Merge pull request #452 from vincent-antaki/documentation-update

Documentation update

Author: vincent-antaki

examples/Handler Methods.ipynb

@@ -25,26 +25,26 @@
     "\n",
     "### [handle_fit_transform](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep.handle_fit)\n",
     "\n",
-    "1. [_will_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method.\n",
-    "2. [_will_fit_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._will_fit_transform): Apply side effects before fit_transform\n",
-    "3. [_fit_transform_data_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): Fit transform data container.\n",
-    "4. [_did_fit_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._did_fit_transform): Apply side effects after fit_transform.\n",
-    "5. [_did_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process): Apply side effects after any step method.\n",
+    "1. [\\_will\\_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method.\n",
+    "2. [\\_will\\_fit_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._will_fit_transform): Apply side effects before fit_transform\n",
+    "3. [\\_fit\\_transform\\_data\\_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): Fit transform data container.\n",
+    "4. [\\_did\\_fit\\_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._did_fit_transform): Apply side effects after fit_transform.\n",
+    "5. [\\_did\\_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process): Apply side effects after any step method.\n",
     "\n",
     "### [handle_fit](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep.handle_fit)\n",
     "\n",
-    "1. [_will_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method.\n",
-    "2. [_will_fit(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._will_fit): Apply side effects before fit.\n",
-    "3. [_fit_data_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): Fit data container.\n",
-    "4. [_did_fit(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._did_fit): Apply side effects after fit.\n",
+    "1. [\\_will\\_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method.\n",
+    "2. [\\_will\\_fit(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._will_fit): Apply side effects before fit.\n",
+    "3. [\\_fit\\_data\\_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): Fit data container.\n",
+    "4. [\\_did\\_fit(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._did_fit): Apply side effects after fit.\n",
     "\n",
     "### [handle_transform](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep.handle_transform)\n",
     "\n",
-    "1. [_will_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method\n",
-    "2. [_will_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_transform_data_container): Apply side effects before transform.\n",
-    "3. [_transform_data_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): Fit transform data container.\n",
-    "4. [_did_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_transform): Apply side effects after transform. \n",
-    "5. [_did_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process): Apply side effects after any step method.\n",
+    "1. [\\_will\\_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process): Apply side effects before any step method\n",
+    "2. [\\_will\\_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_transform_data_container): Apply side effects before transform.\n",
+    "3. [\\_transform\\_data_container(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): Fit transform data container.\n",
+    "4. [\\_did\\_transform(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_transform): Apply side effects after transform. \n",
+    "5. [\\_did\\_process(data_container, context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process): Apply side effects after any step method.\n",
     "\n",
     "### When to use handler methods ? \n",
     "\n",
@@ -169,9 +169,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "2. Implement [_transform_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): \n",
+    "2. Implement [\\_transform\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): \n",
     "\n",
-    "Pass expected outputs to the wrapped step [handle_transform](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.BaseStep.handle_transform) method. Update the data container expected outputs with the outputs."
+    "Pass expected outputs to the wrapped step [handle_transform](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep.handle_transform) method. Update the data container expected outputs with the outputs."
    ]
   },
   {
@@ -198,7 +198,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "2. Implement [_fit_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): \n",
+    "2. Implement [\\_fit\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): \n",
     "\n",
     "Pass expected outputs to the wrapped step [handle_fit](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep.handle_fit) method. Update the data container expected outputs with the outputs."
    ]
@@ -225,7 +225,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "3. Implement [_fit_transform_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): \n",
+    "3. Implement [\\_fit\\_transform\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): \n",
     "\n",
     "Pass expected outputs to the wrapped step [handle_fit_transform](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep.handle_fit_transform) method.\n",
     "Update the data container expected outputs with the outputs."
@@ -379,7 +379,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "2. Implement the [_will_process](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process) lifecycle method to expand the data inside the data container."
+    "2. Implement the [\\_will\\_process](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._will_process) lifecycle method to expand the data inside the data container."
    ]
   },
   {
@@ -397,7 +397,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "3. Implement the [_did_process](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process) lifecycle method to reduce the dimension of the data inside the data container."
+    "3. Implement the [\\_did\\_process](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._did_process) lifecycle method to reduce the dimension of the data inside the data container."
    ]
   },
   {
@@ -514,7 +514,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "1. Create a step that inherits from [HandleOnlyMixin](https://www.neuraxle.org/stable/api/neuraxle.base.html?highlight=handleonlymixin#neuraxle.base.HandleOnlyMixin), and [TruncableSteps](). Initialize TruncableSteps with a preprocessing, and a postprocessing step."
+    "1. Create a step that inherits from [HandleOnlyMixin](https://www.neuraxle.org/stable/api/neuraxle.base.html?highlight=handleonlymixin#neuraxle.base.HandleOnlyMixin), and [TruncableSteps](https://www.neuraxle.org/stable/api/neuraxle.base.html?highlight=truncable%20step#neuraxle.base.TruncableSteps). Initialize TruncableSteps with a preprocessing, and a postprocessing step."
    ]
   },
   {
@@ -536,7 +536,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "2. Implement [_fit_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): "
+    "2. Implement [\\_fit\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_data_container): "
    ]
   },
   {
@@ -558,7 +558,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "3. Implement [_transform_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): "
+    "3. Implement [\\_transform\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep._transform_data_container): "
    ]
   },
   {
@@ -590,7 +590,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "4. Implement [_fit_transform_data_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): "
+    "4. Implement [\\_fit\\_transform\\_data\\_container](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep._fit_transform_data_container): "
    ]
   },
   {

