Remove deprecated visualization functions (#130)

Remove old visualization functions deprecated since #58.

* Remove old tests - fix paths - support pathlib.Path

* fix doc

* move tests/test_visualization_new_structure.py

* cleanup

* Fix broken links

Author: dweindl

doc/conf.py

@@ -9,14 +9,6 @@
 import sys
 import warnings
 
-# Sphinx autosummary does not handle well submodules and functions with
-#  identical names if the function is part of __all__ of the parent module.
-#  This is way, we get autosummary to create the submodule documentation:
-import petab
-from petab.visualize.plot_data_and_simulation import plot_data_and_simulation
-petab.visualize.plot_data_and_simulation = \
-    sys.modules['petab.visualize.plot_data_and_simulation']
-
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,

petab/visualize/__init__.py

@@ -7,25 +7,20 @@
 
 """
 
-from .plot_data_and_simulation import (plot_data_and_simulation,
-                                       plot_petab_problem,
-                                       plot_measurements_by_observable,
-                                       plot_without_vis_spec,
-                                       plot_with_vis_spec,
-                                       plot_problem,
-                                       save_vis_spec)
+from .plot_data_and_simulation import (
+    plot_without_vis_spec,
+    plot_with_vis_spec,
+    plot_problem,
+)
 
 from .plotter import MPLPlotter
 from .plotting import DataProvider, Figure
 
-__all__ = ["plot_data_and_simulation",
-           "plot_petab_problem",
-           "plot_measurements_by_observable",
-           "plot_without_vis_spec",
-           "plot_with_vis_spec",
-           "plot_problem",
-           "save_vis_spec",
-           "MPLPlotter",
-           "DataProvider",
-           "Figure"
-           ]
+__all__ = [
+    "plot_without_vis_spec",
+    "plot_with_vis_spec",
+    "plot_problem",
+    "MPLPlotter",
+    "DataProvider",
+    "Figure"
+]