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Release 1.0.0.rc1 #76

Merged
merged 82 commits into from
Mar 4, 2024
Merged

Release 1.0.0.rc1 #76

merged 82 commits into from
Mar 4, 2024

Commits on Dec 11, 2023

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Commits on Dec 13, 2023

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Commits on Dec 15, 2023

  1. change: Added central tumor location

    A first version has been produced with central tumor locations that seems to work out. Further refinement of the module comming in next push
    YoelPH committed Dec 15, 2023
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Commits on Dec 19, 2023

  1. change! further expand functionality of midline

    The midline model was further expanded to have similar funcitonalities as the old model. Additionally, the code style was made more conformal with the bilateral module.
    Right now the code is not functional.
    YoelPH committed Dec 19, 2023
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Commits on Jan 5, 2024

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Commits on Jan 16, 2024

  1. fix(bil): added new modality sync

    The new modality sync makes sure that both models stay updated
    YoelPH committed Jan 16, 2024
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  2. fix(mid): changed key assignment

    New key assignment for midline model where 'ipsi' is removed to ensure correct assignment
    YoelPH committed Jan 16, 2024
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Commits on Jan 23, 2024

  1. change: Non-mixture midline implemented

    fixed the non mixture midline extension model and added documentation
    YoelPH committed Jan 23, 2024
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Commits on Feb 12, 2024

  1. add: added doc strings

    YoelPH committed Feb 12, 2024
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Commits on Feb 15, 2024

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  3. feat: add delegator/synchronizer mixin

    Related: #74
    rmnldwg committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. feat: add delegation/sync mixin

    We have added a mixin class that allows the delegation and
    synchronization of attributes. This may replace the convoluted and
    unreadable callback functions we used to sync some properties
    
    Related: #74
    rmnldwg committed Feb 16, 2024
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  2. feat(helper): add popfirst() and flatten()

    Two new helper function in relation to getting and setting params.
    rmnldwg committed Feb 16, 2024
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  3. change!: make get_params() uniform and chainable

    The API of all `get_params()` methods is now nice and uniform, allowing
    arbitrary chaining of these methods.
    
    BREAKING CHANGE: The `get_params()` methods don't accept the `param`
    argument anymore.
    rmnldwg committed Feb 16, 2024
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  4. change!: make set_params() uniform and chainable

    The API of all `set_params()` methods is now nice and uniform,
    allowing arbitrary chaining of these methods.
    
    BREAKING CHANGE: The `assign_params()` method has been removed and some
    `set_params()` methods work differently than before.
    rmnldwg committed Feb 16, 2024
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Commits on Feb 19, 2024

  1. change!: make set_params() not return kwargs

    It does make sense to "use up" the positional arguments one by one in
    the `set_params()` methods, but doing the same thing with keyword
    arguments is pointless, difficult and error prone.
    
    BREAKING CHANGE: `set_params()` only returns one tuple of floats.
    rmnldwg committed Feb 19, 2024
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  4. change(graph)!: replace name with get_name()

    In the `Edge` class, the `name` property is replaced by a function
    `get_name()` that is more flexible and allows us to have edge names
    without underscores when we need it.
    
    BREAKING CHANGE: `Edge.name` is replaced by `Edge.get_name()`
    rmnldwg committed Feb 19, 2024
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  5. change(bi)!: reintroduce is_symmetric attribute

    This will once again manage the symmetry of the `Bilateral` class's
    different ipsi- and contralateral attributes.
    rmnldwg committed Feb 19, 2024
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Commits on Feb 20, 2024

  1. change(diag)!: use composite for distributions

    Instead of a dict that holds the T-stages and corresponding
    distributions over diagnose times, this implements them as a composite
    pattern. This replaces the dict-like API entirely with methods. This has
    several advantages:
    1. It is more explicit and thus more readable
    2. The composite pattern is designed to work naturally with tree-like
    structures, which we have here when dealing with bilateral models.
    3. This separates a lot of the logic into separate abstract classes,
    further separating concerns.
    
    BREAKING CHANGES: The old API of setting and getting distributions will
    not work anymore.
    rmnldwg committed Feb 20, 2024
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  2. change(mod)!: use composite for modalities

    Instead of a dict that holds the names and corresponding
    sens/spec for diagnostic modalities, this implements them as a composite
    pattern. This replaces the dict-like API entirely with methods. This has
    several advantages:
    1. It is more explicit and thus more readable
    2. The composite pattern is designed to work naturally with tree-like
    structures, which we have here when dealing with bilateral models.
    3. This separates a lot of the logic into separate abstract classes,
    further separating concerns.
    