examples/Step Saving And Lifecycle.ipynb

@@ -22,14 +22,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "1. [BaseStep.__init__(hyperparams, hyperparams_space, name)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.BaseStep): This is where you initialize all of your props, and fitted state. \n",
+    "1. [BaseStep.\\_\\_init\\_\\_(hyperparams, hyperparams_space, name)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.BaseStep): This is where you initialize all of your props, and fitted state. \n",
     "2. [set_hyperparams(hyperperparams)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._HasHyperparams.set_hyperparams): Configure your steps' hyperparameters before initializing it.\n",
-    "3. [setup(context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.TransformerStep.setup): Initialize the step before it runs. Only from here and not before that heavy things should be created (e.g.: things inside GPU), and NOT in the constructor.\n",
+    "3. [setup(context)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.BaseTransformer.setup): Initialize the step before it runs. Only from here and not before that heavy things should be created (e.g.: things inside GPU), and NOT in the constructor.\n",
     "4. [fit(data_inputs, expected_outputs)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._FittableStep.fit): Fit step with the given data inputs, and expected outputs.\n",
     "\n",
     "5. [transform(data_inputs)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._TransformerStep.transform): Transform given data inputs.\n",
     "6. [save(context, full_dump)](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base._HasSavers.save): Save step using the execution context to create the directory to save the step into.\n",
-    "7. [teardown()](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.TransformerStep.teardown): Teardown step after program execution. Inverse of setup, and it should clear memory. Override this method if you need to clear memory."
+    "7. [teardown()](https://www.neuraxle.org/stable/api/neuraxle.base.html#neuraxle.base.BaseTransformer.teardown): Teardown step after program execution. Inverse of setup, and it should clear memory. Override this method if you need to clear memory."
    ]
   },
   {

neuraxle/base.py

@@ -1426,7 +1426,7 @@ def set_hyperparams(self, hyperparams: HyperparameterSamples) -> 'BaseTransforme
         :return: self
 
         .. note::
-        This is a recursive method that will call :func:`~neuraxle.base._HasHyperparams._set_hyperparams` in the end.
+            This is a recursive method that will call :func:`~neuraxle.base._HasHyperparams._set_hyperparams`.
         .. seealso::
             :class:`~neuraxle.hyperparams.space.HyperparameterSamples`,
             :class:̀_HasChildrenMixin`,
@@ -1488,9 +1488,9 @@ def get_hyperparams(self) -> HyperparameterSamples:
         :return: step hyperparameters
 
         .. note::
-        This is a recursive method that will call :func:`~neuraxle.base._HasHyperparams._get_hyperparams` in the end.
+            This is a recursive method that will call :func:`~neuraxle.base._HasHyperparams._get_hyperparams`.
         .. seealso::
-            * :class:`~neuraxle.hyperparams.space.HyperparameterSamples`
+            :class:`~neuraxle.hyperparams.space.HyperparameterSamples`,
             :class:̀_HasChildrenMixin`,
             :func:`BaseStep.apply`,
             :func:`_HasChildrenMixin._apply`,
@@ -1514,7 +1514,7 @@ def set_params(self, **params) -> 'BaseTransformer':
             hyperparams = s.get_params()
             assert hyperparams == {"learning_rate": 0.1}
 
-        :param **params: arbitrary number of arguments for hyperparameters
+        :param arbitrary number of arguments for hyperparameters
 
