start documentation

.gitignore

@@ -3,3 +3,8 @@
 **/.pytest_cache
 **/.DS_Store
 **/*.pyc
+docs/_build
+build
+dist
+.idea
+src/kyupy.egg-info

README.md

@@ -1,56 +0,0 @@
-KyuPy - Processing VLSI Circuits With Ease
-==========================================
-
-KyuPy is a python package for high-performance processing and analysis of
-non-hierarchical VLSI designs. Its purpose is to provide a rapid prototyping
-platform to aid and accelerate research in the fields of VLSI test, diagnosis
-and reliability. KyuPy is freely available under the MIT license.
-
-
-Main Features
--------------
-
-* Partial [lark](https://github.com/lark-parser/lark) parsers for common files used with synthesized designs:
-  bench, gate-level verilog, standard delay format (SDF), standard test interface language (STIL)
-* Bit-parallel gate-level 2-, 4-, and 8-valued logic simulation
-* GPU-accelerated high-throughput gate-level timing simulation
-* High-performance through the use of [numpy](https://numpy.org) and [numba](https://numba.pydata.org)
-
-
-Getting Started
----------------
-
-KyuPy requires Python 3.6 or newer.
-Install the latest release by running:
-```commandline
-pip3 install --user kyupy
-```
-For best performance, ensure you have [numba](https://pypi.org/project/numba) installed:
-```commandline
-pip3 install --user numba
-```
-GPU/CUDA support may [require some additional setup](https://numba.pydata.org/numba-doc/latest/cuda/index.html).
-If CUDA or numba is not available, KyuPy will automatically fall back to slow, pure python execution.
-
-The Jupyter Notebook [UsageExamples.ipynb](https://github.com/s-holst/kyupy/blob/main/UsageExamples.ipynb) on GitHub
-contains some useful examples to get familiar with the API.
-
-
-Development
------------
-
-To contribute to KyuPy or simply explore the source code, clone the KyuPy [repository](https://github.com/s-holst/kyupy) on GitHub.
-Within your local checkout, run:
-```commandline
-pip3 install --user -e .
-```
-to make the kyupy package available in your python environment.
-The source code comes with tests that can be run with:
-```
-pytest
-```
-
-KyuPy depends on the following packages:
-* [lark-parser](https://pypi.org/project/lark-parser)
-* [numpy](https://pypi.org/project/numpy)
-* [numba](https://pypi.org/project/numba) (optional, required only for GPU/CUDA support)

README.rst

@@ -0,0 +1,28 @@
+KyuPy - Pythonic Processing of VLSI Circuits
+============================================
+
+KyuPy is a Python package for processing and analysis of non-hierarchical gate-level VLSI designs.
+It contains fundamental building blocks for research software in the fields of VLSI test, diagnosis and reliability:
+
+* Efficient data structures for gate-level circuits and related design data.
+* Partial `lark <https://github.com/lark-parser/lark>`_ parsers for common design files like
+  bench, gate-level verilog, standard delay format (SDF), standard test interface language (STIL).
+* Bit-parallel gate-level 2-, 4-, and 8-valued logic simulation.
+* GPU-accelerated high-throughput gate-level timing simulation.
+* High-performance through the use of `numpy <https://numpy.org>`_ and `numba <https://numba.pydata.org>`_.
+
+
+Getting Started
+---------------
+
+KyuPy is available in `PyPI <https://pypi.org/project/kyupy>`_.
+It requires Python 3.6 or newer, `lark-parser <https://pypi.org/project/lark-parser>`_, and `numpy <https://pypi.org/project/numpy>`_.
+Although optional, `numba <https://pypi.org/project/numba>`_ should be installed for best performance.
+GPU/CUDA support in numba may `require some additional setup <https://numba.pydata.org/numba-doc/latest/cuda/index.html>`_.
+If numba is not available, KyuPy will automatically fall back to slow, pure Python execution.
+
+The Jupyter Notebook `UsageExamples.ipynb <https://github.com/s-holst/kyupy/blob/main/UsageExamples.ipynb>`_ contains some useful examples to get familiar with the API.
+
+To work with the latest pre-release source code, clone the `KyuPy GitHub repository <https://github.com/s-holst/kyupy>`_.
+Run ``pip3 install --user -e .`` within your local checkout to make the package available in your Python environment.
+The source code comes with tests that can be run with ``pytest``.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,64 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import sphinx_rtd_theme
+sys.path.insert(0, os.path.abspath('../src'))
+
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'KyuPy'
+copyright = '2020, Stefan Holst'
+author = 'Stefan Holst'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.2'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx_rtd_theme',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+autodoc_default_options = {
+    'member-order': 'bysource',
+}

docs/datastructures.rst

@@ -0,0 +1,30 @@
+Core Data Structures
+====================
+
+KyuPy provides two types of core data structures, one for gate-level circuits, and a few others for representing and storing logic data and signal values.
+The data structures are designed to work together nicely with numpy arrays.
+For example, all the nodes and connections in the circuit graph have numerical indices that can be used to access ndarrays with associated data.
+Circuit graphs also define an ordering of inputs, outputs and other nodes to easily process test vector data and alike.
+
+Module :mod:`kyupy.circuit`
+---------------------------
+
+.. automodule:: kyupy.circuit
+
+.. autoclass:: kyupy.circuit.Node
+   :members:
+
+.. autoclass:: kyupy.circuit.Circuit
+   :members:
+
+Logic Values and Arrays
+-----------------------
+
+.. automodule:: kyupy.logic
+
+.. autoclass:: kyupy.logic.MVArray
+   :members:
+
+.. autoclass:: kyupy.logic.BPArray
+   :members:
+

