зеркало из https://github.com/dotnet/infer.git
Ported tutorial code to Python (#264)
* Added TestPython project. * TestFSharp exposes xUnit tests. * Added Invoker.InvokeInstance. Invoker favors overloads with higher array indexing depth. * Added EpTests.LinearProgrammingTest. * Updated FSharp.Core, Msagl * pr-netcore.yml uses latest version of .NET 3.1 instead of exact version * UseDotNet task * Updated versions of YAML tasks * netcoretest.sh uses "dotnet test"
This commit is contained in:
Tom Minka
GitHub
Родитель
032372ce36
Коммит
82bfc893ed
|
|
@ -258,8 +258,5 @@ InferNet_Copy_Temp/
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apiguide-tmp/
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_site/
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|
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#code generated by iron python examples
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src/IronPythonWrapper/InferNetExamples/InferNetExamples/GeneratedSource/
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|
||||
#Compiler for IronPython
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||||
src/IronPythonWrapper/Compiler
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**/GeneratedSource
|
||||
**/__pycache__
|
||||
|
|
|
|||
23
BUILDING.md
23
BUILDING.md
|
|
@ -55,9 +55,10 @@ When not using Windows, expect build failure messages about examples that use WP
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|||
### Run unit tests
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|
||||
Unit tests are written using the [XUnit](https://xunit.github.io/) framework.
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In order to run unit tests, build the test project and execute one of the following commands:
|
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The easiest way to run all tests is to execute the script `netcoretest.sh` or `monotest.sh`.
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To run unit tests manually, build the test project and execute one of the following commands:
|
||||
```bash
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||||
dotnet ~/.nuget/packages/xunit.runner.console/2.3.1/tools/netcoreapp2.0/xunit.console.dll <path to netcoreapp3.1 assembly with tests> <filter>
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dotnet test Tests -c <configuration> <filter>
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```
|
||||
```bash
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||||
mono ~/.nuget/packages/xunit.runner.console/2.3.1/tools/net452/xunit.console.exe <path to net461 assembly with tests> <filter>
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@ -92,23 +93,7 @@ testing you must filter these out by `-notrait`.
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_BadTest_ is a category of tests that must fail.
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_OpenBug_ is a category of tests that can fail.
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||||
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An example of quick testing of `Microsoft.ML.Probabilistic.Tests.dll` in `Debug` configuration after changing working directory to
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the `Tests` project looks like:
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```bash
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dotnet ~/.nuget/packages/xunit.runner.console/2.3.1/tools/netcoreapp2.0/xunit.console.dll bin/DebugCore/netcoreapp3.1/Microsoft.ML.Probabilistic.Tests.dll -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=Platform -notrait Category=CsoftModel -notrait Category=ModifiesGlobals -notrait Category=DistributedTest -notrait Category=Performance
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dotnet ~/.nuget/packages/xunit.runner.console/2.3.1/tools/netcoreapp2.0/xunit.console.dll bin/DebugCore/netcoreapp3.1/Microsoft.ML.Probabilistic.Tests.dll -trait Category=CsoftModel -trait Category=ModifiesGlobals -trait Category=DistributedTests -trait Category=Performance -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=Platform -parallel none
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```
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To run the same set of tests on Mono:
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```bash
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mono ~/.nuget/packages/xunit.runner.console/2.3.1/tools/net452/xunit.console.exe bin/DebugFull/net461/Microsoft.ML.Probabilistic.Tests.dll -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=Platform -notrait Category=CsoftModel -notrait Category=ModifiesGlobals -notrait Category=DistributedTest -notrait Category=Performance
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mono ~/.nuget/packages/xunit.runner.console/2.3.1/tools/net452/xunit.console.exe bin/DebugFull/net461/Microsoft.ML.Probabilistic.Tests.dll -trait Category=CsoftModel -trait Category=ModifiesGlobals -trait Category=DistributedTests -trait Category=Performance -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=Platform -parallel none
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```
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Helper scripts `netcoretest.sh` and `monotest.sh` for running unit tests on .NET Core and Mono respectively are located in the `test` folder.
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See the scripts for example filters.
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## Fast matrix operations with Intel MKL
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Matrix operations in Infer.NET can be significantly accelerated by building with Intel MKL support.
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|
|
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32
Infer.sln
32
Infer.sln
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@ -4,7 +4,9 @@ VisualStudioVersion = 16.0.29020.237
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{A181C943-2E01-454D-9008-2E3C53AA09CC}"
|
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ProjectSection(SolutionItems) = preProject
|
||||
BUILDING.md = BUILDING.md
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||||
Infer.snk = Infer.snk
|
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README.md = README.md
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TestRunConfig1.testrunconfig = TestRunConfig1.testrunconfig
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EndProjectSection
|
||||
ProjectSection(FolderStartupServices) = postProject
|
||||
|
|
@ -98,6 +100,30 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "LearnersNuGet", "src\Learne
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EndProject
|
||||
Project("{888888A0-9F3D-457C-B088-3A5042F75D52}") = "Tools.PythonScripts", "src\Tools\PythonScripts\Tools.PythonScripts.pyproj", "{D7562CC3-D48A-481D-B40C-07EE51EBBF50}"
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EndProject
|
||||
Project("{888888A0-9F3D-457C-B088-3A5042F75D52}") = "TestPython", "test\TestPython\TestPython.pyproj", "{79B39D08-DF06-47B8-B7EE-15E30EB9A209}"
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EndProject
