Version 7.1.0

Version 7.1.0

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "src/OSPSuite.PKParameters"]
 	path = src/OSPSuite.PKParameters
 	url = https://github.com/Open-Systems-Pharmacology/OSPSuite.PKParameters.git
+[submodule "scripts"]
+	path = scripts
+	url = https://github.com/Open-Systems-Pharmacology/build-scripts.git

OSPSuite.Core.sln

@@ -5,9 +5,11 @@ VisualStudioVersion = 14.0.25123.0
 MinimumVisualStudioVersion = 14.0.24720.0
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{9ED8AA66-5E2F-4900-846B-4D2758832061}"
 	ProjectSection(SolutionItems) = preProject
+		appveyor-coverage.yml = appveyor-coverage.yml
 		appveyor.yml = appveyor.yml
 		copy_to_mobi.bat = copy_to_mobi.bat
 		copy_to_pksim.bat = copy_to_pksim.bat
+		rakefile.rb = rakefile.rb
 		README.md = README.md
 		SolutionInfo.cs = SolutionInfo.cs
 	EndProjectSection

README.md

@@ -4,7 +4,8 @@ Core functionalities of the Open Systems Pharmacology Suite.
 
 ## Code Status
 [![NuGet version](https://img.shields.io/nuget/v/OSPSuite.Core.svg?style=flat)](https://www.nuget.org/packages/OSPSuite.Core)
-[![Build status](https://ci.appveyor.com/api/projects/status/w3ecxmp3grryc5ts/branch/master?svg=true&passingText=master%20-%20passing)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/ospsuite-core/branch/master)
+[![Build status](https://ci.appveyor.com/api/projects/status/w3ecxmp3grryc5ts/branch/develop?svg=true)](https://ci.appveyor.com/project/open-systems-pharmacology-ci/ospsuite-core/branch/develop)
+[![Coverage status](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core/branch/develop/graph/badge.svg)](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core)
 
 ## Code of conduct
 Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc...) is expected to follow the Open Systems Pharmacology [code of conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_CONDUCT.md).

appveyor-coverage.yml

@@ -0,0 +1,44 @@
+configuration: Debug
+
+environment:
+  app_version: '7.1.0'
+
+version: '%app_version%.{build}'
+
+assembly_info:
+  patch: true
+  file: SolutionInfo.*
+  assembly_version: "{version}"
+  assembly_file_version: "{version}"	
+
+cache:
+  packages -> **\packages.config  
+
+before_build:
+  - nuget sources add -name bddhelper -source https://ci.appveyor.com/nuget/ospsuite-bddhelper 
+  - nuget sources add -name utility -source https://ci.appveyor.com/nuget/ospsuite-utility 
+  - nuget sources add -name serializer -source https://ci.appveyor.com/nuget/ospsuite-serializer 
+  - nuget sources add -name databinding -source https://ci.appveyor.com/nuget/ospsuite-databinding 
+  - nuget sources add -name texreporting -source https://ci.appveyor.com/nuget/ospsuite-texreporting 
+  - nuget sources add -name databinding-devexpress -source https://ci.appveyor.com/nuget/ospsuite-databinding-devexpress 
+  - nuget sources add -name funcparser -source https://ci.appveyor.com/nuget/ospsuite-funcparser 
+  - nuget sources add -name simmodel -source https://ci.appveyor.com/nuget/ospsuite-simmodel
+  - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes-282
+  - nuget sources add -name smartxls -source https://ci.appveyor.com/nuget/ospsuite-smartxls
+  - nuget restore
+
+build:
+  verbosity: minimal
+  project: OSPSuite.Core.sln
+
+test_script:
+  - rake cover
+
+install:  
+ - set PATH=C:\Ruby22\bin;C:\\Python34;C:\\Python34\\Scripts;%PATH%"
+ - pip install codecov
+ - git submodule update --init --recursive
+ - ps: >-
+    (new-object net.webclient).DownloadFile('https://download.microsoft.com/download/A/2/D/A2D8587D-0027-4217-9DAD-38AFDB0A177E/msxml.msi', 'C:\\msxml.msi')
+
+    Start-Process msiexec.exe -ArgumentList /i, C:\msxml.msi, /quiet, /qn, /norestart -Wait

appveyor.yml

@@ -9,7 +9,7 @@ assembly_info:
   patch: true
   file: SolutionInfo.*
   assembly_version: "{version}"
-  assembly_file_version: "{version}"	
+  assembly_file_version: "{version}"  
 
