Further update documentation for 0.7.0

CITATION.cff

@@ -4,6 +4,7 @@ type: software
 authors:
 - given-names: "FastML Team"
 title: "hls4ml"
+version: "v0.7.0rc1"
 doi: 10.5281/zenodo.1201549
 repository-code: "https://github.com/fastmachinelearning/hls4ml"
 url: "https://fastmachinelearning.org/hls4ml"
@@ -21,3 +22,35 @@ abstract: |
   hls4ml is an open-source software-hardware codesign workflow
   to interpret and translate machine learning algorithms for
   implementations in hardware, including FPGAs and ASICs.
+references:
+  - type: article
+    title: "Fast inference of deep neural networks on FPGAs with hls4ml"
+    authors:
+    - family-names: "Duarte"
+      given-names: "Javier"
+    - family-names: "Han"
+      given-names: "Song"
+    - family-names: "Harris"
+      given-names: "Philip"
+    - family-names: "Jindariani"
+      given-names: "Sergo"
+    - family-names: "Kreinar"
+      given-names: "Edward"
+    - family-names: "Kreis"
+      given-names: "Benjamin"
+    - family-names: "Ngadiuba"
+      given-names: "Jennifer"
+    - family-names: "Pierini"
+      given-names: "Maurizio"
+    - family-names: "Rivera"
+      given-names: "Ryan"
+    - family-names: "Tran"
+      given-names: "Nhan"
+    - family-names: "Wu"
+      given-names: "Zhenbin"
+    journal: "JINST"
+    volume: "13"
+    start: "P07027"
+    doi: "10.1088/1748-0221/13/07/P07027"
+    year: "2018"
+    number: "07"

README.md

@@ -64,11 +64,12 @@ hls4ml.report.read_vivado_report('my-hls-test')
 # Citation
 If you use this software in a publication, please cite the software
 ```bibtex
-@software{vloncar_2021_5680908,
+@software{fastml_hls4ml,
   author       = {{FastML Team}},
   title        = {fastmachinelearning/hls4ml},
-  year         = 2021,
+  year         = 2023,
   publisher    = {Zenodo},
+  version      = {v0.7.0rc1},
   doi          = {10.5281/zenodo.1201549},
   url          = {https://github.com/fastmachinelearning/hls4ml}
 }

docs/advanced/accelerator.rst

@@ -0,0 +1,77 @@
+=========================
+VivadoAccelerator Backend
+=========================
+
+The ``VivadoAccelerator`` backend of ``hls4ml`` leverages the `PYNQ <http://pynq.io/>`_ software stack to easily deploy models on supported devices.
+Currently ``hls4ml`` supports the following boards:
+
+* `pynq-z2 <https://www.xilinx.com/support/university/xup-boards/XUPPYNQ-Z2.html>`_ (part: ``xc7z020clg400-1``)
+* `zcu102 <https://www.xilinx.com/products/boards-and-kits/ek-u1-zcu102-g.html>`_ (part: ``xczu9eg-ffvb1156-2-e``)
+* `alveo-u50 <https://www.xilinx.com/products/boards-and-kits/alveo/u50.html>`_ (part: ``xcu50-fsvh2104-2-e``)
+* `alveo-u250 <https://www.xilinx.com/products/boards-and-kits/alveo/u250.html>`_ (part: ``xcu250-figd2104-2L-e``)
+* `alveo-u200 <https://www.xilinx.com/products/boards-and-kits/alveo/u200.html>`_ (part: ``xcu200-fsgd2104-2-e``)
+* `alveo-u280 <https://www.xilinx.com/products/boards-and-kits/alveo/u280.html>`_ (part: ``xcu280-fsvh2892-2L-e``)
+
+but, in principle, support can be extended to `any board supported by PYNQ <http://www.pynq.io/board.html>`_.
+For the Zynq-based boards, there are two components: an ARM-based processing system (PS) and FPGA-based programmable logic (PL), with various intefaces between the two.
+
+.. image:: ../img/zynq_interfaces.png
+  :height: 300px
+  :align: center
+  :alt: Zynq PL/PS interfaces
+
+Neural Network Overlay
+======================
+
+In the PYNQ project, programmable logic circuits are presented as hardware libraries called *overlays*.
+The overlay can be accessed through a Python API.
+In ``hls4ml``, we create a custom **neural network overlay**, which sends and receives data via AXI stream.
+The target device is programmed using a bitfile that is generated by the ``VivadoAccelerator`` backend.
+
+.. image:: ../img/pynqframe.png
+  :width: 600px
+  :align: center
+  :alt: PYNQ software stack
+
+Example
+=======
+
+This example is taken from `part 7 of the hls4ml tutorial <https://github.com/fastmachinelearning/hls4ml-tutorial/blob/master/part7_deployment.ipynb>`_.
+Specifically, we'll deploy a model on a ``pynq-z2`` board.
+
+First, we generate the bitfile from a Keras model ``model`` and a config.