|
||||
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "build", "build", "{5759CC85-729E-479A-BF7E-8A0B8937B123}"
|
||||
ProjectSection(SolutionItems) = preProject
|
||||
build\common.props = build\common.props
|
||||
build\copyassemblies.sh = build\copyassemblies.sh
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||||
build\evaluator-netcore.yml = build\evaluator-netcore.yml
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build\evaluator-netframework.yml = build\evaluator-netframework.yml
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test\monotest.sh = test\monotest.sh
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build\netcoretest-fast.yml = build\netcoretest-fast.yml
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||||
test\netcoretest.sh = test\netcoretest.sh
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build\nightly-netcore.yml = build\nightly-netcore.yml
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build\nightly-windows.yml = build\nightly-windows.yml
|
||||
build\nuget-properties.props = build\nuget-properties.props
|
||||
build\pr-factordocs.yml = build\pr-factordocs.yml
|
||||
build\pr-msbuild.yml = build\pr-msbuild.yml
|
||||
build\pr-netcore.yml = build\pr-netcore.yml
|
||||
build\release.yml = build\release.yml
|
||||
build\sign.proj = build\sign.proj
|
||||
build\updateversion.sh = build\updateversion.sh
|
||||
build\vstest-fast.yml = build\vstest-fast.yml
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||||
build\windows-msbuild.yml = build\windows-msbuild.yml
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||||
EndProjectSection
|
||||
EndProject
|
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Global
|
||||
GlobalSection(SolutionConfigurationPlatforms) = preSolution
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Debug|Any CPU = Debug|Any CPU
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|
|
@ -512,6 +538,12 @@ Global
|
|||
{D7562CC3-D48A-481D-B40C-07EE51EBBF50}.Release|Any CPU.ActiveCfg = Release|Any CPU
|
||||
{D7562CC3-D48A-481D-B40C-07EE51EBBF50}.ReleaseCore|Any CPU.ActiveCfg = Release|Any CPU
|
||||
{D7562CC3-D48A-481D-B40C-07EE51EBBF50}.ReleaseFull|Any CPU.ActiveCfg = Release|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.DebugCore|Any CPU.ActiveCfg = Debug|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.DebugFull|Any CPU.ActiveCfg = Debug|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.Release|Any CPU.ActiveCfg = Release|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.ReleaseCore|Any CPU.ActiveCfg = Release|Any CPU
|
||||
{79B39D08-DF06-47B8-B7EE-15E30EB9A209}.ReleaseFull|Any CPU.ActiveCfg = Release|Any CPU
|
||||
EndGlobalSection
|
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GlobalSection(SolutionProperties) = preSolution
|
||||
HideSolutionNode = FALSE
|
||||
|
|
|
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|
|
@ -8,6 +8,7 @@ parameters:
|
|||
Configuration: 'ReleaseCore'
|
||||
|
||||
steps:
|
||||
# TODO: Use .NET Core CLI Task instead: https://docs.microsoft.com/en-us/azure/devops/pipelines/tasks/build/dotnet-core-cli?view=azure-devops
|
||||
- task: Bash@3
|
||||
displayName: 'Running tests'
|
||||
inputs:
|
||||
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|
@ -17,8 +18,9 @@ steps:
|
|||
displayName: Run tests
|
||||
continueOnError: true
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||||
|
||||
# https://docs.microsoft.com/en-us/azure/devops/pipelines/tasks/test/publish-test-results?view=azure-devops&tabs=yaml
|
||||
- task: PublishTestResults@2
|
||||
displayName: 'Publishing test results'
|
||||
inputs:
|
||||
testRunner: XUnit
|
||||
testResultsFiles: 'test/netcoretest-result*.xml'
|
||||
testResultsFormat: vstest
|
||||
testResultsFiles: 'test/**/netcoretest-result*.trx'
|
||||
|
|
@ -16,10 +16,10 @@ queue:
|
|||
trigger: none # disable CI build
|
||||
|
||||
steps:
|
||||
- task: DotNetCoreInstaller@0
|
||||
- task: UseDotNet@2
|
||||
inputs:
|
||||
packageType: 'sdk'
|
||||
version: '3.1.201'
|
||||
version: '3.x'
|
||||
|
||||
- script: |
|
||||
dotnet build /p:DisableImplicitNuGetFallbackFolder=true --configuration $(BuildConfiguration)Core Infer.sln
|
||||
|
|
|
|||
|
|
@ -11,10 +11,10 @@ resources:
|
|||
trigger: none # disable CI build
|
||||
|
||||
steps:
|
||||
- task: DotNetCoreInstaller@0
|
||||
- task: UseDotNet@2
|
||||
inputs:
|
||||
packageType: 'sdk'
|
||||
version: '3.1.201'
|
||||
version: '3.x'
|
||||
|
||||
- script: |
|
||||
echo Checking $(Build.Repository.LocalPath)\src\Runtime\Factors\FactorDocs.xml...
|
||||
|
|
|
|||
|
|
@ -19,9 +19,9 @@ jobs:
|
|||
pool:
|
||||
vmImage: windows-2019
|
||||
steps:
|
||||
- task: NuGetToolInstaller@0
|
||||
- task: NuGetToolInstaller@1
|
||||
inputs:
|
||||
versionSpec: '5.5.1'
|
||||
versionSpec: '>=5.5.1'
|
||||
|
||||
- task: NuGetCommand@2
|
||||
inputs:
|
||||
|
|
@ -43,9 +43,9 @@ jobs:
|
|||
pool:
|
||||
vmImage: windows-2019
|
||||
steps:
|
||||
- task: NuGetToolInstaller@0
|
||||
- task: NuGetToolInstaller@1
|
||||
inputs:
|
||||
versionSpec: '5.5.1'
|
||||
versionSpec: '>=5.5.1'
|
||||
|
||||
- task: NuGetCommand@2
|
||||
inputs:
|
||||
|
|
|
|||
|
|
@ -17,10 +17,10 @@ variables:
|
|||
buildConfiguration: 'Release'
|
||||
|
||||
steps:
|
||||
- task: DotNetCoreInstaller@0
|
||||
- task: UseDotNet@2
|
||||
inputs:
|
||||
packageType: 'sdk'
|
||||
version: '3.1.201'
|
||||
version: '3.x'
|
||||
|
||||
- script: |
|
||||
dotnet build /p:DisableImplicitNuGetFallbackFolder=true --configuration $(buildConfiguration)Core Infer.sln
|
||||
|
|
|
|||
|
|
@ -19,10 +19,10 @@ jobs:
|
|||
pool:
|
||||
vmImage: macOS-10.14
|
||||
steps:
|
||||
- task: DotNetCoreInstaller@0
|
||||
- task: UseDotNet@2
|
||||
inputs:
|
||||
packageType: 'sdk'
|
||||
version: '3.1.201'
|
||||
version: '3.x'
|
||||
|
||||
- script: |
|
||||
dotnet build --configuration $(BuildConfiguration)Core Infer.sln
|
||||
|
|
@ -34,10 +34,10 @@ jobs:
|
|||
pool:
|
||||
vmImage: ubuntu-16.04
|
||||
steps:
|
||||
- task: DotNetCoreInstaller@0
|
||||
- task: UseDotNet@2
|
||||
inputs:
|
||||
packageType: 'sdk'
|
||||
version: '3.1.201'
|
||||
version: '3.x'
|
||||
|
||||
- script: |
|
||||
dotnet build --configuration $(BuildConfiguration)Core Infer.sln
|
||||
|
|
@ -57,9 +57,9 @@ jobs:
|
|||
workingDirectory: build
|
||||
arguments: $(Build.BuildNumber)
|
||||
|
||||
- task: NuGetToolInstaller@0
|
||||
- task: NuGetToolInstaller@1
|
||||
inputs:
|
||||
versionSpec: '5.5.1'
|
||||
versionSpec: '>=5.5.1'
|
||||
|
||||
- task: NuGetCommand@2
|
||||
displayName: 'Restoring NuGet packages'
|
||||
|
|
|
|||
|
|
@ -17,9 +17,9 @@ steps:
|
|||
workingDirectory: build
|
||||
arguments: ${{ parameters.BuildNumber }}
|
||||
|
||||
- task: NuGetToolInstaller@0
|
||||
- task: NuGetToolInstaller@1
|
||||
inputs:
|
||||
versionSpec: '5.5.1'
|
||||
versionSpec: '>=5.5.1'
|
||||
|
||||
- task: NuGetCommand@2
|
||||
displayName: 'Restoring NuGet packages'
|
||||
|
|
|
|||
|
|
@ -45,10 +45,16 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
/// </summary>
|
||||
public Conversion[] Conversions;
|
||||
|
||||
/// <summary>
|
||||
/// Array indexing depth needed to obtain a match.
