Merge pull request #70 from rmnldwg/release-1.0.0.a5

Release 1.0.0.a5

CHANGELOG.md

@@ -2,8 +2,70 @@
 
 All notable changes to this project will be documented in this file.
 
+<a name="1.0.0.a5"></a>
+## [1.0.0.a5] - 2024-02-06
 
-## [Unreleased]
+In this alpha release we fixed more bugs and issues that emerged during more rigorous testing.
+
+Most notably, we backed away from storing the transition matrix in a model's instance. Because it created opaque and confusion calls to functions trying to delete them when parameters were updated.
+
+Instead, the function computing the transition matrix is now globally cached using a hash function from the graph representation. This has the drawback of slightly more computation time when calculating the hash. But the advantage is that e.g. in a bilateral symmetric model, the transition matrix of the two sides is only ever computed once when (synched) parameters are updated.
+
+### Bug Fixes
+
+- (**graph**) Assume `nodes` is dictionary, not a list
+- (**uni**) Update `draw_patients()` method to output LyProX style data
+- (**bi**) Update bilateral data generation method to also generate LyProX style data
+- (**bi**) Syntax error in `init_synchronization`
+- (**uni**) Remove need for transition matrix deletion via a global cache
+- (**uni**) Use cached matrices & simplify stuff
+- (**uni**) Observation matrix only property, not cached anymore
+
+### Documentation
+
+- Fix typos & formatting errors in docstrings
+
+### Features
+
+- (**graph**) Implement graph hash for global cache of transition matrix
+- (**helper**) Add an `arg0` cache decorator that caches based on the first argument only
+- (**matrix**) Use cache for observation & diagnose matrices
+
+### Miscellaneous Tasks
+
+- Update dependencies & classifiers
+
+### Refactor
+
+- Variables inside `generate_transition()`
+
+### Testing
+
+- Make doctests discoverable by unittest
+- Update tests to changed API
+- (**uni**) Assert format & distribution of drawn patients
+- (**uni**) Allow larger delta for synthetic data distribution
+- (**bi**) Check bilateral data generation method
+- Check the bilateral model with symmetric tumor spread
+- Make sure delete & recompute synced edges' tensor work
+- Adapt tests to changed `Edge` API
+- (**bi**) Evaluate transition matrix recomputation
+- Update tests to match new transition matrix code
+- Update trinary unilateral tests
+
+### Change
+
+- ⚠ **BREAKING** Compute transition tensor globally
+- ⚠ **BREAKING** Make transition matrix a method instead of a property
+- ⚠ **BREAKING** Make observation matrix a method instead of a property
+
+### Ci
+
+- Add coverage test dependency back into project
+
+### Remove
+
+- Unused files and directories
 
 
 <a name="1.0.0.a4"></a>

lymph/diagnose_times.py

@@ -231,9 +231,21 @@ def set_params(self, **kwargs) -> None:
             warnings.warn("Distribution is not updateable, skipping...")
 
 
-    def draw(self) -> np.ndarray:
-        """Draw sample of diagnose times from the PMF."""
-        return np.random.choice(a=self.support, p=self.distribution)
+    def draw_diag_times(
+        self,
+        num: int | None = None,
+        rng: np.random.Generator | None = None,
+        seed: int = 42,
+    ) -> np.ndarray:
+        """Draw ``num`` samples of diagnose times from the stored PMF.
+
+        A random number generator can be provided as ``rng``. If ``None``, a new one
+        is initialized with the given ``seed`` (or ``42``, by default).
+        """
+        if rng is None:
+            rng = np.random.default_rng(seed)
+
+        return rng.choice(a=self.support, p=self.distribution, size=num)
 
 
 class DistributionsUserDict(AbstractLookupDict):