Stage documentation improvements (#1362)

* Populate stub stages document 
* Excluded from the list are abstract, deprecated and stages primarily used for testing.
* Fix minor docstring type-os in `morpheus/stages/input/rss_source_stage.py` and `morpheus/stages/postprocess/ml_flow_drift_stage.py`

Closes #1361

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/nv-morpheus/Morpheus/blob/main/docs/source/developer_guide/contributing.md).
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

Authors:
  - David Gardner (https://github.com/dagardner-nv)

Approvers:
  - Devin Robison (https://github.com/drobison00)

URL: #1362

docs/source/examples/doca/README.md

@@ -0,0 +1 @@
+../../../../examples/doca/README.md

docs/source/examples/index.rst

@@ -24,6 +24,7 @@ Examples
 
    abp_nvsmi_detection/README.md
    abp_pcap_detection/README.md
+   doca/README.md
    gnn_fraud_detection_pipeline/README.md
    llm/index
    log_parsing/README.md

docs/source/getting_started.md

@@ -272,7 +272,9 @@ This indicates that the `to-file` stage cannot accept the input type of `morpheu
 
 #### Pipeline Stages
 
-A complete list of the pipeline stages will be added in the future. For now, you can query the available stages for each pipeline type via:
+The CLI allows for an easy way to query the available stages for each pipeline type. Refer to [Morpheus Stages](./stages/morpheus_stages.md) for more extensive documentation of the stages included in Morpheus.
+
+> **Note**: While most stages are available from the CLI, a small subset of stages, and configuration options for stages are unavailable from the CLI and can only be used via the Python API.
 
 ```
 $ morpheus run pipeline-nlp --help

docs/source/stages/morpheus_stages.md

@@ -17,65 +17,81 @@ limitations under the License.
 
 # Stages Documentation
 
-## Boundary
+Stages are the building blocks of Morpheus pipelines. Below is a list of the most commonly used stages. For a full list of stages, refer to the stages API {py:mod}`morpheus.stages`. In addition to this there are several custom stages contained in the [Examples](../examples.md) and [Developer Guides](../developer_guide/guides.md).
 
-- Linear Boundary Stage
+## Table of Contents
+- [Doca](#doca)
+- [General](#general)
+- [Inference](#inference)
+- [Input](#input)
+- [LLM](#llm)
+- [Output](#output)
+- [Post-process](#post-process)
+- [Pre-process](#pre-process)
+
+
+## Doca
+
+- Doca Stage {py:class}`~morpheus.stages.doca.doca_source_stage.DocaSourceStage` A source stage used to receive raw packet data from a ConnectX-6 Dx NIC. This stage is not compiled by default refer to the [Doca Example](../../../examples/doca/README.md) for details on building this stage.
 
 ## General
 
-- Buffer Stage
-- Delay Stage
-- Linear Modules Stage
-- Monitor Stage
-- Multi Port Module Stage
-- Trigger Stage
+- Linear Modules Stage {py:class}`~morpheus.stages.general.linear_modules_stage.LinearModulesStage` Loads an existing, registered, module and wraps it as a Morpheus stage. Refer to [Morpheus Modules](../developer_guide/guides.md#morpheus-modules) for details on modules.
+- Monitor Stage {py:class}`~morpheus.stages.general.monitor_stage.MonitorStage` Display throughput numbers at a specific point in the pipeline.
+- Multi Port Module Stage {py:class}`~morpheus.stages.general.multi_port_modules_stage.MultiPortModulesStage` Loads an existing, registered, multi-port module and wraps it as a multi-port Morpheus stage. Refer to [Morpheus Modules](../developer_guide/guides.md#morpheus-modules) for details on modules.
+- Trigger Stage {py:class}`~morpheus.stages.general.trigger_stage.TriggerStage` Buffer data until the previous stage has completed, useful for testing performance of one stage at a time.
 
 ## Inference
 
-- Auto Encoder Inference Stage
-- Identity Inference Stage
