1.3.7

What's new:

Bug Fixes

• Make models compatible with new data format.
• Correct array shape mismatch in draw_patients.

Miscellaneous Tasks

• Update codecov badge.
• Mention wiki in contribution guide.
• Update email addresses.

Change

• Adjustments to allow bilateral mixture model.
• Make compatible with new data format (again).
• Change dataframe indexing to conform with new standard.

1.3.6

What's New

This release changes nothing about the actual code. Only the way it's built and tested. So, purely a maintenance update.

Miscellaneous Tasks

• Update pre-commit & ruff rules.

Testing

• Update one doctest example.

Build

• Switch to src layout. Fixes #106.
• Rename opt dependencies to tests.
• Use tests dependency pytest-cov over coverage.

Ci

• Update pre-commit config.

1.3.5

What's new:

Bug Fixes

• Assign only tumor spread probs in midline.
• (mid) Warn instead of raise when out of sync. Fixes [#102].

Documentation

• Fix release badge in README.
• Fix outdated links to rmnldwg.

Testing

• Ensure midline params sync.
• Add failing midline params desync. Related [#102].
• Fix desync test case.

Build

• Add git-cliff to dev dependencies.

1.3.4

What's New

Bug Fixes

• Don't use or when param may be 0.
  Since Python's expression a = b or c will assign c to a as soon as
  b is "falsy", e.g. also when b = 0.0, I should not use this to check
  if a parameter in the model is None.

Documentation

• Fix misspelled repo link.
• Remove empty mixins page.
• Better reuse of README.
• Move social card to repo root.
  This is actually for LyProX: I want to display the social card of all
  repos in the lycosystem on LyProX's landing page. Therefore, they all
  need to be in their expected places.

Miscellaneous Tasks

• Add year range to license.

Testing

• Use val != 0.5 to test matrix deletion.
  0.5 is the new initial value for most parameters, so it does not make
  sense to use this to check if upon changing a parameter, the transition
  matrix gets deleted.

Change

• Init most params with 0.5 instead of 0.0.
  In some cases, initializing with 0.0 may have unintended consequences.
  E.g., a probability of 0.0 cannot be renormalized.

Ci

• Use OIDC for publishing.

1.3.3

What's New

Bug Fixes

• Make midext_prob last param in get/set methods
• Midline musn't use last of set_param args.
  Instead, it should use the one at num_dims - 1.

Documentation

• Fix broken quickstart link.
• Add emcee to requirements for quickstart notebook.
• Explain midline extension probability in set/get.

Testing

• midext_prob is last parameter in get/set methods.

1.3.2

What's New

Bug Fixes

• __init__() without named_params now works. Previously, it raised an exception
  because the distribution composite was not initialized.

Testing

• __init__() with named_params must work.

1.3.1

What's New

Bug Fixes

• get_named_params() returns only named params and doesn't raise an error anymore.
• Add deleter to named_params property.

Change

• Move named_params stuff from dedicated mixin to types.Model.
• Raise explicit invalid param name error.
  This ensures that e.g. during sampling, the likelihood does not simply
  return -np.inf because it sees a ValueError.
• Call set_named_params() in likelihoods.
  This ensures that a model definition is respected during inference and
  also when reloading sampled parameters. In case no named_params are
  provided, this will simply behave as set_params().

1.3.0

What's New

The main two new features of this release are the HPV model (thanks @YoelPH for this) and the ability to only set a subset of parameters. See #95 for an explanation why that was necessary.

No breaking changes this time (phew).

Bug Fixes

• (hpv) Some renaming and import correct symbols.
• (hpv) Send kwargs to constructor correctly.
• Partial globals work in set_named_params().
  Setting ipsi_spread via named_params works now. This was tricky to
  implement, as the spread params of the ipsi model are all called
  ipsi_<something>_spread.

Documentation

• Fix typos in readme.
• Fix typo in midline model docstring.
• Fix equation in midline model docstring.
• Change ref to "bilateral" in HPV model.
• Add new mixins to autodoc.
• Add warning about untested HPV model.

Features

• (hpv) Create HPV wrapper.
  The HPV module can be used to build a unilateral lymph model
  where the b_2 parameter is different for HPV positive patients.
  This fixes #42
• (uni) Add basic working named params mixing. Related to #95
• Add named_params to all models. Fixes #95
• Add named_params to model constructors. Related to #95

Testing

• Add basic tests for NamedParamsMixin. Related to #95
• Check partial globals work.
  E.g. ipsi_spread should set the spread of all LNLs in the ipsi
  model. Related to #95

Change

• (mid) Set default use_central=False.
  This is a more sane default and does not result in a ValueError when
  creating the model with the default arguments.
• (hpv) Put data split into HPV class.
• (hpv) Delegate methods via hpv_status arg.
  Instead of re-implementing or copy-pasting methods from the Unilateral
  class, they simply compute those model's corresponding method that was
  selected via the hpv_status (keyword) argument.

1.2.3

What's New

This is very minor and I only release this tiny update, so that I can depend on all models having the binary and trinary constructor in lyscripts.

Features

• (mid) Add missing binary constructor to Midline model. Now all models have a binary and trinary constructor.

Styling

• Add rules to ruff.

Testing

• Make suite testable with pytest.

Ci

• Switch to pytest for testing.

1.2.2

What's New

Bug Fixes

• (mid) Correct contra state dist evo. Fixes #85.
  Previously, the model did not correctly marginalize over the possible
  time when a tumor can grow over the midline. It simply assumed that it
  did from the onset.

Documentation

• (uni) Remove outdated docstring paragraph. Fixes #88.

Miscellaneous Tasks

• Bump pre-commit versions.

Styling

• Use ruff to fix lint and format code.

Build

• Remove upper cap in deps.

Change

• risk() meth requires involvement. Fixes #87.
  We figured it does not make sense to allow passing involvement=None
  into the risk() method just to have it return 1. This is except for
  the midline class, where involvement may reasonably be None while
  midext isn't.
  Also, I ran ruff over some files, fixing some code style issues.