Merge pull request #211 from HicServices/feature/mathnot

Remove MathNet.Numerics, embed the one class we actually used from it

.github/workflows/testpack.yml

@@ -4,12 +4,12 @@ on: push
 
 jobs:
   package:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-dotnet@v4
         with:
-          dotnet-version: '6.0.x'
+          dotnet-version: '8.0.x'
       - name: Test
         run: dotnet test --nologo
       - name: Package

Packages.md

@@ -11,9 +11,7 @@
 | ------- | ------------| ------- | ------- | -------------------------- |
 | CommandLineParser | [GitHub](https://github.com/commandlineparser/commandline) | [MIT](https://opensource.org/licenses/MIT) | Allows command line arguments for main client application and CLI executables |
 | CsvHelper | [GitHub](https://github.com/JoshClose/CsvHelper) | MS-PL / Apache 2.0 | Enables reading/writing CSV files |
-| Generator.Equals    | [GitHub](https://github.com/diegofrata/Generator.Equals)                                    | [MIT](https://opensource.org/licenses/MIT)                                                     | Simplifies object comparators                                                                       |
 | HIC.FAnsiSql                            | [GitHub](https://github.com/HicServices/FAnsiSql)                          | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html)                                           | DBMS abstraction layer                                                                              |
-| MathNet.Numerics | [GitHub](https://github.com/mathnet/mathnet-numerics)| [MIT](https://opensource.org/licenses/MIT) | Generate statistical distributions (e.g. Gaussian) for random data | |
 | Microsoft.SourceLink.GitHub | [GitHub](https://github.com/dotnet/sourcelink) | [1.1.1](https://www.nuget.org/packages/Microsoft.SourceLink.GitHub/1.1.1) | [Apache License 2.0](https://github.com/dotnet/sourcelink/blob/master/License.txt) | Enables source debugging of project nuget package| |
 | YamlDotNet                              | [GitHub](https://github.com/aaubry/YamlDotNet)                             | [MIT](https://opensource.org/licenses/MIT)                                                     | Loading configuration files                                                                         |
 

SynthEHR.Core/Datasets/BiochemistryRecord.cs

@@ -8,7 +8,7 @@
 using System.Data;
 using System.Globalization;
 using System.Linq;
-using MathNet.Numerics.Distributions;
+using Normal = SynthEHR.Statistics.Distributions.Normal;
 
 namespace SynthEHR.Datasets;
 

SynthEHR.Core/Datasets/DataGenerator.cs

@@ -15,7 +15,7 @@
 using System.Text;
 using CsvHelper;
 using CsvHelper.Configuration;
-using MathNet.Numerics.Distributions;
+using Normal = SynthEHR.Statistics.Distributions.Normal;
 
 namespace SynthEHR.Datasets;
 

SynthEHR.Core/Datasets/HospitalAdmissionsRecord.cs

@@ -209,7 +209,7 @@ static HospitalAdmissionsRecord()
             rowCount++;
         }
 
-        var operationsTable = new DataTable();
+        using var operationsTable = new DataTable();
         operationsTable.BeginLoadData();
         operationsTable.Columns.Add("CountOfRecords", typeof(int));
 

SynthEHR.Core/Person.cs

@@ -4,20 +4,18 @@
 // RDMP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 // You should have received a copy of the GNU General Public License along with RDMP. If not, see <https://www.gnu.org/licenses/>.
 
+#nullable enable
 using System;
 using System.Text;
-using Generator.Equals;
 using SynthEHR.Datasets;
 
 namespace SynthEHR;
 
 /// <summary>
 /// Randomly generated person for whom datasets can be built
 /// </summary>
-[Equatable]
-public sealed partial class Person
+public sealed record Person
 {
-
     /// <include file='../Datasets.doc.xml' path='Datasets/Demography/Field[@name="Forename"]'/>
     public string Forename { get; set; }
     /// <include file='../Datasets.doc.xml' path='Datasets/Demography/Field[@name="Surname"]'/>
@@ -36,7 +34,7 @@ public sealed partial class Person
     /// <include file='../Datasets.doc.xml' path='Datasets/Demography/Field[@name="Address"]'/>
     public DemographyAddress Address { get; set; }
     /// <include file='../Datasets.doc.xml' path='Datasets/Demography/Field[@name="PreviousAddress"]'/>
-    public DemographyAddress PreviousAddress { get; set; }
+    public DemographyAddress? PreviousAddress { get; set; }
 
     /// <summary>
     /// Earliest year of birth to generate
@@ -52,25 +50,19 @@ public sealed partial class Person
     /// <summary>
     /// The collection to which the patient belongs, may be null
     /// </summary>
-    private readonly PersonCollection _parent;
+    private readonly PersonCollection? _parent;
 