-- Inference Stage
-- PyTorch Inference Stage
-- Triton Inference Stage
+- Auto Encoder Inference Stage {py:class}`~morpheus.stages.inference.auto_encoder_inference_stage.AutoEncoderInferenceStage` PyTorch inference stage used for Auto Encoder pipeline mode.
+- PyTorch Inference Stage {py:class}`~morpheus.stages.inference.pytorch_inference_stage.PyTorchInferenceStage` PyTorch inference stage used for most pipeline modes with the exception of Auto Encoder.
+- Triton Inference Stage {py:class}`~morpheus.stages.inference.triton_inference_stage.TritonInferenceStage`  Inference stage which utilizes a [Triton Inference Server](https://developer.nvidia.com/nvidia-triton-inference-server).
 
 ## Input
 
-- AppShield Source Stage
-- Autoencoder Source Stage
-- Azure Source Stage
-- Cloud Trail Source Stage
-- Control Message File Source Stage
-- Control Message Kafka Source Stage
-- Duo Source Stage
-- File Source Stage
-- Kafka Source Stage
+- AppShield Source Stage {py:class}`~morpheus.stages.input.appshield_source_stage.AppShieldSourceStage` Load Appshield messages from one or more plugins into a dataframe.
+- Azure Source Stage {py:class}`~morpheus.stages.input.azure_source_stage.AzureSourceStage` Load Azure Active Directory messages.
+- Cloud Trail Source Stage {py:class}`~morpheus.stages.input.cloud_trail_source_stage.CloudTrailSourceStage` Load messages from a Cloudtrail directory.
+- Control Message File Source Stage {py:class}`~morpheus.stages.input.control_message_file_source_stage.ControlMessageFileSourceStage` Recieves control messages from different sources specified by a list of (fsspec)[https://filesystem-spec.readthedocs.io/en/latest/api.html?highlight=open_files#fsspec.open_files] strings.
+- Control Message Kafka Source Stage {py:class}`~morpheus.stages.input.control_message_kafka_source_stage.ControlMessageKafkaSourceStage` Load control messages from a Kafka cluster.
+- Databricks Delta Lake Source Stage {py:class}`~morpheus.stages.input.databricks_deltalake_source_stage.DataBricksDeltaLakeSourceStage` Source stage used to load messages from a DeltaLake table.
+- Duo Source Stage {py:class}`~morpheus.stages.input.duo_source_stage.DuoSourceStage` Load Duo Authentication messages.
+- File Source Stage {py:class}`~morpheus.stages.input.file_source_stage.FileSourceStage` Load messages from a file.
+- HTTP Client Source Stage {py:class}`~morpheus.stages.input.http_client_source_stage.HttpClientSourceStage` Poll a remote HTTP server for incoming data.
+- HTTP Server Source Stage {py:class}`~morpheus.stages.input.http_server_source_stage.HttpServerSourceStage` Start an HTTP server and listens for incoming requests on a specified endpoint.
+- In Memory Source Stage {py:class}`~morpheus.stages.input.in_memory_source_stage.InMemorySourceStage` Input source that emits a pre-defined list of dataframes.
+- Kafka Source Stage {py:class}`~morpheus.stages.input.kafka_source_stage.KafkaSourceStage` Load messages from a Kafka cluster.
+- RSS Source Stage {py:class}`~morpheus.stages.input.rss_source_stage.RSSSourceStage` Load RSS feed items into a pandas DataFrame.
 
-## Output
+## LLM 
 
-- Write To File Stage
-- Write To Kafka Stage
+- LLM Engine Stage {py:class}`~morpheus.stages.llm.llm_engine_stage.LLMEngineStage` Execute an LLM engine within a Morpheus pipeline.
+
+## Output
+- HTTP Client Sink Stage {py:class}`~morpheus.stages.output.http_client_sink_stage.HttpClientSinkStage` Write all messages to an HTTP endpoint.
+- HTTP Server Sink Stage {py:class}`~morpheus.stages.output.http_server_sink_stage.HttpServerSinkStage` Start an HTTP server and listens for incoming requests on a specified endpoint.
+- In Memory Sink Stage {py:class}`~morpheus.stages.output.in_memory_sink_stage.InMemorySinkStage` Collect incoming messages into a list that can be accessed after the pipeline is complete.