+
+.. code-block:: Python
+
+    import hls4ml
+    config = hls4ml.utils.config_from_keras_model(model, granularity='name')
+    hls_model = hls4ml.converters.convert_from_keras_model(model,
+                                                           hls_config=config,
+                                                           output_dir='hls4ml_prj_pynq',
+                                                           backend='VivadoAccelerator',
+                                                           board='pynq-z2')
+    hls4ml.build(bitfile=True)
+
+
+After this command completes, we will need to package up the bitfile, hardware handoff, and Python driver to copy to the PS of the board.
+
+.. code-block:: bash
+
+    mkdir -p package
+    cp hls4ml_prj_pynq/myproject_vivado_accelerator/project_1.runs/impl_1/design_1_wrapper.bit package/hls4ml_nn.bit
+    cp hls4ml_prj_pynq/myproject_vivado_accelerator/project_1.srcs/sources_1/bd/design_1/hw_handoff/design_1.hwh package/hls4ml_nn.hwh
+    cp hls4ml_prj_pynq/axi_stream_driver.py package/
+    tar -czvf package.tar.gz -C package/ .
+
+Then we can copy this package to the PS of the board and untar it.
+
+Finally, on the PS in Python we can create a ``NeuralNetworkOverlay`` object, which will download the bitfile onto the PL of the board.
+We also must provide the shapes of our input and output data, ``X_test.shape`` and ``y_test.shape``, respectively, to allocate the buffers for the data transfer.
+The ``predict`` method will send the input data to the PL and return the output data ``y_hw``.
+
+.. code-block:: Python
+
+    from axi_stream_driver import NeuralNetworkOverlay
+
+    nn = NeuralNetworkOverlay('hls4ml_nn.bit', X_test.shape, y_test.shape)
+    y_hw, latency, throughput = nn.predict(X_test, profile=True)

docs/conf.py

@@ -124,3 +124,4 @@ def get_pypi_version(package, url_pattern=URL_PATTERN):
     'github_version': 'main',  # Version
     'conf_py_path': '/docs/',  # Path in the checkout to the docs root
 }
+html_favicon = 'img/hls4ml_logo.svg'

docs/flows.rst

@@ -2,32 +2,60 @@
 Optimizer Passes and Flows
 ==========================
 
-The ``hls4ml`` package internally represents the model graph with the :py:class:`~hls4ml.model.graph.ModelGraph` class.
-The nodes in this graph are represented by classes derived from the :py:class:`~hls4ml.model.layers.Layer` base class.
+The ``hls4ml`` library will parse models from Keras, PyTorch or ONNX into an internal execution graph. This model graph is represented with the
+:py:class:`~hls4ml.model.graph.ModelGraph` class. The nodes in this graph, corresponding to the layer and operations of the input model are represented
+by classes derived from the :py:class:`~hls4ml.model.layers.Layer` base class.
 
-Layers have only inputs, outputs and attributes.
-All information about the layer's state and configuration is stored in the attributes.
-All weights, variables and data types are attributes and there are mapping views to sort through them.
+Layers are required to have defined inputs and outputs that define how they are connected in the graph and what is the shape of their output. All information
+about the layer's state and configuration is stored in its attributes. All weights, variables and data types are attributes and there are mapping views to sort through them.
 Layers can define expected attributes and can be verified for correctness, or to produce a list of configurable attributes that user can tweak.
 
 Optimizer passes
 ----------------
 
-An :py:class:`~hls4ml.model.optimizer.optimizer.OptimizerPass` transforms a model graph.
-All model/layer transformations should happen in these optimizer passes.
-There are a number of types of optimizer passes:
+To reach a state from which the code can be generated, internal model graph will undergo a series of optimizations (transformations), dubbed *optimization passes*.
+All transformations of the model and any modification to any layer's attributes must be implemented through an optimization pass. All optimizer passes derive from
+the :py:class:`~hls4ml.model.optimizer.optimizer.OptimizerPass` class. Optimizer passes are applied at the level of nodes/layers, however a special class
+:py:class:`~hls4ml.model.optimizer.optimizer.ModelOptimizerPass` exists that is applied on the full model. Subclasses of
+:py:class:`~hls4ml.model.optimizer.optimizer.OptimizerPass` must provide a criteria in ``match`` function that, if satisfied, will perform the transformation from
+``transform`` function. The boolean return value of ``transform`` indicates if the optimizer pass made changes to the model graph, requiring running the optimizers again.
+Example of an optimizer pass that runs on the full model, is :py:class:`~hls4ml.model.optimizer.passes.stamp.MakeStamp`, while an example of the layer optimizer is
+:py:class:`~hls4ml.model.optimizer.passes.fuse_biasadd` class that adds a bias to a :py:class:`~hls4ml.model.layers.Dense`,
+:py:class:`~hls4ml.model.layers.Conv1D`, or :py:class:`~hls4ml.model.layers.Conv2D` layer.
 
- * layer-specific: These are special optimizations for a given layer.
-   An example is the :py:class:`~hls4ml.model.optimizer.passes.fuse_biasadd` class that adds a bias to a :py:class:`~hls4ml.model.layers.Dense`, :py:class:`~hls4ml.model.layers.Conv1D`, or :py:class:`~hls4ml.model.layers.Conv2D` layer.
