adapted diffxpy to new hessian and fim computition interface in batchglm

Author: davidsebfischer

diffxpy/pkg_constants.py

@@ -8,6 +8,9 @@
 BATCHGLM_OPTIM_NEWTON_TR = False
 BATCHGLM_OPTIM_IRLS = False
 BATCHGLM_OPTIM_IRLS_GD = False
-BATCHGLM_OPTIM_IRLS_TR = False
+BATCHGLM_OPTIM_IRLS_TR = True
 BATCHGLM_OPTIM_IRLS_GD_TR = True
+
 BATCHGLM_PROVIDE_BATCHED = True
+BATCHGLM_PROVIDE_FIM = True
+BATCHGLM_PROVIDE_HESSIAN = False

diffxpy/testing/det.py

@@ -2302,7 +2302,8 @@ def plot_genes(
             show=True,
             ncols=2,
             row_gap=0.3,
-            col_gap=0.25
+            col_gap=0.25,
+            return_axs=False
     ):
         """
         Plot observed data and spline fits of selected genes.
@@ -2317,6 +2318,7 @@ def plot_genes(
         :param ncols: Number of columns in plot grid if multiple genes are plotted.
         :param row_gap: Vertical gap between panel rows relative to panel height.
         :param col_gap: Horizontal gap between panel columns relative to panel width.
+        :param return_axs: Whether to return axis objects of plots.
         :return: Matplotlib axis objects.
         """
 
@@ -2390,8 +2392,10 @@ def plot_genes(
 
         plt.close(fig)
 
-        return axs
-
+        if return_axs:
+            return axs
+        else:
+            return
 
     def plot_heatmap(
             self,
@@ -2402,7 +2406,8 @@ def plot_heatmap(
             nticks=10,
             cmap: str = "YlGnBu",
             width=10,
-            height_per_gene=0.5
+            height_per_gene=0.5,
+            return_axs=False
     ):
         """
         Plot observed data and spline fits of selected genes.
@@ -2416,6 +2421,7 @@ def plot_heatmap(
         :param cmap: matplotlib cmap.
         :param width: Width of heatmap figure.
         :param height_per_gene: Height of each row (gene) in heatmap figure.
+        :param return_axs: Whether to return axis objects of plots.
         :return: Matplotlib axis objects.
         """
         import seaborn as sns
@@ -2480,7 +2486,10 @@ def plot_heatmap(
 
         plt.close(fig)
 
-        return ax
+        if return_axs:
+            return axs
+        else:
+            return
 
 
 class DifferentialExpressionTestWaldCont(_DifferentialExpressionTestCont):

diffxpy/testing/tests.py

@@ -170,6 +170,8 @@ def _fit(
             init_b=init_b,
             provide_optimizers=provide_optimizers,
             provide_batched=pkg_constants.BATCHGLM_PROVIDE_BATCHED,
+            provide_fim=pkg_constants.BATCHGLM_PROVIDE_FIM,
+            provide_hessian=pkg_constants.BATCHGLM_PROVIDE_HESSIAN,
             dtype=dtype,
             **constructor_args
         )