|
||||
/// </summary>
|
||||
public uint Depth;
|
||||
|
||||
public void SetTo(Binding info)
|
||||
{
|
||||
foreach (KeyValuePair<Type, Type> entry in info.Types) Types[entry.Key] = entry.Value;
|
||||
info.Conversions.CopyTo(Conversions, 0);
|
||||
Depth = info.Depth;
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
|
|
@ -91,6 +97,7 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
//if (a.Types.Count < b.Types.Count) return true;
|
||||
float aWeight = Conversion.GetWeight(a.Conversions);
|
||||
float bWeight = Conversion.GetWeight(b.Conversions);
|
||||
if (aWeight == bWeight) return a.Depth > b.Depth;
|
||||
return (aWeight < bWeight);
|
||||
}
|
||||
|
||||
|
|
@ -584,15 +591,15 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
}
|
||||
Type formalElement = formal.GetElementType();
|
||||
Type actualElement = actual.GetElementType();
|
||||
binding.Depth++;
|
||||
IEnumerator<Binding> iter3 = InferGenericParameters(formalElement, actualElement, binding, errors, position, allowSubtype, conversionOptions);
|
||||
while (iter3.MoveNext())
|
||||
{
|
||||
binding = iter3.Current;
|
||||
Conversion oldConversion = new Conversion();
|
||||
Conversion elementConversion = default(Conversion);
|
||||
if (position >= 0)
|
||||
{
|
||||
oldConversion = binding.Conversions[position];
|
||||
Conversion elementConversion = binding.Conversions[position];
|
||||
elementConversion = binding.Conversions[position];
|
||||
if (elementConversion.Converter != null)
|
||||
{
|
||||
// if there is an element conversion, promote it to an array conversion
|
||||
|
|
@ -605,8 +612,9 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
}
|
||||
yield return binding;
|
||||
// restore previous state
|
||||
if (position >= 0) binding.Conversions[position] = oldConversion;
|
||||
if (position >= 0) binding.Conversions[position] = elementConversion;
|
||||
}
|
||||
binding.Depth--;
|
||||
yield break;
|
||||
}
|
||||
else
|
||||
|
|
@ -628,6 +636,7 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
int subclassCount = 0;
|
||||
bool anyMatch = false;
|
||||
List<Exception> innerErrors = new List<Exception>();
|
||||
binding.Depth++;
|
||||
foreach (Type parent in choices)
|
||||
{
|
||||
if (!parent.IsGenericType || !formalGenericTypeDefinition.Equals(parent.GetGenericTypeDefinition()))
|
||||
|
|
@ -651,6 +660,7 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
}
|
||||
subclassCount++;
|
||||
}
|
||||
binding.Depth--;
|
||||
if (!anyMatch || innerErrors.Count > 0)
|
||||
{
|
||||
string formalString = StringUtil.TypeToString(formal);
|
||||
|
|
@ -853,7 +863,7 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
|
||||
public override string ToString()
|
||||
{
|
||||
return StringUtil.DictionaryToString(Types, Environment.NewLine);
|
||||
return $"Binding({StringUtil.DictionaryToString(Types, Environment.NewLine)}, Conversions={StringUtil.ArrayToString(Conversions)}, Depth={Depth})";
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
|
|
|
|||
|
|
@ -70,6 +70,20 @@ namespace Microsoft.ML.Probabilistic.Compiler.Reflection
|
|||
}
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
/// Invoke the instance member which best matches the argument types.
|
||||
/// </summary>
|
||||
/// <param name="methodName"></param>
|
||||
/// <param name="target"></param>
|
||||
/// <param name="args"></param>
|
||||
/// <returns></returns>
|
||||
public static object InvokeInstance(string methodName, object target, params object[] args)
|
||||
{
|
||||
return InvokeMember(target.GetType(), methodName,
|
||||
BindingFlags.Public | BindingFlags.Instance | BindingFlags.GetField | BindingFlags.GetProperty | BindingFlags.InvokeMethod |
|
||||
BindingFlags.FlattenHierarchy, target, args);
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
/// Get an element from an array or collection, or invoke a delegate.
|
||||
/// </summary>
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
<DocumentationFile>bin\$(Configuration)\$(TargetFramework)\Microsoft.ML.Probabilistic.FSharp.XML</DocumentationFile>
|
||||
</PropertyGroup>
|
||||
<ItemGroup>
|
||||
<PackageReference Include="FSharp.Core" Version="4.3.4" />
|
||||
<PackageReference Include="FSharp.Core" Version="4.7.2" />
|
||||
<PackageReference Update="System.ValueTuple" Version="4.5.0" />
|
||||
</ItemGroup>
|
||||
<ItemGroup>
|
||||
|
|
|
|||
|
|
@ -58,10 +58,10 @@ namespace Microsoft.ML.Probabilistic.Tutorials
|
|||
z[n].InitialiseTo(zInit[n]);
|
||||
|
||||
// The inference
|
||||
InferenceEngine ie = new InferenceEngine();
|
||||
Console.WriteLine("Dist over pi=" + ie.Infer(weights));
|
||||
Console.WriteLine("Dist over means=\n" + ie.Infer(means));
|
||||
Console.WriteLine("Dist over precs=\n" + ie.Infer(precs));
|
||||
InferenceEngine engine = new InferenceEngine();
|
||||
Console.WriteLine("Dist over pi=" + engine.Infer(weights));
|
||||
Console.WriteLine("Dist over means=\n" + engine.Infer(means));
|
||||
Console.WriteLine("Dist over precs=\n" + engine.Infer(precs));
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
|
|
|
|||
|
|
@ -26,9 +26,9 @@
|
|||
</PropertyGroup>
|
||||
|
||||
<ItemGroup>
|
||||
<PackageReference Include="Microsoft.Msagl" Version="1.1.1" />
|
||||
<PackageReference Include="Microsoft.Msagl.Drawing" Version="1.1.1" />
|
||||
<PackageReference Include="Microsoft.Msagl.GraphViewerGdi" Version="1.1.1" />
|
||||
<PackageReference Include="Microsoft.Msagl" Version="1.1.3" />
|
||||
<PackageReference Include="Microsoft.Msagl.Drawing" Version="1.1.3" />
|
||||
<PackageReference Include="Microsoft.Msagl.GraphViewerGdi" Version="1.1.3" />
|
||||
<Reference Include="System.Drawing" />
|
||||
<Reference Include="System.Windows.Forms" />
|
||||
<EmbeddedResource Update="*.resx">
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace BayesPointTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic.Distributions
|
||||
|
|
@ -18,7 +18,7 @@ open Microsoft.ML.Probabilistic.FSharp
|
|||
|
||||
module bayes =
|
||||
// The training model
|
||||
let bayesTestFunc() =
|
||||
let BayesPointMachineExample() =
|
||||
Console.WriteLine("\n=====================Running Bayes Point Machine Tutorial====================\n");
|
||||
let noise = 0.1
|
||||
let len = Variable.New<int>()
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace ClinicalTrialTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic.Models
|
||||
|
|
@ -51,7 +51,7 @@ module clinical =
|
|||
Variable.IfBlock isEffective f1 f2
|
||||
()
|
||||
|
||||
let clinicalTestFunc() =
|
||||
let clinicalTrialTutorial() =
|
||||
Console.WriteLine("\n====================Running Clinical Trial Tutorial==========================\n");
|
||||
|
||||
// The inference
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
namespace DifficultyAbilityExample
|
||||
namespace TestFSharp
|
||||
|
||||
open System.Collections.Generic
|
||||
open Microsoft.ML.Probabilistic
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace GaussianRangesTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic
|
||||
|
|
@ -19,7 +19,7 @@ open Microsoft.ML.Probabilistic.FSharp
|
|||
|
||||
// The model
|
||||
module ranges =
|
||||
let rangesTestFunc() =
|
||||
let learningAGaussianWithRanges() =
|
||||
Console.WriteLine("\n======================Running Gaussian Ranges Tutorial=======================\n");
|
||||
// The model
|
||||
let len = Variable.New<int>()
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace MixtureGaussiansTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic
|
||||
|
|
@ -35,7 +35,7 @@ module mixture =
|
|||
//-----------------------------------
|
||||
// The model
|
||||
//----------------------------------
|
||||
let mixtureTestFunc() =
|
||||
let mixtureOfGaussiansTutorial() =
|
||||
Console.WriteLine("\n=================Running Mixture of Gaussians Tutorial=======================\n");
|
||||
// Define a range for the number of mixture components
|
||||
let k = Range(2)
|
||||
|
|
|
|||
|
|
@ -1,22 +0,0 @@
|
|||
// Licensed to the .NET Foundation under one or more agreements.