     /// <summary>
     /// Generates a new random person using the seeded random.  This overload ensures that the <see cref="Person"/> generated
     /// does not already exist in the <paramref name="collection"/> (in terms of CHI / ANOCHI numbers).
     /// </summary>
     /// <param name="r"></param>
     /// <param name="collection"></param>
-    public Person(Random r,PersonCollection collection):this(r)
+    public Person(Random? r, PersonCollection? collection = null)
     {
         _parent = collection;
-    }
+        r ??= Random.Shared;
 
-    /// <summary>
-    /// Generates a new random person using the seeded random
-    /// </summary>
-    /// <param name="r"></param>
-    public Person(Random r)
-    {
         Gender = r.Next(2) switch
         {
             0 => 'F',
@@ -85,7 +77,7 @@ public Person(Random r)
 
         //1 in 10 patients is dead
         if (r.Next(10) == 0)
-            DateOfDeath = DataGenerator.GetRandomDateAfter(DateOfBirth, r);
+            DateOfDeath = DataGenerator.GetRandomDateAfter(DateOfBirth,r);
         else
             DateOfDeath = null;
 
@@ -96,7 +88,7 @@ public Person(Random r)
         Address = new DemographyAddress(r);
 
         //one in 10 people doesn't have a previous address
-        if(r.Next(10) != 0)
+        if (r.Next(10) != 0)
             PreviousAddress = new DemographyAddress(r);
     }
 
@@ -105,45 +97,37 @@ public Person(Random r)
     /// </summary>
     /// <param name="r"></param>
     /// <returns></returns>
-    public string GetRandomForename(Random r)
-    {
-        return Gender == 'F' ? CommonGirlForenames[r.Next(100)] : CommonBoyForenames[r.Next(100)];
-    }
+    public string GetRandomForename(Random r) => Gender == 'F' ? CommonGirlForenames[r.Next(100)] : CommonBoyForenames[r.Next(100)];
 
     /// <summary>
     /// Returns a random date after the patients date of birth (and before their death if they are dead).
     /// </summary>
     /// <param name="r"></param>
     /// <returns></returns>
-    public DateTime GetRandomDateDuringLifetime(Random r)
-    {
-        return DateOfDeath == null
+    public DateTime GetRandomDateDuringLifetime(Random r) =>
+        DateOfDeath == null
             ? DataGenerator.GetRandomDateAfter(DateOfBirth, r)
             : DataGenerator.GetRandomDate(DateOfBirth, (DateTime)DateOfDeath, r);
-    }
 
     /// <summary>
     /// Returns a random surname from a list of common surnames
     /// </summary>
     /// <param name="r"></param>
     /// <returns></returns>
-    public static string GetRandomSurname(Random r)
-    {
-        return CommonSurnames[r.Next(100)];
-    }
+    public static string GetRandomSurname(Random r) => CommonSurnames[r.Next(100)];
 
     /// <summary>
     /// If the person died before onDate it returns NULL (as of onDate we did not know when the person would die).  if onDate is > date of death it
     /// returns the date of death (we knew when they died - you cannot predict the future, but you can remember the past)
     /// </summary>
     /// <param name="onDate"></param>
     /// <returns></returns>
-    public DateTime? GetDateOfDeathOrNullOn(DateTime onDate)
-    {
-        return onDate >= DateOfDeath ? DateOfDeath :
+    public DateTime? GetDateOfDeathOrNullOn(DateTime onDate) =>
+        onDate >= DateOfDeath
+            ? DateOfDeath
+            :
             //we cannot predict the future, they are dead today, but you are pretending the date is onDate
             null;
-    }
 
     /// <summary>
     /// Returns a new random ANOCHI which does not exist in <see cref="_parent"/> (if we have one)
@@ -154,12 +138,10 @@ private string GetNovelANOCHI(Random r)
     {
         var anochi = GenerateANOCHI(r);
 
-        while(_parent != null && _parent.AlreadyGeneratedANOCHIs.Contains(anochi))
+        while (_parent?.AlreadyGeneratedANOCHIs.Add(anochi) == false)
             anochi = GenerateANOCHI(r);
-        _parent?.AlreadyGeneratedANOCHIs.Add(anochi);
 
         return anochi;
-
     }
 
     /// <summary>
@@ -171,16 +153,15 @@ private string GetNovelCHI(Random r)
     {
         var chi = GetRandomCHI(r);
 
-        while(_parent != null && _parent.AlreadyGeneratedCHIs.Contains(chi))
+        while (_parent?.AlreadyGeneratedCHIs.Add(chi) == false)
             chi = GetRandomCHI(r);
-        _parent?.AlreadyGeneratedCHIs.Add(chi);
 
         return chi;
     }
 
     private static string GenerateANOCHI(Random r)
     {
-        var toReturn = new StringBuilder();
+        var toReturn = new StringBuilder(12);
 
         for (var i = 0; i < 10; i++)
             toReturn.Append(r.Next(10));

SynthEHR.Core/Statistics/Distributions/IContinuousDistribution.cs

@@ -0,0 +1,57 @@
+// <copyright file="IContinuousDistribution.cs" company="Math.NET">
+// Math.NET Numerics, part of the Math.NET Project
+// http://numerics.mathdotnet.com
+// http://github.com/mathnet/mathnet-numerics
+//
+// Copyright (c) 2009-2014 Math.NET
+//
+// Permission is hereby granted, free of charge, to any person
+// obtaining a copy of this software and associated documentation
+// files (the "Software"), to deal in the Software without
+// restriction, including without limitation the rights to use,
+// copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the
+// Software is furnished to do so, subject to the following
+// conditions:
+//
+// The above copyright notice and this permission notice shall be
+// included in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+// OTHER DEALINGS IN THE SOFTWARE.
+// </copyright>
+
+namespace SynthEHR.Statistics.Distributions;
+
+/// <summary>
+/// Continuous Univariate Probability Distribution.
+/// </summary>
+internal interface IContinuousDistribution : IUnivariateDistribution
+{
+    /// <summary>
+    /// Gets the mode of the distribution.
+    /// </summary>
+    double Mode { get; }
+
+    /// <summary>
+    /// Gets the smallest element in the domain of the distribution which can be represented by a double.
+    /// </summary>
+    double Minimum { get; }
+
+    /// <summary>
+    /// Gets the largest element in the domain of the distribution which can be represented by a double.
+    /// </summary>
+    double Maximum { get; }
+
+    /// <summary>
+    /// Draws a random sample from the distribution.
+    /// </summary>
+    /// <returns>a sample from the distribution.</returns>
+    double Sample();
+}

SynthEHR.Core/Statistics/Distributions/IDistribution.cs

@@ -0,0 +1,41 @@
+// <copyright file="IUnivariateDistribution.cs" company="Math.NET">
+// Math.NET Numerics, part of the Math.NET Project
+// http://numerics.mathdotnet.com
+// http://github.com/mathnet/mathnet-numerics
+//
+// Copyright (c) 2009-2013 Math.NET
+//
+// Permission is hereby granted, free of charge, to any person
+// obtaining a copy of this software and associated documentation
+// files (the "Software"), to deal in the Software without
+// restriction, including without limitation the rights to use,
+// copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the
+// Software is furnished to do so, subject to the following
+// conditions:
+//
+// The above copyright notice and this permission notice shall be
+// included in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+// OTHER DEALINGS IN THE SOFTWARE.
+// </copyright>
+
+namespace SynthEHR.Statistics.Distributions;
+
+/// <summary>
+/// Probability Distribution.
+/// </summary>
+internal interface IDistribution
+{
+    /// <summary>
+    /// Gets or sets the random number generator which is used to draw random samples.
+    /// </summary>
+    System.Random RandomSource { get; set; }
+}

SynthEHR.Core/Statistics/Distributions/IUnivariateDistribution.cs

@@ -0,0 +1,66 @@
+// <copyright file="IUnivariateDistribution.cs" company="Math.NET">
+// Math.NET Numerics, part of the Math.NET Project
+// http://numerics.mathdotnet.com
+// http://github.com/mathnet/mathnet-numerics
+//
+// Copyright (c) 2009-2013 Math.NET
+//
+// Permission is hereby granted, free of charge, to any person
+// obtaining a copy of this software and associated documentation
+// files (the "Software"), to deal in the Software without
+// restriction, including without limitation the rights to use,
+// copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the
+// Software is furnished to do so, subject to the following
+// conditions:
+//
+// The above copyright notice and this permission notice shall be
+// included in all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+// OTHER DEALINGS IN THE SOFTWARE.
+// </copyright>
+
+namespace SynthEHR.Statistics.Distributions;
+
+/// <summary>
+/// Univariate Probability Distribution.
+/// </summary>
+internal interface IUnivariateDistribution:IDistribution
+{
+    /// <summary>
+    /// Gets the mean of the distribution.
+    /// </summary>
+    double Mean { get; }
+
+    /// <summary>
+    /// Gets the variance of the distribution.
+    /// </summary>
+    double Variance { get; }
+
+    /// <summary>
+    /// Gets the standard deviation of the distribution.
+    /// </summary>
+    double StdDev { get; }
+
+    /// <summary>
+    /// Gets the entropy of the distribution.
+    /// </summary>
+    double Entropy { get; }
+
+    /// <summary>
+    /// Gets the skewness of the distribution.
+    /// </summary>
+    double Skewness { get; }
+
+    /// <summary>
+    /// Gets the median of the distribution.
+    /// </summary>
+    double Median { get; }
+}