- * backend-specific: These are only used for particular backends. An example is :py:class:`~hls4ml.backends.vivado.passes.repack_stream.ReshapeStream`.
- * model-level: These model-level optimizer passes are run on every type of layer.
- * templates: These add the HLS code for a particular backend, e.g., :py:class:`~hls4ml.backends.vivado.passes.core_templates.DenseFunctionTemplate`.
- * decorators
+Optimizers can be general, independent of the backend, in which case they are located in :py:mod:`hls4ml.model.optimizer.passes`, or they may be backend-specific,
+in which case they are located in a folder dependent on the backend, e.g., :py:mod:`hls4ml.backends.vivado.passes` or
+:py:mod:`hls4ml.backends.quartus.passes`. A common set of optimizers that are used by FPGA backends are located in :py:mod:`hls4ml.backends.fpga.passes`.
+
+Certain optimizers are used frequently enough that it makes sense to define special classes, which inherit from :py:class:`~hls4ml.model.optimizer.optimizer.OptimizerPass`
+
+ * :py:class:`~hls4ml.model.optimizer.optimizer.GlobalOptimizerPass`: An optimizer pass that matches each node. This is useful, for example,
+   to transform the types for a particular backend.
+ * :py:class:`~hls4ml.model.optimizer.optimizer.LayerOptimizerPass`: An optimizer pass that matches each node of a particular layer type. This is
+   useful, for example, to write out the HLS code for a particular node that remains in the final graph.
+ * :py:class:`~hls4ml.model.optimizer.optimizer.ConfigurableOptimizerPass`:  An optimizer pass that has some configurable parameters.
+ * :py:class:`~hls4ml.backends.template.Template`:  An optimizer pass that populates a code template and assigns it to an attribute of a given layer. This is commonly used
+   to generate code blocks in later stages of the conversion.
+
+Note that :py:class:`~hls4ml.model.optimizer.optimizer.LayerOptimizerPass` and :py:class:`~hls4ml.model.optimizer.optimizer.ModelOptimizerPass`
+also exist as decorators that wrap a function.
+
+New optimizers can be registered with the :py:func:`~hls4ml.model.optimizer.optimizer.register_pass`. Optimizers should be assigned to a flow (see below).
 
 Flows
 -----
-A :py:class:`~hls4ml.model.flow.flow.Flow` is an ordered set of optimizers that may depend on other flows.
+A :py:class:`~hls4ml.model.flow.flow.Flow` is an ordered set of optimizers that represent a single stage in the conversion process. The optimizers from a flow are applied
+until they no longer make changes to the model graph after which the next flow (stage) can start. Flows may depend on other flows being applied before them,
+ensuring the model graph is in a desired state before a flow starts. The function :py:func:`~hls4ml.model.flow.flow.register_flow` is used to register a new flow. Flows
+are applied on a model graph with :py:func:`~hls4ml.model.graph.ModelGraph.apply_flow`.
+
 There are common model-level flows that can run regardless of the backend, and there are backend-specific flows.
-Each backend provides provides a default flow for processing.
-For example, the Vivado backend defaults to an `IP flow <https://github.com/fastmachinelearning/hls4ml/blob/7c0a065935904f50bd7e4c547f85354b36276092/hls4ml/backends/vivado/vivado_backend.py#L148-L160>`_ that requires additional flows and produces an IP.
+The `convert and optimize <https://github.com/fastmachinelearning/hls4ml/blob/7c0a065935904f50bd7e4c547f85354b36276092/hls4ml/model/optimizer/__init__.py#L14-L20>`_
+flows do not depend on a backend.
+
+Each backend provides provides a default flow that defines the default target for that backend. For example, the Vivado backend defaults to an
+`IP flow <https://github.com/fastmachinelearning/hls4ml/blob/7c0a065935904f50bd7e4c547f85354b36276092/hls4ml/backends/vivado/vivado_backend.py#L148-L160>`_
+that requires additional flows and produces an IP. It runs no optimizers itself, but it requires that many other flows (sub-flows) to have run.
+The convert and optimize flows defined above are some of these required sub-flows.
+
 Another example is FIFO buffer depth optimization explained in the :ref:`FIFO Buffer Depth Optimization` section.

docs/index.rst

@@ -2,11 +2,11 @@
     :hidden:
     :caption: Introduction
 
-    release_notes
+    concepts
     status
     setup
+    release_notes
     command
-    concepts
     details
     flows
     reference
@@ -24,6 +24,7 @@
 
     advanced/fifo_depth
     advanced/extension
+    advanced/accelerator
 
 .. toctree::
     :hidden:

docs/reference.rst

@@ -9,11 +9,12 @@ If you use this software in a publication, please cite the software
 
 ..  code-block:: bibtex
 
-    @software{vloncar_2021_5680908,
+    @software{fastml_hls4ml,
     author       = {{FastML Team}},
     title        = {fastmachinelearning/hls4ml},
-    year         = 2021,
+    year         = 2023,
     publisher    = {Zenodo},
+    version      = {v0.7.0rc1},
     doi          = {10.5281/zenodo.1201549},
     url          = {https://github.com/fastmachinelearning/hls4ml}
     }