wavefactor 2.10.0__tar.gz → 2.11.0__tar.gz

{wavefactor-2.10.0/wavefactor.egg-info → wavefactor-2.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wavefactor
-Version: 2.10.0
+Version: 2.11.0
 Summary: Bayesian Multiresolution Wavelet Spatial Factor Model for Spatial Transcriptomics
 License-Expression: GPL-3.0-or-later
 Classifier: Programming Language :: Python :: 3
@@ -24,6 +24,9 @@ Requires-Dist: pandas>=1.3.0
 Requires-Dist: scikit-learn>=1.0.0
 Provides-Extra: testing
 Requires-Dist: pytest>=7.0.0; extra == "testing"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.25.0; extra == "docs"
 Dynamic: license-file
 
 # WaveFactor: Bayesian Multiresolution Wavelet Spatial Factor Model
@@ -86,7 +89,7 @@ Options:
 
 **Preprint**: Coming soon, stay tuned!
 
-**Research Poster (2026 November)**: [View PDF](docs/assets/2026Nov-WaveFactor-Poster.pdf)
+**Research Poster (2026 November)**: [View PDF](https://github.com/shimlab/WaveFactor/blob/main/docs/assets/2026Nov-WaveFactor-Poster.pdf)
 
 ---
 

{wavefactor-2.10.0 → wavefactor-2.11.0}/README.md

@@ -58,7 +58,7 @@ Options:
 
 **Preprint**: Coming soon, stay tuned!
 
-**Research Poster (2026 November)**: [View PDF](docs/assets/2026Nov-WaveFactor-Poster.pdf)
+**Research Poster (2026 November)**: [View PDF](https://github.com/shimlab/WaveFactor/blob/main/docs/assets/2026Nov-WaveFactor-Poster.pdf)
 
 ---
 

wavefactor-2.11.0/VERSION

@@ -0,0 +1 @@
+2.11.0

{wavefactor-2.10.0 → wavefactor-2.11.0}/pyproject.toml

@@ -38,6 +38,10 @@ dependencies = [
 testing = [
     "pytest>=7.0.0",
 ]
+docs = [
+    "mkdocs-material>=9.5.0",
+    "mkdocstrings[python]>=0.25.0",
+]
 
 [tool.setuptools.packages.find]
 where = ["."]

{wavefactor-2.10.0 → wavefactor-2.11.0}/tests/test_model.py

@@ -31,7 +31,7 @@ def test_wavefactor_estimator_fit_transform():
 
     coords = np.column_stack([xx.ravel(), yy.ravel()])
 
-    # Fit WaveFactor (defaults to init="prior")
+    # Fit WaveFactor (defaults to init="random")
     model = WaveFactor(
         n_factors=K,
         n_length_scales=D,
@@ -53,7 +53,7 @@ def test_wavefactor_estimator_fit_transform():
     assert model.loadings_.shape == (K, N_genes)
     assert len(model.elbo_history_) > 0
     assert np.isfinite(model.elbo_)
-    assert model.init == "prior"
+    assert model.init == "random"
 
     # Test result object
     res = model.get_result()
@@ -113,12 +113,12 @@ def test_estimator_get_set_params():
     assert params["n_factors"] == 5
     assert params["n_length_scales"] == 3
     assert params["max_iter"] == 200
-    assert params["init"] == "prior"
+    assert params["init"] == "random"
 
-    model.set_params(n_factors=8, max_iter=500, init="random")
+    model.set_params(n_factors=8, max_iter=500, init="prior")
     assert model.n_factors == 8
     assert model.max_iter == 500
-    assert model.init == "random"
+    assert model.init == "prior"
 
 
 def test_estimator_invalid_init():

