attribute to BioProvDocument
• Update W3C-PROV tutorial
• Improve test coverage
• Debug Program deserializer

v0.1.12

• Patching errors for JSON IO
  • Create File, Program, Run deserializers
• Implement path replacing methods for multi-user support

v0.1.11

• Fix Run.start_time and Run.end_time testing
• Improve Program tests
• Allow users to have multiple environments
• Improving internal PROV relationships

v0.1.10

• Refactoring hashes using hashlib
• Removing EnvProv.env_set attribute
• Implementing file hashes
• Debug EnvProv JSON deserializer
• Updating introductory tutorial

v0.1.9

• Improve Env constructor in Project deserializer
• Improve Program behaviour when dealing with not found Programs
• Implement utils.serializer_filter function
• Improve pretty printing of commands

v0.1.8

• Improve BioProvDocument constructor
• Improve Sample and Program serializers
• Improve internal PROV relationships

v0.1.7

• Fix documentation build
• Refactor f-strings
• Draft of complete Prov document (all relationships)

v0.1.6

• Add more Provenance classes
• Improve Provenance graph
• Add contributing guidelines
• Refactor config and prov modules
• Add CLI options to show config
• Rename src.program to src.main
• Refactoring tests: joining src.program and src.sample tests into src.main

v0.1.5

• Add W3C-PROV tutorial
• Small tweaks to default arguments in Program and File module

v0.1.4

• Fix PresetProgram.add_parameter bug
• Add basic Tutorial
• Refactor SeqStats data class
• Improve Provenance classes

v0.1.3

• Patching more JSON IO bugs

v0.1.2

• Refactor functions in src.files module
• Add support for BioPython AlignIO module
• Patching src.program module
• Improving JSON serializers