Enhanced subdomain integration for the weak form library

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
   hooks:
     - id: reorder-python-imports
 - repo: https://github.com/ambv/black
-  rev: 21.5b1
+  rev: 22.3.0
   hooks:
     - id: black
 - repo: https://gitlab.com/pycqa/flake8

docs/JOSS2/paper.md

@@ -103,7 +103,7 @@ The goal of the `PySINDy` package is to enable anyone with access to measurement
 
 # Acknowledgments
 `PySINDy` is a fork of [`sparsereg`](https://github.com/Ohjeah/sparsereg) [@markus_quade_sparsereg].
-SLB, AAK, KK, and UF acknowledge support from the Army Research Office (ARO  W911NF-19-1-0045). JLC acknowledges support from funding support from the Department of Defense (DoD) through the National Defense Science \& Engineering Graduate (NDSEG) Fellowship Program. 
+SLB, AAK, KK, and UF acknowledge support from the Army Research Office (ARO  W911NF-19-1-0045). JLC acknowledges support from funding support from the Department of Defense (DoD) through the National Defense Science \& Engineering Graduate (NDSEG) Fellowship Program. ZGN is a Washington Research Foundation Postdoctoral Fellow.
 
 ![Summary of SINDy features organized by (a) `PySINDy` structure and (b) functionality. (a) Hierarchy from the sparse regression problem solved by SINDy, to the submodules of `PySINDy`, to the individual optimizers, libraries, and differentiation methods implemented in the code.
 (b) Flow chart for organizing the SINDy variants and functionality in the literature. Bright color boxes indicate the features that have been implemented through this work, roughly organized by functionality. Semi-transparent boxes indicate features that have not yet been implemented.\label{fig:package-structure}](Fig1.png)

pysindy/feature_library/base.py

@@ -327,6 +327,11 @@ def __init__(
         )
         self.libraries_ = libraries
         self.inputs_per_library_ = inputs_per_library
+        for lib in self.libraries_:
+            if hasattr(lib, "spatiotemporal_grid"):
+                if lib.spatiotemporal_grid is not None:
+                    self.n_samples = lib.K
+                    self.spatiotemporal_grid = lib.spatiotemporal_grid
 
     def _combinations(self, lib_i, lib_j):
         """
@@ -422,9 +427,12 @@ def transform(self, x):
             generated from applying the custom functions to the inputs.
 
         """
+        n_samples = x.shape[0]
         for lib in self.libraries_:
             check_is_fitted(lib)
-        n_samples = x.shape[0]
+            if hasattr(lib, "spatiotemporal_grid"):
+                if lib.spatiotemporal_grid is not None:  # check if weak form
+                    n_samples = self.n_samples
 
         # preallocate matrix
         xp = np.zeros((n_samples, self.n_output_features_))

pysindy/feature_library/generalized_library.py

@@ -251,6 +251,9 @@ def transform(self, x):
 
         n_samples, n_features = x.shape
 
+        if isinstance(self.libraries_[0], WeakPDELibrary):
+            n_samples = self.libraries_[0].K * self.libraries_[0].num_trajectories
+
         if float(__version__[:3]) >= 1.0:
             n_input_features = self.n_features_in_
         else: