Task/rename bad medicine (#195)

* rename badmedicine to SynthEHR
* fix missing file rename

---------

Co-authored-by: James A Sutherland <[email protected]>

.github/workflows/testpack.yml

@@ -14,11 +14,11 @@ jobs:
         run: dotnet test --nologo
       - name: Package
         run: |
-          dotnet publish BadMedicine/BadMedicine.csproj -o linux-x64 -r linux-x64 -c Release --self-contained --nologo -p:PublishSingleFile=true -p:GenerateDocumentationFile=false
-          dotnet publish BadMedicine/BadMedicine.csproj -o win-x64 -r win-x64 -c Release --self-contained --nologo -p:PublishSingleFile=true -p:GenerateDocumentationFile=false
-          dotnet pack BadMedicine.Core/BadMedicine.Core.csproj -p:DebugType=full -p:SymbolPackageFormat=snupkg -p:PackageVersion=$(fgrep AssemblyInformationalVersion SharedAssemblyInfo.cs|cut -d'"' -f2) -o . --include-source --include-symbols --nologo -c Release
-          tar czf badmedicine-cli-linux-x64.tgz ./linux-x64
-          zip -9rj badmedicine-cli-win-x64.zip win-x64
+          dotnet publish SynthEHR/SynthEHR.csproj -o linux-x64 -r linux-x64 -c Release --self-contained --nologo -p:PublishSingleFile=true -p:GenerateDocumentationFile=false
+          dotnet publish SynthEHR/SynthEHR.csproj -o win-x64 -r win-x64 -c Release --self-contained --nologo -p:PublishSingleFile=true -p:GenerateDocumentationFile=false
+          dotnet pack SynthEHR.Core/SynthEHR.Core.csproj -p:DebugType=full -p:SymbolPackageFormat=snupkg -p:PackageVersion=$(fgrep AssemblyInformationalVersion SharedAssemblyInfo.cs|cut -d'"' -f2) -o . --include-source --include-symbols --nologo -c Release
+          tar czf SynthEHR-cli-linux-x64.tgz ./linux-x64
+          zip -9rj SynthEHR-cli-win-x64.zip win-x64
       - name: Nuget push
         if: contains(github.ref,'refs/tags/')
         run: nuget push HIC.*.nupkg -skipDuplicate -Source https://api.nuget.org/v3/index.json -ApiKey ${{ secrets.NUGET_KEY }}
@@ -27,7 +27,7 @@ jobs:
         if: contains(github.ref, 'refs/tags/v')
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          file: badmedicine-cli-*
+          file: SynthEHR-cli-*
           tag: ${{ github.ref }}
           overwrite: true
           file_glob: true

.gitignore

@@ -1,13 +1,13 @@
-BadMedicine/obj/
-BadMedicine/bin/
+SynthEHR/obj/
+SynthEHR/bin/
 *.user
-BadMedicine/.vs/
+SynthEHR/.vs/
 .vs/
 Visual Studio 2017/
-BadMedicineTests/obj/
+SynthEHRTests/obj/
 *.vspx
 *.psess
-BadMedicineTests/bin/
-BadMedicine.Core/obj/
-BadMedicine.Core/bin/
+SynthEHRTests/bin/
+SynthEHR.Core/obj/
+SynthEHR.Core/bin/
 .idea/

CHANGELOG.md

@@ -4,7 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.2.2] - 2024-035-16
+## [2.0.0] - Unreleased
+
+- Rename package to SynthEHR
+
+## [1.2.2] - 2024-05-16
 
 -Add warning about naming deprecation, see [README](./README.md#Deprecation)
 
@@ -16,7 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Now targets .Net 8.0
 - Some bugfixes change random data generation, cross-version consistency not preserved
-- BadMedicine itself now AOT/trim clean, but dependencies are not
+- SynthEHR itself now AOT/trim clean, but dependencies are not
 - Improve BucketList performance
 - Add Equ 2.3.0
 - Bump HIC.FAnsiSql from 3.0.1 to 3.2.0
@@ -88,15 +92,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Patient birth dates now go from 1914 (Person.MinimumYearOfBirth) allowing for patients aged up to 100 years
 
-[Unreleased]: https://github.com/HicServices/BadMedicine/compare/v1.2.2...main
-[1.2.2]: https://github.com/HicServices/BadMedicine/compare/v1.2.1...v1.2.2
-[1.2.1]: https://github.com/HicServices/BadMedicine/compare/v1.2.0...v1.2.1
-[1.2.0]: https://github.com/HicServices/BadMedicine/compare/v1.1.2...v1.2.0
-[1.1.2]: https://github.com/HicServices/BadMedicine/compare/v1.1.1...v1.1.2
-[1.1.1]: https://github.com/HicServices/BadMedicine/compare/v1.1.0...v1.1.1
-[1.1.0]: https://github.com/HicServices/BadMedicine/compare/v1.0.0...v1.1.0
-[1.0.0]: https://github.com/HicServices/BadMedicine/compare/v0.1.6...v1.0.0
-[0.1.6]: https://github.com/HicServices/BadMedicine/compare/v0.1.5...v0.1.6
-[0.1.5]: https://github.com/HicServices/BadMedicine/compare/v0.1.4...v0.1.5
-[0.1.4]: https://github.com/HicServices/BadMedicine/compare/v0.1.3...v0.1.4
-[0.1.3]: https://github.com/HicServices/BadMedicine/compare/0.0.1.2...v0.1.3
+[Unreleased]: https://github.com/HicServices/SynthEHR/compare/v2.0.0...main
+[2.0.0]: https://github.com/HicServices/SynthEHR/compare/v1.2.2...v2.0.0
+[1.2.2]: https://github.com/HicServices/SynthEHR/compare/v1.2.1...v1.2.2
+[1.2.1]: https://github.com/HicServices/SynthEHR/compare/v1.2.0...v1.2.1
+[1.2.0]: https://github.com/HicServices/SynthEHR/compare/v1.1.2...v1.2.0
+[1.1.2]: https://github.com/HicServices/SynthEHR/compare/v1.1.1...v1.1.2
+[1.1.1]: https://github.com/HicServices/SynthEHR/compare/v1.1.0...v1.1.1
+[1.1.0]: https://github.com/HicServices/SynthEHR/compare/v1.0.0...v1.1.0
+[1.0.0]: https://github.com/HicServices/SynthEHR/compare/v0.1.6...v1.0.0
+[0.1.6]: https://github.com/HicServices/SynthEHR/compare/v0.1.5...v0.1.6
+[0.1.5]: https://github.com/HicServices/SynthEHR/compare/v0.1.4...v0.1.5
+[0.1.4]: https://github.com/HicServices/SynthEHR/compare/v0.1.3...v0.1.4
+[0.1.3]: https://github.com/HicServices/SynthEHR/compare/0.0.1.2...v0.1.3

README.md

@@ -1,21 +1,16 @@
-# BadMedicine
+# SynthEHR (Previously BadMedicine)
 
-## <a name="Deprecation"></a> Deprecation Notice
-
-BadMedicine v1.2.2 will be the final release under this name.
-
-The project will be renamed SynthEHR in all future releases, starting at v2.0.0
-
-The project will be able to be found on [Github](https://gituhb.com/HICServices/SynthEHR) and on [Nuget](https://www.nuget.org/packages/HIC.SynthEHR/)
-
-[![Build Status](https://github.com/HICServices/BadMedicine/actions/workflows/testpack.yml/badge.svg?branch=develop)](https://travis-ci.org/HicServices/BadMedicine) [![NuGet Badge](https://buildstats.info/nuget/HIC.BadMedicine)](https://www.nuget.org/packages/HIC.BadMedicine/)
+[![Build Status](https://github.com/HICServices/SynthEHR/actions/workflows/testpack.yml/badge.svg?branch=develop)](https://travis-ci.org/HicServices/SynthEHR) [![NuGet Badge](https://buildstats.info/nuget/HIC.SynthEHR)](https://www.nuget.org/packages/HIC.SynthEHR/)
 
 Library and CLI for randomly generating medical data like you might get out of an Electronic Health Records (EHR) system.  It is intended for generating data for demos and testing ETL / cohort generation/ data management tools.
 
-BadMedicine differs from other random data generators e.g. Mockaroo, SQL Data Generator etc in that data generated is based on (simple) models generated from live EHR datasets collected for over 30 years in Tayside and Fife (UK).  This makes the data generated recognisable (codes used, frequency of codes etc) from a clinical perspective and representative of the problems (ontology mapping etc) that data analysts would encounter working with real medical data.
+SynthEHR differs from other random data generators e.g. Mockaroo, SQL Data Generator etc in that data generated is based on (simple) models generated from live EHR datasets collected for over 30 years in Tayside and Fife (UK).  This makes the data generated recognisable (codes used, frequency of codes etc) from a clinical perspective and representative of the problems (ontology mapping etc) that data analysts would encounter working with real medical data.
 
 Datasets generated are not suitable for training AI algorithms etc (See [What is Modelled?](#what-is-modelled))
 
+## Rename
+As of v2.0.0 BadMedicine was renamed to SynthEHR. Previous versions of the software can be found at [nuget.org](https://www.nuget.org/packages/HIC.BadMedicine).
+
 ## Datasets
 
 The following synthetic datasets can be produced.
@@ -31,32 +26,32 @@ The following synthetic datasets can be produced.
 
 ## Usage:
 
-BadMedicine is available as a [nuget package](https://www.nuget.org/packages/HIC.BadMedicine/) for linking as a library
+SynthEHR is available as a [nuget package](https://www.nuget.org/packages/HIC.SynthEHR/) for linking as a library
 
-The standalone CLI (BadMedicine.exe) is available in the [releases section of Github](https://github.com/HicServices/BadMedicine/releases)
+The standalone CLI (SynthEHR.exe) is available in the [releases section of Github](https://github.com/HicServices/SynthEHR/releases)
 
 Usage is as follows:
 
 ```
-BadMedicine.exe c:\temp\
+SynthEHR.exe c:\temp\
 ```
 
 You can change how much data is produced (e.g. 500 patients, 10000 records per dataset):
 
 ```
-BadMedicine.exe c:\temp\ 500 10000
+SynthEHR.exe c:\temp\ 500 10000
 ```
 
 Or run only a single dataset:
 
 ```
-BadMedicine.exe c:\omg 5000 200000 -l -d CarotidArteryScan
+SynthEHR.exe c:\omg 5000 200000 -l -d CarotidArteryScan
 ```
 
 You can seed the generator (Guids generated will still differ)
 
 ```
-BadMedicine.exe c:\omg 5000 200000 -l -d CarotidArteryScan -s 5000
+SynthEHR.exe c:\omg 5000 200000 -l -d CarotidArteryScan -s 5000
 ```
 
 ## Building
@@ -65,16 +60,16 @@ Building requires MSBuild 15 or later (or Visual Studio 2017 or later).  You wil
 
 You can build a OS specific binary
 
-First build BadMedicine.csproj
+First build SynthEHR.csproj
 ```
-dotnet publish BadMedicine.csproj -r win-x64 --self-contained
+dotnet publish SynthEHR.csproj -r win-x64 --self-contained
 cd .\bin\Debug\netcoreapp2.2\win-x64\
 ```
 ## Direct to Database
 
 You can generate data directly into a relational database (instead of onto disk).
 
-To turn this mode on rename the file `BadMedicine.template.yaml` to `BadMedicine.yaml` and provide the connection strings to your database e.g.:
+To turn this mode on rename the file `SynthEHR.template.yaml` to `SynthEHR.yaml` and provide the connection strings to your database e.g.:
 
 ```yaml
 Database:
@@ -85,12 +80,12 @@ Database:
   # Your DBMS provider ('MySql', 'PostgreSql','Oracle' or 'MicrosoftSQLServer')
   DatabaseType: MicrosoftSQLServer
   # Database to create/use on the server
-  DatabaseName: BadMedicineTestData
+  DatabaseName: SynthEHRTestData
 ```
 
 ## Library Usage
 
-You can generate test data for your program yourself by referencing the [nuget package](https://www.nuget.org/packages/HIC.BadMedicine/):
+You can generate test data for your program yourself by referencing the [nuget package](https://www.nuget.org/packages/HIC.SynthEHR/):
 
 ```csharp
 //Seed the random generator if you want to always produce the same randomisation
@@ -113,7 +108,7 @@ Assert.IsNotNull(a.Condition1);
 
 ## What is Modelled?
 
-Data generated by BadMedicine is driven by Aggregate distributions of real health data collected in Tayside (UK).  This means that codes appear in data with the frequency that match real data.  For example in the Hospital Admissions data we can see that ICD9 codes (denoted by dash) cease being recorded in ~1997 in favour of ICD10 codes and we can see the most common admission conditions are sensible:
+Data generated by SynthEHR is driven by Aggregate distributions of real health data collected in Tayside (UK).  This means that codes appear in data with the frequency that match real data.  For example in the Hospital Admissions data we can see that ICD9 codes (denoted by dash) cease being recorded in ~1997 in favour of ICD10 codes and we can see the most common admission conditions are sensible:
 
 ![alt text](./Images/MainConditionDistribution.png)
 

SharedAssemblyInfo.cs

@@ -1,12 +1,12 @@
 using System.Reflection;
 
 [assembly: AssemblyCompany("Health Informatics Centre, University of Dundee")]
-[assembly: AssemblyProduct("Bad Medicine")]
+[assembly: AssemblyProduct("SynthEHR")]
 [assembly: AssemblyCopyright("Copyright (c) 2018 - 2024")]
 [assembly: AssemblyTrademark("")]
 [assembly: AssemblyCulture("")]
 
 // These should be replaced with correct values by the release process
-[assembly: AssemblyVersion("1.2.2")]
-[assembly: AssemblyFileVersion("1.2.2")]
-[assembly: AssemblyInformationalVersion("1.2.2")]
+[assembly: AssemblyVersion("2.0.0")]
+[assembly: AssemblyFileVersion("2.0.0")]
+[assembly: AssemblyInformationalVersion("2.0.0")]

BadMedicine.Core/BucketList.cs → SynthEHR.Core/BucketList.cs

@@ -4,7 +4,7 @@
 using System.Linq;
 using System.Threading;
 
-namespace BadMedicine;
+namespace SynthEHR;
 
 /// <summary>
 /// Picks random object of Type T based on a specified probability for each element.

BadMedicine.Core/Datasets/Appointment.cs → SynthEHR.Core/Datasets/Appointment.cs

@@ -6,7 +6,7 @@
 
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Data class describing an appointment including a guid identifier

BadMedicine.Core/Datasets/Biochemistry.cs → SynthEHR.Core/Datasets/Biochemistry.cs

@@ -6,7 +6,7 @@
 
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <include file='../../Datasets.doc.xml' path='Datasets/Biochemistry'/>
 /// <inheritdoc/>

BadMedicine.Core/Datasets/BiochemistryRecord.cs → SynthEHR.Core/Datasets/BiochemistryRecord.cs

@@ -10,7 +10,7 @@
 using System.Linq;
 using MathNet.Numerics.Distributions;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Data class representing a single row in <see cref="Biochemistry"/> (use if you want to use randomly generated data directly

BadMedicine.Core/Datasets/CarotidArteryScan.cs → SynthEHR.Core/Datasets/CarotidArteryScan.cs

@@ -7,7 +7,7 @@
 using System;
 using System.Linq;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Test data based on the Scottish Vascular Labs CARSCAN database table

BadMedicine.Core/Datasets/DataGenerator.cs → SynthEHR.Core/Datasets/DataGenerator.cs

@@ -17,7 +17,7 @@
 using CsvHelper.Configuration;
 using MathNet.Numerics.Distributions;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Base class for all randomly generated datasets.  Handles generating random data types and writing

BadMedicine.Core/Datasets/DataGeneratorFactory.cs → SynthEHR.Core/Datasets/DataGeneratorFactory.cs

@@ -2,7 +2,7 @@
 using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Finds Types and Creates instances of <see cref="IDataGenerator"/> implementations