|
||||
// The .NET Foundation licenses this file to you under the MIT license.
|
||||
// See the LICENSE file in the project root for more information.
|
||||
|
||||
#light
|
||||
open System
|
||||
open System.Diagnostics
|
||||
|
||||
let coreAssemblyInfo = FileVersionInfo.GetVersionInfo(typeof<Object>.Assembly.Location)
|
||||
printfn "%s .NET version %s mscorlib %s" (if Environment.Is64BitProcess then "64-bit" else "32-bit") (Environment.Version.ToString ()) coreAssemblyInfo.ProductVersion
|
||||
|
||||
//main Smoke Test .............................................
|
||||
|
||||
let _ = TwoCoinsTutorial.coins.twoCoinsTestFunc()
|
||||
let _ = TruncatedGaussianTutorial.truncated.truncatedTestFunc()
|
||||
let _ = GaussianRangesTutorial.ranges.rangesTestFunc()
|
||||
let _ = ClinicalTrialTutorial.clinical.clinicalTestFunc()
|
||||
let _ = BayesPointTutorial.bayes.bayesTestFunc()
|
||||
let _ = MixtureGaussiansTutorial.mixture.mixtureTestFunc()
|
||||
let _ = DifficultyAbilityExample.DifficultyAbility.main()
|
||||
|
||||
Console.ReadLine() |> ignore
|
||||
|
|
@ -2,7 +2,9 @@
|
|||
<Import Project="$(MSBuildThisFileDirectory)..\..\build\common.props" />
|
||||
|
||||
<PropertyGroup>
|
||||
<OutputType>Exe</OutputType>
|
||||
<AssemblyName>TestFSharp</AssemblyName>
|
||||
<RootNamespace>TestFSharp</RootNamespace>
|
||||
<OutputType>Exe</OutputType>
|
||||
<PlatformTarget>AnyCPU</PlatformTarget>
|
||||
<Configurations>Debug;Release;DebugFull;DebugCore;ReleaseFull;ReleaseCore</Configurations>
|
||||
</PropertyGroup>
|
||||
|
|
@ -26,21 +28,49 @@
|
|||
</PropertyGroup>
|
||||
</Otherwise>
|
||||
</Choose>
|
||||
|
||||
|
||||
<PropertyGroup Condition=" '$(TargetFramework)' == 'netcoreapp3.1'">
|
||||
<DefineConstants>$(DefineConstants);NETCORE;NETSTANDARD;NETSTANDARD2_0</DefineConstants>
|
||||
</PropertyGroup>
|
||||
|
||||
<PropertyGroup Condition=" '$(TargetFramework)' == 'net461'">
|
||||
<DefineConstants>$(DefineConstants);NET45;NETFULL</DefineConstants>
|
||||
</PropertyGroup>
|
||||
|
||||
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU' OR '$(Configuration)|$(Platform)'=='DebugFull|AnyCPU' OR '$(Configuration)|$(Platform)'=='DebugCore|AnyCPU'">
|
||||
<DebugType>full</DebugType>
|
||||
<DebugSymbols>true</DebugSymbols>
|
||||
<DefineConstants>$(DefineConstants);DEBUG</DefineConstants>
|
||||
</PropertyGroup>
|
||||
|
||||
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU' OR '$(Configuration)|$(Platform)'=='ReleaseFull|AnyCPU' OR '$(Configuration)|$(Platform)'=='ReleaseCore|AnyCPU'">
|
||||
<DebugType>portable</DebugType>
|
||||
<DebugSymbols>true</DebugSymbols>
|
||||
<Optimize>true</Optimize>
|
||||
</PropertyGroup>
|
||||
|
||||
<ItemGroup>
|
||||
<PackageReference Include="FSharp.Core" Version="4.3.4" />
|
||||
<PackageReference Update="System.ValueTuple" Version="4.5.0" />
|
||||
<Compile Include="..\..\src\Shared\SharedAssemblyFileVersion.fs">
|
||||
<Link>SharedAssemblyFileVersion.fs</Link>
|
||||
</Compile>
|
||||
</ItemGroup>
|
||||
<ItemGroup>
|
||||
<ProjectReference Include="..\..\src\Runtime\Runtime.csproj" />
|
||||
<ProjectReference Include="..\..\src\Compiler\Compiler.csproj" />
|
||||
<ProjectReference Include="..\..\src\FSharpWrapper\FSharpWrapper.fsproj" />
|
||||
</ItemGroup>
|
||||
<ItemGroup>
|
||||
<PackageReference Include="FSharp.Core" Version="4.7.2" />
|
||||
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.6.1" />
|
||||
<PackageReference Include="xunit" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.runner.visualstudio" Version="2.4.2">
|
||||
<PrivateAssets>all</PrivateAssets>
|
||||
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
|
||||
</PackageReference>
|
||||
<PackageReference Update="System.ValueTuple" Version="4.5.0" />
|
||||
</ItemGroup>
|
||||
<ItemGroup>
|
||||
<Compile Include="DifficultyAbility.fs" />
|
||||
<Compile Include="..\..\src\Shared\SharedAssemblyFileVersion.fs">
|
||||
<Link>SharedAssemblyFileVersion.fs</Link>
|
||||
</Compile>
|
||||
<Compile Include="AssemblyInfo.fs" />
|
||||
<Compile Include="BayesPointMachine.fs" />
|
||||
<Compile Include="ClinicalTrial.fs" />
|
||||
|
|
@ -48,7 +78,7 @@
|
|||
<Compile Include="MixtureofGaussians.fs" />
|
||||
<Compile Include="TruncatedGaussian.fs" />
|
||||
<Compile Include="TwoCoins.fs" />
|
||||
<Compile Include="Program.fs" />
|
||||
<Compile Include="TestTutorials.fs" />
|
||||
<None Include="App.config">
|
||||
<CopyToOutputDirectory>Always</CopyToOutputDirectory>
|
||||
</None>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,29 @@
|
|||
// Licensed to the .NET Foundation under one or more agreements.
