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Release 1.0.0.rc1 #76
Commits on Dec 11, 2023
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Commits on Dec 13, 2023
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Commits on Dec 15, 2023
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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
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Commits on Dec 19, 2023
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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.
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Commits on Jan 5, 2024
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Commits on Jan 16, 2024
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fix(bil): added new modality sync
The new modality sync makes sure that both models stay updated
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fix(mid): changed key assignment
New key assignment for midline model where 'ipsi' is removed to ensure correct assignment
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Commits on Jan 23, 2024
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change: Non-mixture midline implemented
fixed the non mixture midline extension model and added documentation
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Commits on Feb 12, 2024
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Commits on Feb 15, 2024
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Commits on Feb 16, 2024
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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
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feat(helper): add
popfirst()
andflatten()
Two new helper function in relation to getting and setting params.
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change!: make
get_params()
uniform and chainableThe 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.
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change!: make
set_params()
uniform and chainableThe 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.
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Commits on Feb 19, 2024
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change!: make
set_params()
not return kwargsIt 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.
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change(graph)!: replace
name
withget_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()`
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change(bi)!: reintroduce
is_symmetric
attributeThis will once again manage the symmetry of the `Bilateral` class's different ipsi- and contralateral attributes.
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Commits on Feb 20, 2024
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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.
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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.
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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.
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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.
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Commits on Feb 21, 2024
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change(mod)!: shorten to sens/spec
Also, add a `clear_modalities()` and a `clear_distributions()` method to the respective composites.
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feat(graph)!: add
__hash__
to edge, node, graphThis removed the dedicated `parameter_hash()` method.
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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.
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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.
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Commits on Feb 22, 2024
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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.
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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
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Commits on Feb 23, 2024
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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`.
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Commits on Feb 24, 2024
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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.
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Commits on Feb 25, 2024
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Commits on Feb 26, 2024
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Commits on Feb 27, 2024
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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.
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Commits on Feb 28, 2024
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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.
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fix(mid): finish
draw_patients
methodSome bugs in the method for drawing synthetic patients from the `Midline` were fixed. This seems to be working now.
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Commits on Feb 29, 2024
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Commits on Mar 4, 2024
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docs: add CSS for nicer signatures
The parameters of call signatures now each get their own line, making it much more readable.
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