Merge pull request #5 from sglvladi/v2.0a1

V2.0a1
sglvladi · Mar 27, 2023 · 27c8213 · 27c8213
2 parents a74cc99 + e31d632
commit 27c8213
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diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -0,0 +1,52 @@
+name: Wheels
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: pypa/cibuildwheel@v2.12.1
+        env:
+          CIBW_ARCHS_MACOS: auto universal2
+
+      - name: Verify clean directory
+        run: git diff --exit-code
+        shell: bash
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
diff --git a/.gitignore b/.gitignore
@@ -21,6 +21,8 @@ htmlcov/
 
 # IDE
 .idea/
+.vs/
+x64/
 
 # Notebooks
 examples/.ipynb_checkpoints
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,9 +1,14 @@
 version: 2
 
+formats: all
+
 sphinx:
    configuration: docs/source/conf.py
 
-formats: all
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
 
 python:
   install:

diff --git a/cpp_test/cpp_test.cpp b/cpp_test/cpp_test.cpp
diff --git a/cpp_test/cpp_test.vcxproj b/cpp_test/cpp_test.vcxproj
@@ -0,0 +1,142 @@
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+<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <ItemGroup Label="ProjectConfigurations">
+    <ProjectConfiguration Include="Debug|Win32">
+      <Configuration>Debug</Configuration>
+      <Platform>Win32</Platform>
+    </ProjectConfiguration>
+    <ProjectConfiguration Include="Release|Win32">
+      <Configuration>Release</Configuration>
+      <Platform>Win32</Platform>
+    </ProjectConfiguration>
+    <ProjectConfiguration Include="Debug|x64">
+      <Configuration>Debug</Configuration>
+      <Platform>x64</Platform>
+    </ProjectConfiguration>
+    <ProjectConfiguration Include="Release|x64">
+      <Configuration>Release</Configuration>
+      <Platform>x64</Platform>
+    </ProjectConfiguration>
+  </ItemGroup>
+  <PropertyGroup Label="Globals">
+    <VCProjectVersion>16.0</VCProjectVersion>
+    <Keyword>Win32Proj</Keyword>
+    <ProjectGuid>{191debca-a285-4744-bfb2-f9d0b8655d4b}</ProjectGuid>
+    <RootNamespace>cpptest</RootNamespace>
+    <WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
+  </PropertyGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
+    <ConfigurationType>Application</ConfigurationType>
+    <UseDebugLibraries>true</UseDebugLibraries>
+    <PlatformToolset>v143</PlatformToolset>
+    <CharacterSet>Unicode</CharacterSet>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
+    <ConfigurationType>Application</ConfigurationType>
+    <UseDebugLibraries>false</UseDebugLibraries>
+    <PlatformToolset>v143</PlatformToolset>
+    <WholeProgramOptimization>true</WholeProgramOptimization>
+    <CharacterSet>Unicode</CharacterSet>
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+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
+    <ConfigurationType>Application</ConfigurationType>
+    <UseDebugLibraries>true</UseDebugLibraries>
+    <PlatformToolset>v143</PlatformToolset>
+    <CharacterSet>Unicode</CharacterSet>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
+    <ConfigurationType>Application</ConfigurationType>
+    <UseDebugLibraries>false</UseDebugLibraries>
+    <PlatformToolset>v143</PlatformToolset>
+    <WholeProgramOptimization>true</WholeProgramOptimization>
+    <CharacterSet>Unicode</CharacterSet>
+  </PropertyGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+  <ImportGroup Label="ExtensionSettings">
+  </ImportGroup>
+  <ImportGroup Label="Shared">
+  </ImportGroup>
+  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+  </ImportGroup>
+  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+  </ImportGroup>
+  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+  </ImportGroup>
+  <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+    <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+  </ImportGroup>
+  <PropertyGroup Label="UserMacros" />
+  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+    <ClCompile>
+      <WarningLevel>Level3</WarningLevel>
+      <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions>WIN32;_DEBUG;_CONSOLE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <ConformanceMode>true</ConformanceMode>
+    </ClCompile>
+    <Link>
+      <SubSystem>Console</SubSystem>
+      <GenerateDebugInformation>true</GenerateDebugInformation>
+    </Link>
+  </ItemDefinitionGroup>
+  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+    <ClCompile>
+      <WarningLevel>Level3</WarningLevel>
+      <FunctionLevelLinking>true</FunctionLevelLinking>
+      <IntrinsicFunctions>true</IntrinsicFunctions>
+      <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions>WIN32;NDEBUG;_CONSOLE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <ConformanceMode>true</ConformanceMode>
+    </ClCompile>
+    <Link>
+      <SubSystem>Console</SubSystem>
+      <EnableCOMDATFolding>true</EnableCOMDATFolding>
+      <OptimizeReferences>true</OptimizeReferences>
+      <GenerateDebugInformation>true</GenerateDebugInformation>
+    </Link>
+  </ItemDefinitionGroup>
+  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+    <ClCompile>
+      <WarningLevel>Level3</WarningLevel>
+      <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions>_DEBUG;_CONSOLE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <ConformanceMode>true</ConformanceMode>
+      <AdditionalIncludeDirectories>$(SolutionDir)src;$(SolutionDir)include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+    </ClCompile>
+    <Link>
+      <SubSystem>Console</SubSystem>
+      <GenerateDebugInformation>true</GenerateDebugInformation>
+    </Link>
+  </ItemDefinitionGroup>
+  <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+    <ClCompile>
+      <WarningLevel>Level3</WarningLevel>
+      <FunctionLevelLinking>true</FunctionLevelLinking>
+      <IntrinsicFunctions>true</IntrinsicFunctions>
+      <SDLCheck>true</SDLCheck>
+      <PreprocessorDefinitions>NDEBUG;_CONSOLE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+      <ConformanceMode>true</ConformanceMode>
+      <AdditionalIncludeDirectories>$(SolutionDir)src;$(SolutionDir)include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+    </ClCompile>
+    <Link>
+      <SubSystem>Console</SubSystem>
+      <EnableCOMDATFolding>true</EnableCOMDATFolding>
+      <OptimizeReferences>true</OptimizeReferences>
+      <GenerateDebugInformation>true</GenerateDebugInformation>
+    </Link>
+  </ItemDefinitionGroup>
+  <ItemGroup>
+    <ClCompile Include="cpp_test.cpp" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\pyehm.vcxproj">
+      <Project>{8f558650-7c8f-469e-9ba9-8e92f6b3d921}</Project>
+    </ProjectReference>
+  </ItemGroup>
+  <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+  <ImportGroup Label="ExtensionTargets">
+  </ImportGroup>
+</Project>
diff --git a/cpp_test/cpp_test.vcxproj.filters b/cpp_test/cpp_test.vcxproj.filters
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <ItemGroup>
+    <Filter Include="Source Files">
+      <UniqueIdentifier>{4FC737F1-C7A5-4376-A066-2A32D752A2FF}</UniqueIdentifier>
+      <Extensions>cpp;c;cc;cxx;c++;cppm;ixx;def;odl;idl;hpj;bat;asm;asmx</Extensions>
+    </Filter>
+    <Filter Include="Header Files">
+      <UniqueIdentifier>{93995380-89BD-4b04-88EB-625FBE52EBFB}</UniqueIdentifier>
+      <Extensions>h;hh;hpp;hxx;h++;hm;inl;inc;ipp;xsd</Extensions>
+    </Filter>
+    <Filter Include="Resource Files">
+      <UniqueIdentifier>{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}</UniqueIdentifier>
+      <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav;mfcribbon-ms</Extensions>
+    </Filter>
+  </ItemGroup>
+  <ItemGroup>
+    <ClCompile Include="cpp_test.cpp">
+      <Filter>Source Files</Filter>
+    </ClCompile>
+  </ItemGroup>
+</Project>
diff --git a/cpp_test/cpp_test.vcxproj.user b/cpp_test/cpp_test.vcxproj.user
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="Current" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <PropertyGroup />
+</Project>
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -13,18 +13,20 @@
 import re
 import os
 import sys
+
+from pyehm import __version__
+
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../../'))
 
