Remove rpy2 dependency

It's not needed anymore.

Signed-off-by: Peter Goetz <pego@amazon.com>

binder/environment.yml

@@ -14,7 +14,6 @@ dependencies:
   - pydot
   - seaborn
   - pygraphviz
-  - rpy2
   - ipython
   - jupyter
   - notebook

docs/source/conf.py

@@ -94,7 +94,6 @@ exclude_patterns = [
     ".DS_Store",
     ".ipynb_checkpoints",
     "example_notebooks/dowhy_ranking_methods.ipynb",
-    "example_notebooks/dowhy_causal_discovery_example.ipynb",  # need to check why str_to_dot fails here
     "example_notebooks/dowhy_twins_example.ipynb",
 ]
 

docs/source/example_notebooks/dowhy_causal_discovery_example.ipynb

@@ -18,9 +18,6 @@
     "import dowhy\n",
     "from dowhy import CausalModel\n",
     "\n",
-    "from rpy2.robjects import r as R\n",
-    "%load_ext rpy2.ipython\n",
-    "\n",
     "import numpy as np\n",
     "import pandas as pd\n",
     "import graphviz\n",

pyproject.toml

@@ -101,7 +101,6 @@ optional = true
 #
 # Dependencies for Documentation Generation
 #
-rpy2 = "^3.5.2"
 sphinx = "^5.3.0"
 sphinxcontrib-googleanalytics = { git = "https://github.com/sphinx-contrib/googleanalytics.git", branch = "master" }
 nbsphinx = "^0.8.9"
@@ -111,6 +110,7 @@ ipykernel = "^6.15.1"
 sphinx-copybutton = "0.5.0"
 seaborn = "^0.12.1"
 tensorflow = "^2.11.0"
+cdt ="^0.6.0"
 
 #
 # Versions defined for security reasons

tests/test_notebooks.py

@@ -11,7 +11,6 @@ notebooks_list = [f.name for f in os.scandir(NOTEBOOKS_PATH) if f.name.endswith(
 advanced_notebooks = [
     # requires stdin input for identify in weighting sampler
     "do_sampler_demo.ipynb",
-    # requires Rpy2 for lalonde
     "dowhy_refutation_testing.ipynb",
     "dowhy_lalonde_example.ipynb",
     "lalonde_pandas_api.ipynb",
@@ -27,11 +26,10 @@ advanced_notebooks = [
     "dowhy_twins_example.ipynb",
 ]
 
+# TODO: should probably move more notebooks here to ignore, because
+#       most get tested by the documentation generation.
 ignore_notebooks = [
-    # requires Rpy2 for causal discovery
-    # daily tests of dowhy_causal_discovery_example.ipynb are failing due to cdt/rpy2 config.
-    # comment out, since we are switching causal discovery implementations
-    "dowhy_causal_discovery_example.ipynb"
+    "dowhy_causal_discovery_example.ipynb",  # This is being tested as part of documentation generation
 ]
 
 # Adding the dowhy root folder to the python path so that jupyter notebooks