|
||||
// The .NET Foundation licenses this file to you under the MIT license.
|
||||
// See the LICENSE file in the project root for more information.
|
||||
|
||||
#light
|
||||
namespace TestFSharp
|
||||
open System
|
||||
open System.Diagnostics
|
||||
open Xunit
|
||||
|
||||
module main =
|
||||
[<Fact>]
|
||||
let testTutorials() =
|
||||
let coreAssemblyInfo = FileVersionInfo.GetVersionInfo(typeof<Object>.Assembly.Location)
|
||||
printfn "%s .NET version %s mscorlib %s" (if Environment.Is64BitProcess then "64-bit" else "32-bit") (Environment.Version.ToString ()) coreAssemblyInfo.ProductVersion
|
||||
|
||||
//main Smoke Test .............................................
|
||||
|
||||
coins.twoCoinsTutorial()
|
||||
truncated.truncatedGaussianTutorial()
|
||||
ranges.learningAGaussianWithRanges()
|
||||
clinical.clinicalTrialTutorial()
|
||||
bayes.BayesPointMachineExample()
|
||||
mixture.mixtureOfGaussiansTutorial()
|
||||
DifficultyAbility.main()
|
||||
|
||||
//Console.ReadLine() |> ignore
|
||||
|
||||
testTutorials()
|
||||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace TruncatedGaussianTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic.Models
|
||||
|
|
@ -17,7 +17,7 @@ open Microsoft.ML.Probabilistic.FSharp
|
|||
|
||||
// The Model
|
||||
module truncated =
|
||||
let truncatedTestFunc() =
|
||||
let truncatedGaussianTutorial() =
|
||||
Console.WriteLine("\n====================Running Truncated Gaussian Tutorial======================\n");
|
||||
let threshold = (Variable.New<float>()).Named("threshold")
|
||||
let x = Variable.GaussianFromMeanAndVariance(0.0,1.0).Named("x")
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
|
||||
#light
|
||||
|
||||
namespace TwoCoinsTutorial
|
||||
namespace TestFSharp
|
||||
|
||||
open System
|
||||
open Microsoft.ML.Probabilistic.Models
|
||||
|
|
@ -16,8 +16,7 @@ open Microsoft.ML.Probabilistic.FSharp
|
|||
//-----------------------------------------------------------------------------------
|
||||
|
||||
module coins =
|
||||
|
||||
let twoCoinsTestFunc() =
|
||||
let twoCoinsTutorial() =
|
||||
Console.WriteLine("\n========================Running Two Coins Tutorial========================\n");
|
||||
let firstCoin = Variable.Bernoulli(0.5)
|
||||
let secondCoin = Variable.Bernoulli(0.5)
|
||||
|
|
|
|||
|
|
@ -58,8 +58,11 @@
|
|||
</ItemGroup>
|
||||
|
||||
<ItemGroup>
|
||||
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="15.8.0" />
|
||||
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.6.1" />
|
||||
<PackageReference Include="xunit" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.runner.visualstudio" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.runner.visualstudio" Version="2.4.2">
|
||||
<PrivateAssets>all</PrivateAssets>
|
||||
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
|
||||
</PackageReference>
|
||||
</ItemGroup>
|
||||
</Project>
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003" ToolsVersion="4.0">
|
||||
<PropertyGroup>
|
||||
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
|
||||
<SchemaVersion>2.0</SchemaVersion>
|
||||
<ProjectGuid>79b39d08-df06-47b8-b7ee-15e30eb9a209</ProjectGuid>
|
||||
<ProjectHome>.</ProjectHome>
|
||||
<StartupFile>test_tutorials.py</StartupFile>
|
||||
<SearchPath>
|
||||
</SearchPath>
|
||||
<WorkingDirectory>.</WorkingDirectory>
|
||||
<OutputPath>.</OutputPath>
|
||||
<Name>TestPython</Name>
|
||||
<RootNamespace>TestPython</RootNamespace>
|
||||
<TestFramework>pytest</TestFramework>
|
||||
<UnitTestPattern>Test*.py</UnitTestPattern>
|
||||
<UnitTestRootDirectory>.</UnitTestRootDirectory>
|
||||
</PropertyGroup>
|
||||
<PropertyGroup Condition=" '$(Configuration)' == 'Debug' ">
|
||||
<DebugSymbols>true</DebugSymbols>
|
||||
<EnableUnmanagedDebugging>false</EnableUnmanagedDebugging>
|
||||
</PropertyGroup>
|
||||
<PropertyGroup Condition=" '$(Configuration)' == 'Release' ">
|
||||
<DebugSymbols>true</DebugSymbols>
|
||||
<EnableUnmanagedDebugging>false</EnableUnmanagedDebugging>
|
||||
</PropertyGroup>
|
||||
<ItemGroup>
|
||||
<Compile Include="test_tutorials.py" />
|
||||
</ItemGroup>
|
||||
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)\Python Tools\Microsoft.PythonTools.targets" />
|
||||
<!-- Uncomment the CoreCompile target to enable the Build command in
|
||||
Visual Studio and specify your pre- and post-build commands in
|
||||
the BeforeBuild and AfterBuild targets below. -->
|
||||
<!--<Target Name="CoreCompile" />-->
|
||||
<Target Name="BeforeBuild">
|
||||
</Target>
|
||||
<Target Name="AfterBuild">
|
||||
</Target>
|
||||
</Project>
|
||||
|
|
@ -0,0 +1,259 @@
|
|||
# For help using pythonnet:
|
||||
# https://pythonnet.github.io/
|
||||
# To stop the debugger in .NET code, follow the instructions at:
|
||||
# https://mail.python.org/archives/list/pythonnet@python.org/message/AZ4BKHN72PIRAG32ERFY3XS52NVNCL47/
|
||||
import clr
|
||||
from System import Boolean, Double, Int32, Array
|
||||
|
||||
folder = "../Tests/bin/DebugFull/net461/"
|
||||
clr.AddReference(folder+"Microsoft.ML.Probabilistic")
|
||||
clr.AddReference(folder+"Microsoft.ML.Probabilistic.Compiler")
|
||||
from Microsoft.ML.Probabilistic import *
|
||||
from Microsoft.ML.Probabilistic.Distributions import VectorGaussian, Beta, Bernoulli, Discrete
|
||||
from Microsoft.ML.Probabilistic.Math import Rand, Vector, DenseVector, PositiveDefiniteMatrix
|
||||
from Microsoft.ML.Probabilistic.Models import Variable, InferenceEngine, Range, VariableArray
|
||||
from Microsoft.ML.Probabilistic.Compiler.Reflection import Invoker
|
||||
|
||||
def TwoCoins():
|
||||
firstCoin = Variable.Bernoulli(0.5)
|
||||