         .. note::
             This is a recursive method that will call :func:`~neuraxle.base._HasHyperparams._set_params` in the end.
@@ -2121,8 +2121,10 @@ def invalidate(self) -> 'BaseTransformer':
             * the step name has changed func:`~neuraxle.base.BaseStep.set_name`
 
         :return: self
+
         .. note::
             This is a recursive method used in :class:̀_HasChildrenMixin`.
+
         .. seealso::
             :func:`~neuraxle.base._HasRecursiveMethods.apply`,
             :func:`~neuraxle.base._HasChildrenMixin._apply`
@@ -2195,6 +2197,7 @@ def reverse(self) -> 'BaseTransformer':
         Note: the reverse may fail if there is a pending mutate that was set earlier with ``.will_mutate_to``.
 
         :return: a copy of self, reversed. Each contained object will also have been reversed if self is a pipeline.
+
         .. seealso::
             :func:`~neuraxle.base._TransformerStep.inverse_transform`
         """
@@ -3003,9 +3006,9 @@ def _refresh_steps(self):
     def should_save(self):
         """
         Returns if the step needs to be saved or not.
-        If self should be saved or any of his sub steps, return True.
 
-        :return:
+        :return: If self or any of his sub steps should be saved, returns True.
+
         .. seealso::
             :class:`TruncableJoblibStepSaver`
         """

neuraxle/data_container.py

@@ -34,7 +34,9 @@
 
 
 class AbsentValuesNullObject:
-    """This object, when passed to the default_value_data_inputs argument of the DataContainer.batch method, will return the minibatched data containers such that the last batch won't have the full batch_size if it was incomplete with trailing None values at the end."""
+    """
+    This object, when passed to the default_value_data_inputs argument of the DataContainer.batch method, will return the minibatched data containers such that the last batch won't have the full batch_size if it was incomplete with trailing None values at the end.
+    """
     pass
 
 
@@ -53,7 +55,7 @@ class DataContainer:
 
     .. seealso::
         :class:`~neuraxle.base.BaseHasher`,
-        :class: `neuraxle.base.BaseStep`
+        :class:`~neuraxle.base.BaseStep`,
         :class:`~neuraxle.data_container.DataContainer.AbsentValuesNullObject`
     """
 
@@ -92,7 +94,7 @@ def set_data_inputs(self, data_inputs: Iterable):
 
         :param data_inputs: data inputs
         :type data_inputs: Iterable
-        :return:
+        :return: self
         """
         self.data_inputs = data_inputs
         return self
@@ -103,7 +105,7 @@ def set_expected_outputs(self, expected_outputs: Iterable):
 
         :param expected_outputs: expected outputs
         :type expected_outputs: Iterable
-        :return:
+        :return: self
         """
         self.expected_outputs = expected_outputs
         return self
@@ -114,7 +116,7 @@ def set_current_ids(self, current_ids: List[str]):
 
         :param current_ids: data inputs
         :type current_ids: List[str]
-        :return:
+        :return: self
         """
         self.current_ids = current_ids
         return self
@@ -124,17 +126,18 @@ def set_summary_id(self, summary_id: str):
         Set summary id.
 
         :param summary_id: str
-        :return:
+        :return: self
         """
         self.summary_id = summary_id
         return self
 
     def set_sub_data_containers(self, sub_data_containers: List['DataContainer']):
         """
         Set sub data containers
-        :return:
+        :return: self
         """
         self.sub_data_containers = sub_data_containers
+        return self
 
     def hash_summary(self):
         """
@@ -206,8 +209,8 @@ def minibatches(
         :return: an iterator of DataContainer
         :rtype: Iterable[DataContainer]
 
-        ..seealso
-            :class:`~neuraxle.data_container.DataContainer.AbsentValuesNullObject`,
+        .. seealso::
+            :class:`~neuraxle.data_container.DataContainer.AbsentValuesNullObject`
         """
         for i in range(0, len(self.data_inputs), batch_size):
             data_container = DataContainer(
@@ -369,7 +372,7 @@ class ExpandedDataContainer(DataContainer):
     Sub class of DataContainer to expand data container dimension.
 
     .. seealso::
-        :class:`DataContainer`,
+        :class:`DataContainer`
     """
 
     def __init__(self, data_inputs, current_ids, expected_outputs, summary_id, old_current_ids):
@@ -426,7 +429,7 @@ class ZipDataContainer(DataContainer):
     Sub class of DataContainer to zip two data sources together.
 
     .. seealso::
-        :class:`DataContainer`,
+        :class: `DataContainer`
     """
 
     @staticmethod