    BREAKING CHANGES: The old API of setting and getting modalities will
    not work anymore.
    rmnldwg committed Feb 20, 2024
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  3. feat(type): add model ABC to inherit from

    I added an abstract base class from which all model-like classes should
    inherit. It defines all the methods that need to be present in a model.
    
    The idea behind this is that any subclass of this can be part of a
    composite that correctly delegates getting/setting parameters,
    diagnose time distributions, and modalities.
    rmnldwg committed Feb 20, 2024
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  4. change(uni)!: transform to composite pattern

    Use the new composite pattern for the distribution over diagnose times
    and modalities.
    
    BREAKING CHANGE: `Unilateral` has no attributes `modalities` or
    `diag_time_dists` anymore.
    rmnldwg committed Feb 20, 2024
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Commits on Feb 21, 2024

  1. change(mod)!: shorten to sens/spec

    Also, add a `clear_modalities()` and a `clear_distributions()` method to
    the respective composites.
    rmnldwg committed Feb 21, 2024
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  2. feat(graph)!: add __hash__ to edge, node, graph

    This removed the dedicated `parameter_hash()` method.
    rmnldwg committed Feb 21, 2024
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  3. change(matrix): use hashables over arg0 cache

    Instead of using this weird `arg0_cache` for the observation and
    transition matrix, I use the necessary arguments only, which are all
    hashable now.
    rmnldwg committed Feb 21, 2024
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  5. fix(diag): correct max time & params

    The `max_time` is now correctly accessed and set. Also, the distribution
    params are not used up by synched distributions, but only by the
    distributions in composite leafs.
    rmnldwg committed Feb 21, 2024
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Commits on Feb 22, 2024

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  2. test: fix long-running test

    rmnldwg committed Feb 22, 2024
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  3. chore: move timing data

    rmnldwg committed Feb 22, 2024
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  4. fix!: make likelihood work with emcee again

    The way the likelihood was defined, it did not actually play nicely with
    how the emcee package works. This is now fixed.
    rmnldwg committed Feb 22, 2024
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  13. merge: branch '74-synchronization-is-unreadable-and-error-prone' into…

    … 'dev'
    
    This unexpectedly turned out to be another large refactoring of much
    of the codebase...
    
    However, now the management of the modalities and the distributions
    over diagnose times both are implemented using a composite pattern.
    This also decouples the respective logics from the individual models.
    Eventually, this should also allow one to build mixtures of these
    models and just use setters and getters of diagnose distributions and
    modalities without much changes.
    
    Another big feature of this merge is that the midline model is now
    back again! Though it is still largely untested and it is still
    lacking the treatment of the midline extension as a random variable.
    
    Fixes: #74
    rmnldwg committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. feat: complete set/get methods on model classes

    The `Unilateral, `Bilateral`, and `Midline` model now all have the six
    methods `set_tumor_spread_params`, `set_lnl_spread_params`,
    `set_spread_params`, `set_params`, `get_tumor_spread_params`,
    `get_lnl_spread_params`, `get_spread_params`, and `get_params`.
    rmnldwg committed Feb 23, 2024
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Commits on Feb 24, 2024

  1. feat(mid): reimplement the midline evolution

    The midline evolution that Lars Widmer worked on is now reimplemented.
    However, although this implementation is analogous to the one used in
    previsou version of the code and should thus work, it is still untested
    at this point.
    rmnldwg committed Feb 24, 2024
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Commits on Feb 25, 2024

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Commits on Feb 26, 2024

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  2. test(mid): check llh function

    rmnldwg committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. feat: add helper to draw diagnoses

    The new helper function`draw_diagnoses` is a re-implementation of the
    `Unilateral` class's method with the same name for easier reusing.
    rmnldwg committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. feat(mid): allow marg over unknown midext

    This is implemented differently than before: If data with unknown
    midline extension is added, it gets loaded into an attribute named
    `unknown`, which is a `Bilateral` model only used to store that data and
    generate diagnose matrices.
    rmnldwg committed Feb 28, 2024
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  2. fix(mid): finish draw_patients method

    Some bugs in the method for drawing synthetic patients from the
    `Midline` were fixed. This seems to be working now.
    rmnldwg committed Feb 28, 2024
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Commits on Feb 29, 2024

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Commits on Mar 4, 2024

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  2. chore: update changelog

    rmnldwg committed Mar 4, 2024
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  3. docs: add CSS for nicer signatures

    The parameters of call signatures now each get their own line, making it
    much more readable.
    rmnldwg committed Mar 4, 2024
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