secondCoin = Variable.Bernoulli(0.5)
|
||||
bothHeads = firstCoin.op_BitwiseAnd(firstCoin, secondCoin)
|
||||
engine = InferenceEngine()
|
||||
print("Probability both coins are heads: %s" % engine.Infer(bothHeads))
|
||||
bothHeads.ObservedValue = False
|
||||
print("Probability distribution over firstCoin: %s" % engine.Infer(firstCoin))
|
||||
|
||||
def TruncatedGaussianEfficient():
|
||||
threshold = Variable.New[Double]()
|
||||
x = Variable.GaussianFromMeanAndVariance(0.0, 1.0)
|
||||
Variable.ConstrainTrue(x.op_GreaterThan(x,threshold))
|
||||
engine = InferenceEngine()
|
||||
for thresh in [i*0.1 for i in range(11)]:
|
||||
threshold.ObservedValue = thresh
|
||||
print("Dist over x given thresh of %s = %s" % (thresh, engine.Infer(x)))
|
||||
|
||||
def LearningAGaussian():
|
||||
# Restart the infer.NET random number generator
|
||||
Rand.Restart(12347)
|
||||
data = [Rand.Normal(0.0, 1.0) for i in range(100)]
|
||||
|
||||
mean = Variable.GaussianFromMeanAndVariance(0.0, 1.0).Named("mean")
|
||||
precision = Variable.GammaFromShapeAndScale(1.0, 1.0).Named("precision")
|
||||
|
||||
for i in range(len(data)):
|
||||
x = Variable.GaussianFromMeanAndPrecision(mean, precision)
|
||||
x.ObservedValue = data[i]
|
||||
|
||||
engine = InferenceEngine()
|
||||
print("mean=%s" % engine.Infer(mean))
|
||||
print("precision=%s" % engine.Infer(precision))
|
||||
|
||||
def LearningAGaussianWithRanges():
|
||||
# Restart the infer.NET random number generator
|
||||
Rand.Restart(12347)
|
||||
data = [Rand.Normal(0.0, 1.0) for i in range(100)]
|
||||
|
||||
mean = Variable.GaussianFromMeanAndVariance(0.0, 1.0).Named("mean")
|
||||
precision = Variable.GammaFromShapeAndScale(1.0, 1.0).Named("precision")
|
||||
|
||||
data_range = Range(len(data)).Named("n")
|
||||
x = Variable.Array[Double](data_range)
|
||||
v = Variable.GaussianFromMeanAndPrecision(mean, precision).ForEach(data_range)
|
||||
x.set_Item(data_range, v)
|
||||
x.ObservedValue = data
|
||||
|
||||
engine = InferenceEngine()
|
||||
print("mean=%s" % engine.Infer(mean))
|
||||
print("precision=%s" %engine.Infer(precision))
|
||||
|
||||
def BayesPointMachine(incomes, ages, w, y):
|
||||
j = y.Range
|
||||
xData = [Vector.FromArray(income, age, 1) for income, age in zip(incomes, ages)]
|
||||
x = VariableObserved(xData, j)
|
||||
# The following does not work in pythonnet:
|
||||
#x = Variable.Observed[Vector](Array[Vector](xData))
|
||||
|
||||
noise = 0.1
|
||||
ip = Variable.InnerProduct(w, x.get_Item(j))
|
||||
v = Variable.GaussianFromMeanAndVariance(ip, noise)
|
||||
v = v.op_GreaterThan(v, 0.0)
|
||||
y.set_Item(j, v)
|
||||
|
||||
def BayesPointMachineExample():
|
||||
incomes = [63, 16, 28, 55, 22, 20]
|
||||
ages = [38, 23, 40, 27, 18, 40]
|
||||
will_buy = [True, False, True, True, False, False]
|
||||
|
||||
# The following does not work in pythonnet:
|
||||
#y = Variable.Observed[bool](will_buy)
|
||||
#y = Variable.Observed[bool].Overloads[Array[bool]](will_buy)
|
||||
y = VariableObserved(will_buy)
|
||||
|
||||
eye = PositiveDefiniteMatrix.Identity(3)
|
||||
m = Vector.Zero(3)
|
||||
vg = VectorGaussian(m, eye)
|
||||
w = Variable.Random[Vector](vg)
|
||||
BayesPointMachine(incomes, ages, w, y)
|
||||
|
||||
engine = InferenceEngine()
|
||||
wPosterior = engine.Infer(w)
|
||||
print("Dist over w=\n%s" % wPosterior)
|
||||
|
||||
incomesTest = [ 58, 18, 22 ]
|
||||
agesTest = [ 36, 24, 37 ]
|
||||
ytest = Variable.Array[bool](Range(len(agesTest)))
|
||||
BayesPointMachine(incomesTest, agesTest, Variable.Random[Vector](wPosterior), ytest)
|
||||
print("output=\n%s" % engine.Infer(ytest));
|
||||
|
||||
def ClinicalTrial():
|
||||
# Data from clinical trial
|
||||
control_group_data = [False, False, True, False, False]
|
||||
control_group = VariableObserved(control_group_data)
|
||||
|
||||
treated_group_data = [True, False, True, True, True]
|
||||
treated_group = VariableObserved(treated_group_data)
|
||||
|
||||
i = control_group.Range
|
||||
j = treated_group.Range
|
||||
|
||||
# Prior on being effective treatment
|
||||
is_effective = Variable.Bernoulli(0.5)
|
||||
|
||||
# if block
|
||||
if_var = Variable.If(is_effective)
|
||||
# Model if treatment is effective
|
||||
probIfControl = Variable.Beta(1.0, 1.0)
|
||||
t = Variable.Bernoulli(probIfControl).ForEach(i)
|
||||
control_group.set_Item(i, t)
|
||||
|
||||
probIfTreated = Variable.Beta(1.0, 1.0)
|
||||
t = Variable.Bernoulli(probIfTreated).ForEach(j)
|
||||
treated_group.set_Item(j, t)
|
||||
if_var.Dispose()
|
||||
|
||||
# A bit of background
|
||||
if_var = Variable.IfNot(is_effective)
|
||||
# Model if treatment is not effective
|
||||
prob_all = Variable.Beta(1.0, 1.0)
|
||||
control_group.set_Item(i, Variable.Bernoulli(prob_all).ForEach(i))
|
||||
treated_group.set_Item(j, Variable.Bernoulli(prob_all).ForEach(j))
|
||||
if_var.Dispose()
|
||||
|
||||
# Clinical accuracy
|
||||
engine = InferenceEngine()
|
||||
print("Probability treatment has an effect = %s" % engine.Infer(is_effective))
|
||||
print("Probability of good outcome if given treatment = %s" % engine.Infer[Beta](probIfTreated).GetMean())
|
||||
print("Probability of good outcome if control = %s" % engine.Infer[Beta](probIfControl).GetMean())
|
||||
|
||||
def MixtureOfGaussians():
|
||||
# Define a range for the number of mixture components
|
||||
k = Range(2)
|
||||
|
||||
# Mixture component means
|
||||
means = Variable.Array[Vector](k)
|
||||
means_k = Variable.VectorGaussianFromMeanAndPrecision(Vector.FromArray(0.0, 0.0), PositiveDefiniteMatrix.IdentityScaledBy(2, 0.01)).ForEach(k)
|
||||
means.set_Item(k, means_k)
|
||||
|
||||
# Mixture component precisions
|
