TODO - Things to do

[amsesk]

For Release 1.0.0

• Implement plotly-python GCT plots
• Expand test suite to completion
  • build_taxdb.py
  • codons.py
  • config.py
  • consensus.py
  • db.py
  • dependencies.py
  • error.py
  • flexwindow.py (does not yet test data where trade-off values change results.)
  • gct.py
  • infotable.py
  • kmers.py
  • library.py
  • main.py
  • modcomm.py
  • module.py
  • parsers.py
  • plotter.py
  • reuse.py
  • sequence.py
• Relax format restrictions of spexpand to allow new lines and extra tabs/spaces
• Allow module objects to be called externally as library-like elements (i.e., things like get_head() need to failable and recoverable
• Correctly implement SCGidUpdater
• Log command line and subprocess error correctly
• Update docs with info about spdbify and implement in python instead of rust
• NoTargetError raised in flexwindow.py is not appropriate for all the times it is raised, needs to be subdivided into different error classes
• FlexibleSelectionWindows behave unexpectedly when target means are sufficiently distorted by outlying high/low values. Can lead to 0-width window axes that stall gct. Current fix deletes these windows from analysis, but a more thorough fix should remove outliers in these cases. This should also make windows better.
• SCGid.Codons.Annotate blastn command doesn't log blastn call errors
• Add information about -s flag in scgid kmers annotate with examples