-
 # -- Project information -----------------------------------------------------
 
 project = 'PyEHM'
-copyright = '2021, Lyudmil Vladimirov'
+copyright = '2021-2023, Lyudmil Vladimirov'
 author = 'Lyudmil Vladimirov'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1b1'
+release = __version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -89,4 +91,4 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-html_css_files = ['css/custom.css']
+html_css_files = ['css/custom.css']
diff --git a/docs/source/reference.rst b/docs/source/reference.rst
@@ -13,31 +13,51 @@ The interfaces of these classes are documented below.
 
 .. autoclass:: pyehm.core.EHM2
     :members:
-    :show-inheritance:
-    :inherited-members:
 
-Utils API
----------
-The :mod:`pyehm.utils` module contains helper classes and functions used by :mod:`pyehm.core`.
+Net API
+-------
+The :mod:`pyehm.net` module contains classes that implement the structures (nets, nodes, trees) constructed by the
+:class:`~.EHM` and :class:`~.EHM2` classes.
 
-.. autoclass:: pyehm.utils.EHMNetNode
+.. autoclass:: pyehm.net.EHMNetNode
     :members:
 
-.. autoclass:: pyehm.utils.EHM2NetNode
+.. autoclass:: pyehm.net.EHM2NetNode
+    :members:
+
+.. autoclass:: pyehm.net.EHMNet
     :members:
-    :show-inheritance:
 
-.. autoclass:: pyehm.utils.EHMNet
+.. autoclass:: pyehm.net.EHM2Net
     :members:
 
-.. autoclass:: pyehm.utils.EHM2Tree
+.. autoclass:: pyehm.net.EHM2Tree
     :members:
 
+Utils API
+---------
+The :mod:`pyehm.utils` module contains helper classes and functions.
+
 .. autoclass:: pyehm.utils.Cluster
     :members:
 
 .. autofunction:: pyehm.utils.gen_clusters
 
+.. autofunction:: pyehm.utils.to_nx_graph
+
+Plotting API
+------------
+The :mod:`pyehm.plot` module contains helper functions for plotting the nets and trees constructed by the
+:class:`~.EHM` and :class:`~.EHM2` classes.
+
+.. warning::
+    The plotting functions require `Graphviz <https://graphviz.org/>`_ to be installed and on the ``PATH``.
+
+.. autofunction:: pyehm.plotting.plot_net
+
+.. autofunction:: pyehm.plotting.plot_tree
+
+
 
 Plugins
 -------

diff --git a/include/Eigen/Cholesky b/include/Eigen/Cholesky
@@ -0,0 +1,45 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+#include "Jacobi"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are also accessible via the following methods:
+  *  - MatrixBase::llt()
+  *  - MatrixBase::ldlt()
+  *  - SelfAdjointView::llt()
+  *  - SelfAdjointView::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Cholesky/LLT_LAPACKE.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H