||||
precs = Variable.Array[PositiveDefiniteMatrix](k).Named("precs")
|
||||
precs_k = Variable.WishartFromShapeAndScale(100.0, PositiveDefiniteMatrix.IdentityScaledBy(2, 0.01)).ForEach(k)
|
||||
precs.set_Item(k, precs_k)
|
||||
|
||||
# Mixture weights
|
||||
weights = Variable.Dirichlet(k, [ 1.0, 1.0 ]).Named("weights")
|
||||
|
||||
# Create a variable array which will hold the data
|
||||
n = Range(300).Named("n")
|
||||
data = Variable.Array[Vector](n).Named("x")
|
||||
|
||||
# Create latent indicator variable for each data point
|
||||
z = Variable.Array[Int32](n).Named("z")
|
||||
|
||||
# The mixture of Gaussians model
|
||||
forEachBlock = Variable.ForEach(n)
|
||||
z.set_Item(n, Variable.Discrete(weights))
|
||||
switchBlock = Variable.Switch(z.get_Item(n))
|
||||
data.set_Item(n, Variable.VectorGaussianFromMeanAndPrecision(means.get_Item(z.get_Item(n)), precs.get_Item(z.get_Item(n))))
|
||||
switchBlock.CloseBlock()
|
||||
forEachBlock.CloseBlock()
|
||||
|
||||
# Attach some generated data
|
||||
data.ObservedValue = GenerateData(n.SizeAsInt)
|
||||
|
||||
# Initialise messages randomly to break symmetry
|
||||
zInit = Variable.Array[Discrete](n).Named("zInit")
|
||||
zInit.ObservedValue = [Discrete.PointMass(Rand.Int(k.SizeAsInt), k.SizeAsInt) for i in range(n.SizeAsInt)]
|
||||
# The following does not work in pythonnet:
|
||||
#z.get_Item(n).InitialiseTo[Discrete].Overloads[Variable[Discrete]](zInit.get_Item(n))
|
||||
InitialiseTo(z.get_Item(n), zInit.get_Item(n))
|
||||
|
||||
# The inference
|
||||
engine = InferenceEngine();
|
||||
print("Dist over pi=%s" % engine.Infer(weights))
|
||||
print("Dist over means=\n%s" % engine.Infer(means))
|
||||
print("Dist over precs=\n%s" % engine.Infer(precs))
|
||||
|
||||
def GenerateData(nData):
|
||||
trueM1 = Vector.FromArray(2.0, 3.0)
|
||||
trueM2 = Vector.FromArray(7.0, 5.0)
|
||||
trueP1 = PositiveDefiniteMatrix(ToClr([ [ 3.0, 0.2 ], [ 0.2, 2.0 ] ]))
|
||||
trueP2 = PositiveDefiniteMatrix(ToClr([ [ 2.0, 0.4 ], [ 0.4, 4.0 ] ]))
|
||||
trueVG1 = VectorGaussian.FromMeanAndPrecision(trueM1, trueP1)
|
||||
trueVG2 = VectorGaussian.FromMeanAndPrecision(trueM2, trueP2)
|
||||
truePi = 0.6
|
||||
trueB = Bernoulli(truePi)
|
||||
|
||||
# Restart the infer.NET random number generator
|
||||
Rand.Restart(12347)
|
||||
return [trueVG1.Sample() if trueB.Sample() else trueVG2.Sample() for j in range(nData)]
|
||||
|
||||
def VariableObserved(list, range=None):
|
||||
t = type(list[0])
|
||||
array = Array[t](list)
|
||||
if range == None:
|
||||
args = [array]
|
||||
else:
|
||||
args = [array, range]
|
||||
return Invoker.InvokeStatic(Variable, "Observed", args)
|
||||
|
||||
def InitialiseTo(variable, distribution):
|
||||
Invoker.InvokeInstance("InitialiseTo", variable, distribution)
|
||||
|
||||
def ToClr(matrix):
|
||||
# See https://github.com/pythonnet/pythonnet/blob/ec424bb0a8f0217c496898395880cf9b99d073e6/src/tests/test_array.py#L1112
|
||||
nr = len(matrix)
|
||||
nc = len(matrix[0]) if nr > 0 else 0
|
||||
t = type(matrix[0][0])
|
||||
items = Array.CreateInstance(t, nr, nc)
|
||||
for i in range(nr):
|
||||
for j in range(nc):
|
||||
items.SetValue(t(matrix[i][j]), (i, j))
|
||||
return items
|
||||
|
||||
def __list_methods(obj):
|
||||
for m in dir(obj):
|
||||
try:
|
||||
print(m)
|
||||
except:
|
||||
pass
|
||||
|
||||
def __list_method_overloads(method):
|
||||
for m in f'{method.__overloads__}'.split('\n'):
|
||||
print(' '.join(m.split(' ')[1:]))
|
||||
|
||||
# Using pytest in Visual Studio:
|
||||
# https://devblogs.microsoft.com/python/whats-new-for-python-in-visual-studio-16-3-preview-2/
|
||||
# pytest searches for tests in files named test_*.py or *_test.py
|
||||
# pytest collects functions with names prefixed by "test", either outside a class or in a class with name prefixed by "Test"
|
||||
|
||||
def test_tutorials():
|
||||
TwoCoins()
|
||||
TruncatedGaussianEfficient()
|
||||
LearningAGaussian()
|
||||
LearningAGaussianWithRanges()
|
||||
BayesPointMachineExample()
|
||||
ClinicalTrial()
|
||||
MixtureOfGaussians()
|
||||
|
||||
if __name__ == '__main__':
|
||||
test_tutorials()
|
||||
|
|
@ -39,6 +39,29 @@ namespace Microsoft.ML.Probabilistic.Tests
|
|||
return Util.ArrayInit(count, i => (min + i * inc));
|
||||
}
|
||||
|
||||
/// <summary>
|
||||
/// Demonstrate that EP can solve a linear program
|
||||
/// </summary>
|
||||
[Fact]
|
||||
public void LinearProgrammingTest()
|
||||
{
|
||||
// Could repeat inference incrementally while decreasing precision
|
||||
double precision = 1e-20;
|
||||
// maximize x+y
|
||||
// subject to x + 2*y = 1
|
||||
// x >= 0
|
||||
// y >= 0
|
||||
Variable<double> x = Variable.GaussianFromMeanAndPrecision(1.0/precision/precision, precision);
|
||||
Variable<double> y = Variable.GaussianFromMeanAndPrecision(1.0/precision/precision, precision);
|
||||
Variable.ConstrainEqual(x + 2 * y, 1);
|
||||
Variable.ConstrainPositive(x);
|
||||
Variable.ConstrainPositive(y);
|
||||
|
||||
InferenceEngine engine = new InferenceEngine();
|
||||
Console.WriteLine($"x = {engine.Infer(x)}");
|
||||
Console.WriteLine($"y = {engine.Infer(y)}");
|
||||
}
|
||||
|
||||
[Fact]
|
||||
public void TruncatedGammaPowerTest()
|
||||
{
|
||||
|
|
|
|||
|
|
@ -49,12 +49,15 @@
|
|||
</PropertyGroup>
|
||||
|
||||
<ItemGroup>
|
||||
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="15.8.0" />
|
||||
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.6.1" />
|
||||
<PackageReference Include="Newtonsoft.Json" Version="11.0.2" />
|
||||
<PackageReference Include="xunit" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.runner.visualstudio" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.abstractions" Version="2.0.1" />
