Create plotly versions of selected matplotlib visualizations (#610)

* Create ploty versions of selected matplotlib visualizations * update r install instructions * fix pandas float deprecation warnings * fixarray ndim > 0 float extraction deprecationwarning --------- Co-authored-by: Stephan Grein <[email protected]>
ICB-DCM · Nov 8, 2023 · 46ef9ae · 46ef9ae
1 parent 604a443
commit 46ef9ae
Show file tree

Hide file tree

Showing 15 changed files with 2,005 additions and 361 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 23.7.0
   hooks:
   - id: black
     description: The uncompromising code formatter
@@ -27,7 +27,7 @@ repos:
     name: isort (pyi)
     types: [pyi]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.1
+  rev: 1.7.0
   hooks:
     - id: nbqa-black
     - id: nbqa-pyupgrade

diff --git a/pyabc/transition/jump.py b/pyabc/transition/jump.py
@@ -142,4 +142,4 @@ def pdf(
             ]
         )
 
-        return pds if pds.size != 1 else float(pds)
+        return pds if pds.size != 1 else float(pds[0])
diff --git a/pyabc/visualization/__init__.py b/pyabc/visualization/__init__.py
@@ -13,11 +13,18 @@
     plot_contour_matrix,
     plot_contour_matrix_lowlevel,
 )
-from .credible import plot_credible_intervals, plot_credible_intervals_for_time
+from .credible import (
+    plot_credible_intervals,
+    plot_credible_intervals_for_time,
+    plot_credible_intervals_plotly,
+)
 from .data import plot_data_callback, plot_data_default
 from .distance import plot_distance_weights
-from .effective_sample_size import plot_effective_sample_sizes
-from .epsilon import plot_epsilons
+from .effective_sample_size import (
+    plot_effective_sample_sizes,
+    plot_effective_sample_sizes_plotly,
+)
+from .epsilon import plot_epsilons, plot_epsilons_plotly
 from .histogram import (
     plot_histogram_1d,
     plot_histogram_1d_lowlevel,
@@ -29,26 +36,44 @@
 from .kde import (
     plot_kde_1d,
     plot_kde_1d_highlevel,
+    plot_kde_1d_highlevel_plotly,
+    plot_kde_1d_plotly,
     plot_kde_2d,
     plot_kde_2d_highlevel,
+    plot_kde_2d_highlevel_plotly,
+    plot_kde_2d_plotly,
     plot_kde_matrix,
     plot_kde_matrix_highlevel,
+    plot_kde_matrix_highlevel_plotly,
+    plot_kde_matrix_plotly,
+)
+from .model_probabilities import (
+    plot_model_probabilities,
+    plot_model_probabilities_plotly,
 )
-from .model_probabilities import plot_model_probabilities
 from .sample import (
     plot_acceptance_rates_trajectory,
+    plot_acceptance_rates_trajectory_plotly,
     plot_lookahead_acceptance_rates,
     plot_lookahead_evaluations,
     plot_lookahead_final_acceptance_fractions,
     plot_sample_numbers,
+    plot_sample_numbers_plotly,
     plot_sample_numbers_trajectory,
+    plot_sample_numbers_trajectory_plotly,
     plot_total_sample_numbers,
+    plot_total_sample_numbers_plotly,
 )
 from .sankey import plot_sensitivity_sankey
 from .walltime import (
     plot_eps_walltime,
     plot_eps_walltime_lowlevel,
+    plot_eps_walltime_lowlevel_plotly,
+    plot_eps_walltime_plotly,
     plot_total_walltime,
+    plot_total_walltime_plotly,
     plot_walltime,
     plot_walltime_lowlevel,
+    plot_walltime_lowlevel_plotly,
+    plot_walltime_plotly,
 )