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@rmnldwg rmnldwg released this 06 Mar 10:33
· 114 commits to main since this release
1.0.0.rc2
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Learn about vigilant mode.

What's New

Implementing the lymixture brought to light a shortcoming in the way the data and diagnose matrices are computed and stored. As mentioned in issue #77, their rows are now aligned with the patient data, which may have some advantages for different use cases.

Also, since this is probably the last pre-release, I took the liberty to go over some method names once more and make them clearer.

All changes: 1.0.0.rc1...1.0.0.rc2

Bug Fixes

  • Don't use fake T-stage for BN model. Related #77.
    Since we now have access to the full diagnose matrix by default, there
    is no need for the Bayesian network T-stage fix anymore.
  • (uni) Reload data when modalities change.
    Because we only store those diagnoses that are relevant to the model
    under the "_model" header in the patient_data table, we need to reload
    the patient data whenever we modify the modalities.

Documentation

  • Update to slightly changed API.
  • (bi) Add bilateral quickstart to docs.

Features

  • (mod) Add utils to check for modality changes.

Performance

  • (uni) Make data & diagnose matrices faster. Related #77.
    The last change caused a dramatic slowdown (factor 500) of the data and
    diagnose matrix access, because it needed to index them from a
    DataFrame. Now, I implemented a basic caching scheme with a patient
    data cache version that brought back the original speed.
    Also, apparently del dataframe[column] is much slower than
    dataframe.drop(columns). I replaced the former with the latter and now
    the tests are fast again.

Refactor

  • ⚠ BREAKING Rename methods for brevity & clarity.
    Method names have been changed, e.g comp_dist_evolution() has been
    renamed to state_dist_evo() which is both shorter and (imho) clearer.
  • (uni) Move data/diag matrix generation.

Testing

  • Update to slightly changed API.
  • (uni) Check reset of data on modality change.
    Added a test to make sure the patient data gets reloaded when the
    modalities change. This test is still failing.
  • Finally suppress all PerformanceWarnings.

Change

  • ⚠ BREAKING Store data & diagnose matrices in data. Fixes #77.
    Instead of weird, dedicated UserDicts, I simply use the patient data
    to store the data encoding and diagnose probabilities for each patient.
    This has the advantage that the entire matrix (irrespective of T-stage)
    is aligned with the patients.
  • ⚠ BREAKING (bi) Shorten kwargs.
    The (uni|ipsi|contra)lateral_kwargs in the Bilateral constructor
    were shortened by removing the "lateral".

Merge

  • Branch 'main' into 'dev'.
  • Branch '77-diagnose-matrices-not-aligned-with-data' into 'dev'.

Remove

  • Unused helpers.
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