Add installation of patches to documentation

docs/source/doc/debugging.rst

@@ -3,32 +3,59 @@ Debugging
 
 This is a small list of debug code snippets.
 
-Enable tensorflow eager execution
+Debugging nans with tensorflow
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+It is a little problematic, because some nans occur during the
+runtime without being an error. Often these are cases where an
+operation has different implementations based on the value of the
+input, because it would otherwise lead to a loss of precision.
+
+Therefore we wrote some patches, which put try-except blocks
+around these code parts and if a error occurs, disable check_numeric
+for this part.
+
+For patching tensorflow_probability
+(replace the variables by the correct path):
+
+::
+
+    cd scripts/debugging_patches
+    patch -d {$CONDA_PATH}/envs/{$ENVIRONMENT_NAME}/ -p 0 < filter_nan_errors1.patch
+    patch -d {$CONDA_PATH}/envs/{$ENVIRONMENT_NAME}/ -p 0 < filter_nan_errors2.patch
+    patch -d {$CONDA_PATH}/envs/{$ENVIRONMENT_NAME}/ -p 0 < filter_nan_errors3.patch
+
+And then uncomment these line of codes in the run_script. Check_numerics
+has to enabled only before the optimization, not before the initial
+sampling, because the nan occuring during the sampling of the gamma
+distribution hasn't been patched.
+
 ::
 
-	tf.config.run_functions_eagerly(True)
-	tf.debugging.enable_check_numerics(stack_height_limit=30, path_length_limit=50)
+    tf.config.run_functions_eagerly(True)
+    tf.debugging.enable_check_numerics(stack_height_limit=30, path_length_limit=50)
+
+For debugging the VI, it is reasonable to increase the step size, to run
+more quickly into errors
 
 
 Basic usage of logger
 ^^^^^^^^^^^^^^^^^^^^^
 
 ::
 
-	# Change to debug mode i.e all log.debug is printed
-	logging.basicConfig(level=logging.DEBUG)
+    # Change to debug mode i.e all log.debug is printed
+    logging.basicConfig(level=logging.DEBUG)
 
-	# Use log.debug instead of print
-	log.debug(f"My var {var}")
+    # Use log.debug instead of print
+    log.debug(f"My var {var}")
 
 
 Force cpu or other device
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ::
 
-	my_devices = tf.config.experimental.list_physical_devices(device_type="CPU")
-	tf.config.experimental.set_visible_devices(devices=my_devices, device_type="CPU")
-	tf.config.set_visible_devices([], "GPU")
+    my_devices = tf.config.experimental.list_physical_devices(device_type="CPU")
+    tf.config.experimental.set_visible_devices(devices=my_devices, device_type="CPU")
+    tf.config.set_visible_devices([], "GPU")