@@ -22,7 +22,7 @@ public readonly struct GeneratorType(Type type)
     }
 
     /// <summary>
-    /// List of generator types. Add yourself to this if outside BadMedicine.Core, to avoid reliance on reflection breaking AOT.
+    /// List of generator types. Add yourself to this if outside SynthEHR.Core, to avoid reliance on reflection breaking AOT.
     /// </summary>
     public static readonly List<GeneratorType> Generators =
     [

BadMedicine.Core/Datasets/Demography.cs → SynthEHR.Core/Datasets/Demography.cs

@@ -6,7 +6,7 @@
 
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <include file='../../Datasets.doc.xml' path='Datasets/Demography'/>
 /// <inheritdoc/>

BadMedicine.Core/Datasets/DemographyAddress.cs → SynthEHR.Core/Datasets/DemographyAddress.cs

@@ -6,7 +6,7 @@
 
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Data model for a 5 line address in which some lines might be null

BadMedicine.Core/Datasets/DemographyPostcode.cs → SynthEHR.Core/Datasets/DemographyPostcode.cs

@@ -4,7 +4,7 @@
 // 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/>.
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Data model for a UK postcode

BadMedicine.Core/Datasets/HospitalAdmissions.cs → SynthEHR.Core/Datasets/HospitalAdmissions.cs

@@ -1,6 +1,6 @@
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Generates synthetic random data that is representative of patient hospital admissions data

BadMedicine.Core/Datasets/HospitalAdmissionsRecord.cs → SynthEHR.Core/Datasets/HospitalAdmissionsRecord.cs

@@ -8,10 +8,10 @@
 using System.Collections.Generic;
 using System.Data;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
-/// Random record for when a <see cref="BadMedicine.Person"/> entered hospital.  Basic logic is implemented here to ensure that <see cref="DischargeDate"/>
+/// Random record for when a <see cref="SynthEHR.Person"/> entered hospital.  Basic logic is implemented here to ensure that <see cref="DischargeDate"/>
 /// is after <see cref="AdmissionDate"/> and that the person was alive at the time.
 /// </summary>
 public sealed class HospitalAdmissionsRecord

BadMedicine.Core/Datasets/IDataGenerator.cs → SynthEHR.Core/Datasets/IDataGenerator.cs

@@ -8,7 +8,7 @@
 using System.Data;
 using System.IO;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Interface for classes which generate test data to disk.

BadMedicine.Core/Datasets/Maternity.cs → SynthEHR.Core/Datasets/Maternity.cs

@@ -1,6 +1,6 @@
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <include file='../../Datasets.doc.xml' path='Datasets/Maternity'/>
 /// <inheritdoc/>

BadMedicine.Core/Datasets/MaternityRecord.cs → SynthEHR.Core/Datasets/MaternityRecord.cs

@@ -1,7 +1,7 @@
 using System;
 using System.Data;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <summary>
 /// Describes a single maternity event for a specific <see cref="Person"/>
@@ -57,7 +57,7 @@ public sealed class MaternityRecord
     /// <summary>
     /// Generates a new random biochemistry test.
     /// </summary>
-    /// <param name="p">The person who is undergoing maternity activity.  Should be Female and of a sufficient age that the operation could have taken place during their lifetime (see <see cref="Maternity.IsEligible(BadMedicine.Person)"/></param>
+    /// <param name="p">The person who is undergoing maternity activity.  Should be Female and of a sufficient age that the operation could have taken place during their lifetime (see <see cref="Maternity.IsEligible(SynthEHR.Person)"/></param>
     /// <param name="r"></param>
     public MaternityRecord(Person p, Random r)
     {

BadMedicine.Core/Datasets/Prescribing.cs → SynthEHR.Core/Datasets/Prescribing.cs

@@ -6,7 +6,7 @@
 
 using System;
 
-namespace BadMedicine.Datasets;
+namespace SynthEHR.Datasets;
 
 /// <include file='../../Datasets.doc.xml' path='Datasets/Prescribing'/>
 /// <inheritdoc/>