+- Databricks Delta Lake Sink Stage {py:class}`~morpheus.stages.output.write_to_databricks_deltalake_stage.DataBricksDeltaLakeSinkStage` Write messages to a DeltaLake table.
+- Write To Elastic Search Stage {py:class}`~morpheus.stages.output.write_to_elasticsearch_stage.WriteToElasticsearchStage` Write the messages as documents to Elasticsearch.
+- Write To File Stage {py:class}`~morpheus.stages.output.write_to_file_stage.WriteToFileStage` Write all messages to a file.
+- Write To Kafka Stage {py:class}`~morpheus.stages.output.write_to_kafka_stage.WriteToKafkaStage` Write all messages to a Kafka cluster.
+- Write To Vector DB Stage {py:class}`~morpheus.stages.output.write_to_vector_db.WriteToVectorDBStage` Write all messages to a Vector Database.
 
 ## Post-process
 
-- Add Classifications Stage
-- Add Scores Stage
-- Filter Detections Stage
-- Generate Viz Frames Stage
-- ML Flow Drift Stage
-- Serialize Stage
-- Timeseries Stage
-- Validation Stage
+- Add Classifications Stage {py:class}`~morpheus.stages.postprocess.add_classifications_stage.AddClassificationsStage` Add detected classifications to each message.
+- Add Scores Stage {py:class}`~morpheus.stages.postprocess.add_scores_stage.AddScoresStage` Add probability scores to each message.
+- Filter Detections Stage {py:class}`~morpheus.stages.postprocess.filter_detections_stage.FilterDetectionsStage` Filter message by a classification threshold.
+- Generate Viz Frames Stage {py:class}`~morpheus.stages.postprocess.generate_viz_frames_stage.GenerateVizFramesStage` Write out visualization DataFrames.
+- MLflow Drift Stage {py:class}`~morpheus.stages.postprocess.ml_flow_drift_stage.MLFlowDriftStage` Report model drift statistics to MLflow.
+- Serialize Stage {py:class}`~morpheus.stages.postprocess.serialize_stage.SerializeStage` Include & exclude columns from messages.
+- Timeseries Stage {py:class}`~morpheus.stages.postprocess.timeseries_stage.TimeSeriesStage` Perform time series anomaly detection and add prediction.
 
 ## Pre-process
 
-- Deserialize Stage
-- Drop Null Stage
-- Preprocess AE Stage
-- Preprocess Base Stage
-- Preprocess FIL Stage
-- Preprocess NLP Stage
-- Train AE Stage
-
-## Training
-
-- Training Stage
+- Deserialize Stage {py:class}`~morpheus.stages.preprocess.deserialize_stage.DeserializeStage` Partition messages based on the pipeline config's `pipeline_batch_size` parameter.
+- Drop Null Stage {py:class}`~morpheus.stages.preprocess.drop_null_stage.DropNullStage` Drop null data entries from a DataFrame.
+- Preprocess AE Stage {py:class}`~morpheus.stages.preprocess.preprocess_ae_stage.PreprocessAEStage` Prepare Autoencoder input DataFrames for inference.
+- Preprocess FIL Stage {py:class}`~morpheus.stages.preprocess.preprocess_fil_stage.PreprocessFILStage` Prepare FIL input DataFrames for inference.
+- Preprocess NLP Stage {py:class}`~morpheus.stages.preprocess.preprocess_nlp_stage.PreprocessNLPStage` Prepare NLP input DataFrames for inference.
+- Train AE Stage {py:class}`~morpheus.stages.preprocess.train_ae_stage.TrainAEStage` Train an Autoencoder model on incoming data.

morpheus/stages/input/rss_source_stage.py

@@ -31,7 +31,7 @@
 @register_stage("from-rss")
 class RSSSourceStage(PreallocatorMixin, SingleOutputSource):
     """
-    Load RSS feed items into a pandas DataFrame.
+    Load RSS feed items into a DataFrame.
 
     Parameters
     ----------

morpheus/stages/postprocess/ml_flow_drift_stage.py

@@ -34,7 +34,7 @@
 @register_stage("mlflow-drift", modes=[PipelineModes.FIL, PipelineModes.NLP, PipelineModes.OTHER])
 class MLFlowDriftStage(PassThruTypeMixin, SinglePortStage):
     """
-    Report model drift statistics to ML Flow.
+    Report model drift statistics to MLflow.
 
     Caculates model drift over time and reports the information to MLflow.