{wavefactor-2.10.0 → wavefactor-2.11.0}/wavefactor/engine.py

@@ -112,7 +112,7 @@ def init_parameters(
     dimensions: Dict[str, Any],
     priors: Optional[Dict[str, Any]] = None,
     rng: Optional[np.random.RandomState] = None,
-    init: str = "prior",
+    init: str = "random",
 ) -> Dict[str, Any]:
     """
     Initializes CAVI variational parameters and model prior hyperparameters.
@@ -127,9 +127,9 @@ def init_parameters(
         Generative prior hyperparameters.
     rng : Optional[np.random.RandomState], default=None
         Random number generator.
-    init : str, default="prior"
-        Initialisation mode: "prior" (prior-based variational warmup, default)
-        or "random" (legacy uniform random initialisation).
+    init : str, default="random"
+        Initialisation mode: "random" (uniform pseudo-random initialisation, default)
+        or "prior" (prior-based variational warmup).
     """
     if init not in ("prior", "random"):
         raise ValueError(f"Unknown init mode '{init}'. Expected 'prior' or 'random'.")
@@ -359,7 +359,7 @@ def run_cavi(
     n_jobs: int = -1,
     random_state: Optional[int] = None,
     verbose: bool = True,
-    init: str = "prior",
+    init: str = "random",
 ) -> Dict[str, Any]:
     """
     Orchestrates multi-start Coordinate Ascent Variational Inference.
@@ -384,9 +384,9 @@ def run_cavi(
         Seed for deterministic random number generation.
     verbose : bool, default=True
         Whether to print progress messages.
-    init : str, default="prior"
-        Initialisation mode: "prior" (prior-based variational warmup, default)
-        or "random" (legacy uniform random initialisation).
+    init : str, default="random"
+        Initialisation mode: "random" (uniform pseudo-random initialisation, default)
+        or "prior" (prior-based variational warmup).
 
     Returns
     -------

{wavefactor-2.10.0 → wavefactor-2.11.0}/wavefactor/model.py

@@ -62,10 +62,6 @@ class WaveFactor(BaseEstimator):
         Shape hyperparameter matrix for noise precision Gamma prior, shape (R, G).
     beta_tau : Optional[np.ndarray], default=None
         Rate hyperparameter matrix for noise precision Gamma prior, shape (R, G).
-    grid_side_length : int, optional
-        Side length L of the square L x L spatial grid (must be a power of 2,
-        e.g. 16, 32, 64, 128). Total grid cells = L * L. If None, automatically
-        computed as the smallest power of 2 that encloses the spatial coordinates.
     max_iter : int, default=1000
         Maximum CAVI optimization iterations per start.
     tol : float, default=1e-5
@@ -78,12 +74,13 @@ class WaveFactor(BaseEstimator):
         Random seed for deterministic initialization and reproducibility.
     verbose : bool, default=True
         Whether to log progress during CAVI optimization.
-    init : str, default="prior"
+    init : str, default="random"
         Variational parameter initialisation strategy. Options:
+        - "random": Uniform pseudo-random initialization on [-10, 10] (default).
+          Provides broad exploration across the non-convex ELBO landscape,
+          promotes factor diversity, and prevents factor redundancy / cloning.
         - "prior": Sample variational states from generative prior expectations
-          with mild jitter to break symmetry. Resolves scale explosion and noise
-          swamping in high-dimensional settings.
-        - "random": Legacy uniform pseudo-random initialization on [-10, 10].
+          with mild jitter. Useful when strong directional priors are specified.
     """
 
     def __init__(
@@ -102,7 +99,7 @@ class WaveFactor(BaseEstimator):
         n_jobs: int = -1,
         random_state: Optional[int] = None,
         verbose: bool = True,
-        init: str = "prior",
+        init: str = "random",
     ):
         self.n_factors = n_factors
         self.n_length_scales = n_length_scales

{wavefactor-2.10.0 → wavefactor-2.11.0/wavefactor.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wavefactor
-Version: 2.10.0
+Version: 2.11.0
 Summary: Bayesian Multiresolution Wavelet Spatial Factor Model for Spatial Transcriptomics
 License-Expression: GPL-3.0-or-later
 Classifier: Programming Language :: Python :: 3
@@ -24,6 +24,9 @@ Requires-Dist: pandas>=1.3.0
 Requires-Dist: scikit-learn>=1.0.0
 Provides-Extra: testing
 Requires-Dist: pytest>=7.0.0; extra == "testing"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.25.0; extra == "docs"
 Dynamic: license-file
 
 # WaveFactor: Bayesian Multiresolution Wavelet Spatial Factor Model
@@ -86,7 +89,7 @@ Options:
 
 **Preprint**: Coming soon, stay tuned!
 
-**Research Poster (2026 November)**: [View PDF](docs/assets/2026Nov-WaveFactor-Poster.pdf)
+**Research Poster (2026 November)**: [View PDF](https://github.com/shimlab/WaveFactor/blob/main/docs/assets/2026Nov-WaveFactor-Poster.pdf)
 
 ---
 

{wavefactor-2.10.0 → wavefactor-2.11.0}/wavefactor.egg-info/requires.txt

@@ -4,5 +4,9 @@ PyWavelets>=1.1.0
 pandas>=1.3.0
 scikit-learn>=1.0.0
 
+[docs]
+mkdocs-material>=9.5.0
+mkdocstrings[python]>=0.25.0
+
 [testing]
 pytest>=7.0.0

wavefactor-2.10.0/VERSION

@@ -1 +0,0 @@
-2.10.0