|
||||
<PackageReference Include="xunit.analyzers" Version="0.9.0" />
|
||||
<PackageReference Include="xunit.runner.visualstudio" Version="2.4.2">
|
||||
<PrivateAssets>all</PrivateAssets>
|
||||
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
|
||||
</PackageReference>
|
||||
<PackageReference Include="xunit.abstractions" Version="2.0.3" />
|
||||
<PackageReference Include="xunit.analyzers" Version="0.10.0" />
|
||||
<PackageReference Include="xunit.assert" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.core" Version="2.3.1" />
|
||||
<PackageReference Include="xunit.extensibility.core" Version="2.3.1" />
|
||||
|
|
@ -79,6 +82,12 @@
|
|||
<None Update="Data\IRT2PL_10_1000.mat" CopyToOutputDirectory="PreserveNewest" />
|
||||
<None Update="Data\IRT2PL_10_250.mat" CopyToOutputDirectory="PreserveNewest" />
|
||||
<None Update="Data\test.mat" CopyToOutputDirectory="PreserveNewest" />
|
||||
<None Update="sequential.xunit.runner.json">
|
||||
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
|
||||
</None>
|
||||
<None Update="xunit.runner.json">
|
||||
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
|
||||
</None>
|
||||
|
||||
<None Remove="Bugs\*.txt" />
|
||||
<Content Include="Bugs\*.txt" />
|
||||
|
|
|
|||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"$schema": "https://xunit.net/schema/current/xunit.runner.schema.json",
|
||||
"methodDisplay": "method"
|
||||
}
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
{
|
||||
"$schema": "https://xunit.net/schema/current/xunit.runner.schema.json",
|
||||
"methodDisplay": "method",
|
||||
"parallelizeTestCollections": false
|
||||
}
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
{
|
||||
"$schema": "https://xunit.net/schema/current/xunit.runner.schema.json",
|
||||
"methodDisplay": "method"
|
||||
}
|
||||
|
|
@ -16,28 +16,25 @@ then
|
|||
fi
|
||||
|
||||
compath=/bin/${configuration}/netcoreapp3.1/
|
||||
dlls="Learners/LearnersTests${compath}Microsoft.ML.Probabilistic.Learners.Tests.dll Tests${compath}Microsoft.ML.Probabilistic.Tests.dll TestPublic${compath}TestPublic.dll"
|
||||
|
||||
# dotnet command
|
||||
dotnet='dotnet --fx-version 3.1.3'
|
||||
|
||||
# path to the xunit runner
|
||||
runner=~/.nuget/packages/xunit.runner.console/2.3.1/tools/netcoreapp2.0/xunit.console.dll
|
||||
projects="Learners/LearnersTests Tests TestPublic TestFSharp"
|
||||
|
||||
# filter for parallel test run
|
||||
parallel_filter='-notrait Platform=x86 -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=CsoftModel -notrait Category=ModifiesGlobals -notrait Category=DistributedTest -notrait Category=Performance'
|
||||
#parallel_filter='-notrait Platform=x86 -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest -notrait Category=CsoftModel -notrait Category=ModifiesGlobals -notrait Category=DistributedTest -notrait Category=Performance'
|
||||
parallel_filter='--filter (Platform!=x86)&(Category!=OpenBug)&(Category!=BadTest)&(Category!=CompilerOptionsTest)&(Category!=CsoftModel)&(Category!=ModifiesGlobals)&(Category!=DistributedTest)&(Category!=Performance)'
|
||||
|
||||
# filter for sequential test run
|
||||
sequential_filter='-notrait Platform=x86 -trait Category=CsoftModel -trait Category=ModifiesGlobals -trait Category=DistributedTests -trait Category=Performance -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest'
|
||||
#sequential_filter='-notrait Platform=x86 -trait Category=CsoftModel -trait Category=ModifiesGlobals -trait Category=DistributedTests -trait Category=Performance -notrait Category=OpenBug -notrait Category=BadTest -notrait Category=CompilerOptionsTest'
|
||||
sequential_filter='--filter (Platform!=x86)&(Category!=OpenBug)&(Category!=BadTest)&(Category!=CompilerOptionsTest)&(Category=CsoftModel|Category=ModifiesGlobals|Category=DistributedTests|Category=Performance)'
|
||||
|
||||
exitcode=0
|
||||
index=0
|
||||
|
||||
echo -e "\033[44;37m=====================PARALLEL TESTS RUNNING============================\033[0m"
|
||||
for assembly in $dlls
|
||||
cp "Tests/parallel.xunit.runner.json" "Tests/xunit.runner.json"
|
||||
for project in $projects
|
||||
do
|
||||
# Please note that due to xUnit issue we need to run tests for each assembly separately
|
||||
$dotnet "$runner" "$assembly" $parallel_filter -xml "netcoretest-result${index}.xml"
|
||||
# Please note that due to xUnit issue we need to run tests for each project separately
|
||||
dotnet test "$project" -c "$configuration" $parallel_filter --logger "trx;logfilename=netcoretest-result${index}.trx"
|
||||
if [ 0 -ne $? ]
|
||||
then
|
||||
echo -e "\033[5;41;1;37mParallel running failure!\033[0m"
|
||||
|
|
@ -49,7 +46,9 @@ do
|
|||
done
|
||||
|
||||
echo -e "\033[44;37m=====================SEQUENTIAL TESTS RUNNING=========================\033[0m"
|
||||
$dotnet "$runner" "Tests${compath}Microsoft.ML.Probabilistic.Tests.dll" $sequential_filter -parallel none -xml "netcoretest-result${index}.xml"
|
||||
# See https://xunit.github.io/docs/configuration-files
|
||||
cp "Tests/sequential.xunit.runner.json" "Tests/xunit.runner.json"
|
||||
dotnet test Tests -c "$configuration" $sequential_filter --logger "trx;logfilename=netcoretest-result${index}.trx"
|
||||
if [ 0 -ne $? ]
|
||||
then
|
||||
echo -e "\033[5;41;1;37mSequential running failure!\033[0m"
|
||||
|
|
@ -57,5 +56,6 @@ then
|
|||
else
|
||||
echo -e "\033[32;1mSequential running success!\033[0m"
|
||||
fi
|
||||
cp "Tests/parallel.xunit.runner.json" "Tests/xunit.runner.json"
|
||||
|
||||
exit $exitcode
|
||||
|
|
|
|||
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