docs/index.rst

@@ -0,0 +1,12 @@
+.. include:: ../README.rst
+
+API Reference
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   datastructures
+   parsers
+   simulators
+

docs/parsers.rst

@@ -0,0 +1,12 @@
+Parsers
+=======
+
+bench
+
+verilog
+
+SDF
+
+STIL
+
+

docs/simulators.rst

@@ -0,0 +1,8 @@
+Simulators
+==========
+
+Logic Sim
+
+Wave Sim
+
+

setup.py

@@ -1,14 +1,13 @@
 from setuptools import setup, find_packages
 
-with open('README.md', 'r') as f:
+with open('README.rst', 'r') as f:
     long_description = f.read()
 
 setup(
     name='kyupy',
-    version='0.0.1',
+    version='0.0.2',
     description='High-performance processing and analysis of non-hierarchical VLSI designs',
     long_description=long_description,
-    long_description_content_type='text/markdown',
     packages=find_packages(where='src'),
     package_dir={'': 'src'},
     url='https://github.com/s-holst/kyupy',

src/kyupy/circuit.py

@@ -1,3 +1,10 @@
+"""Data structures for representing non-hierarchical gate-level circuits.
+
+The class :class:`Circuit` is a container of nodes connected by lines.
+A node is an instance of class :class:`Node`,
+and a line is an instance of class :class:`Line`.
+"""
+
 from collections import deque
 
 
@@ -19,36 +26,51 @@ class IndexList(list):
 
 
 class Node:
-    """A Node is a named entity in a circuit (e.g. a gate, a standard cell,
-    a named signal, or a fan-out point) that has connections to other nodes.
-    Each node contains:
-
-    * `self.index`: a circuit-unique integer index.
-    * `self.kind`: a type describing its function (e.g. 'AND', 'NOR').
-      The type '__fork__' is special. It signifies a named signal
-      or a fan-out in the circuit. Any other type is considered a physical cell.
-    * `self.name`: a name. Names must be unique among all forks and all cells
-      in the circuit. However, a fork (`self.kind=='__fork__'`) and a cell with
-      the same name may coexist.
-    * `self.ins`: a list of input connections (objects of class `Line`)
-    * `self.outs`: a list of output connections (objects of class `Line`).
+    """A named entity in a circuit (e.g. a gate, a standard cell,
+    a named signal, or a fan-out point) that is connected to other nodes via lines.
+
+    The constructor automatically adds the new node to the given circuit.
     """
     def __init__(self, circuit, name, kind='__fork__'):
         if kind == '__fork__':
-            if name in circuit.forks:
-                raise ValueError(f'fork of name {name} already exists.')
+            assert name not in circuit.forks, f'fork of name {name} already in circuit.'
             circuit.forks[name] = self
         else:
-            if name in circuit.cells:
-                raise ValueError(f'cell of name {name} already exists.')
+            assert name not in circuit.cells, f'cell of name {name} already in circuit.'
             circuit.cells[name] = self
-        self.index = len(circuit.nodes)
         circuit.nodes.append(self)
         self.circuit = circuit
+        """The :class:`Circuit` object the node is part of.
+        """
         self.name = name
+        """The name of the node.
+
+        Names must be unique among all forks and all cells in the circuit.
+        However, a fork (:code:`kind=='__fork__'`) and a cell with the same name may coexist.
+        """
         self.kind = kind
+        """A string describing the type of the node.
+        
+        Common types are the names from a standard cell library or general gate names like 'AND' or 'NOR'.
+        If :code:`kind` is set to '__fork__', it receives special treatment.
+        A `fork` describes a named signal or a fan-out point in the circuit and not a physical `cell` like a gate.
+        In the circuit, the namespaces of forks and cells are kept separate.
+        While :code:`name` must be unique among all forks and all cells, a fork can have the same name as a cell.
+        The :code:`index`, however, is unique among all nodes; a fork cannot have the same index as a cell.
+        """
+        self.index = len(circuit.nodes) - 1
+        """A unique and consecutive integer index of the node within the circuit.
+
+        It can be used to store additional data about the node :code:`n`
+        by allocating an array or list :code:`my_data` of length :code:`len(n.circuit.nodes)` and
+        accessing it by :code:`my_data[n.index]`.
+        """
         self.ins = GrowingList()
+        """A list of input connections (:class:`Line` objects).
+        """
         self.outs = GrowingList()
+        """A list of output connections (:class:`Line` objects).
+        """
 
     def __repr__(self):
         ins = ' '.join([f'<{line.index}' if line is not None else '<None' for line in self.ins])
@@ -56,6 +78,13 @@ class Node:
         return f'{self.index}:{self.kind}"{self.name}" {ins} {outs}'
 
     def remove(self):
+        """Removes the node from its circuit.
+
+        Lines may still reference the removed node.
+        The user must connect such lines to other nodes or remove the lines from the circuit.
+        To keep the indices consecutive, the node with the highest index within the circuit
+        will be assigned the index of the removed node.
+        """
         if self.circuit is not None:
             del self.circuit.nodes[self.index]
             if self.kind == '__fork__':
@@ -66,8 +95,9 @@ class Node:
 
 
 class Line:
-    """A Line is a directional 1:1 connection between two Nodes. It always
-    connects an output of a node (called `driver`) to an input of a node
+    """A directional 1:1 connection between two nodes.
+
+    It always connects an output of a node (called `driver`) to an input of a node
     (called `reader`) and has a circuit-unique index (`self.index`).
 
     Furthermore, `self.driver_pin` and `self.reader_pin` are the