 cache:
   packages -> **\packages.config  
@@ -24,15 +24,22 @@ before_build:
   - nuget sources add -name funcparser -source https://ci.appveyor.com/nuget/ospsuite-funcparser 
   - nuget sources add -name simmodel -source https://ci.appveyor.com/nuget/ospsuite-simmodel
   - nuget sources add -name cvodes -source https://ci.appveyor.com/nuget/ospsuite-simmodel-solver-cvodes-282
+  - nuget sources add -name smartxls -source https://ci.appveyor.com/nuget/ospsuite-smartxls
   - nuget restore
 
 build:
   publish_nuget: true
   verbosity: minimal
   include_nuget_references: true
+  project: OSPSuite.Core.sln
 
 skip_branch_with_pr: true
 
+branches:
+  only:
+    - master
+    - develop
+
 test:
   assemblies:
     - OSPSuite.Core.Tests.dll
@@ -49,6 +56,12 @@ skip_commits:
   files:
     - '*.md'
 
+pull_requests: 
+  do_not_increment_build_number: true     
+
+nuget: 
+  disable_publish_on_pr: true  
+
 notifications:
   - provider: Slack
     incoming_webhook:      

copy_to_mobi.bat

@@ -1,9 +1,4 @@
 @echo off
-
-set SolutionDir=%~d0%~p0
-set SrcDir=%SolutionDir%src\
-set AppDebugDir=%SolutionDir%..\MoBi\src\MoBi\bin\Debug\
-
-copy "%SrcDir%OSPSuite.UI\bin\debug\OSPSuite*.dll" "%AppDebugDir%"
-copy "%SrcDir%OSPSuite.UI\bin\debug\OSPSuite*.pdb" "%AppDebugDir%"
+cls
+rake copy_to_mobi
 pause

copy_to_pksim.bat

@@ -1,9 +1,4 @@
 @echo off
-
-set SolutionDir=%~d0%~p0
-set SrcDir=%SolutionDir%src\
-set AppDebugDir=%SolutionDir%..\PK-Sim\src\PKSim\bin\Debug
-
-copy "%SrcDir%OSPSuite.UI\bin\debug\OSPSuite*.dll" "%AppDebugDir%"
-copy "%SrcDir%OSPSuite.UI\bin\debug\OSPSuite*.pdb" "%AppDebugDir%"
+cls
+rake copy_to_pksim
 pause

rakefile.rb

@@ -0,0 +1,47 @@
+require_relative 'scripts/coverage'
+require_relative 'scripts/copy-dependencies'
+
+task :cover do 
+  filter = []
+  filter << "+[OSPSuite.Core]*"
+  filter << "+[OSPSuite.Infrastructure]*"
+  filter << "+[OSPSuite.Presentation]*"
+
+  #exclude namespaces that are tested from applications
+  filter << "-[OSPSuite.Infrastructure]OSPSuite.Infrastructure.Reporting*"
+  filter << "-[OSPSuite.Infrastructure]OSPSuite.Infrastructure.Serialization.ORM*"
+  filter << "-[OSPSuite.Presentation]OSPSuite.Presentation.MenuAndBars*"
+  filter << "-[OSPSuite.Presentation]OSPSuite.Presentation.Presenters.ContextMenus*"
+
+  Coverage.cover(filter, "OSPSuite.Core.Tests.csproj")
+end
+
+task :copy_to_pksim do
+	copy_to_app '../PK-Sim/src/PKSim/bin/Debug/'
+end
+
+task :copy_to_mobi do
+	copy_to_app '../MoBi/src/MoBi/bin/Debug/'
+end
+
+private
+
+def copy_to_app(app_target_relative_path)
+  app_target_path = File.join(solution_dir, app_target_relative_path)
+  source_dir = File.join(src_dir, 'OSPSuite.UI', 'bin', 'Debug')
+
+  copy_depdencies source_dir,  app_target_path do
+    copy_file 'OSPSuite.*.dll'
+    copy_file 'OSPSuite.*.pdb'
+  end
+
+end
+
+def solution_dir
+	File.dirname(__FILE__)
+end
+
+def src_dir
+	File.join(solution_dir, 'src')
+end
+

src/OSPSuite.Assets/OSPSuite.Assets.csproj

@@ -34,8 +34,9 @@
     <WarningLevel>4</WarningLevel>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="OSPSuite.Utility">
-      <HintPath>..\..\packages\OSPSuite.Utility.2.0.0.1\lib\net45\OSPSuite.Utility.dll</HintPath>
+    <Reference Include="OSPSuite.Utility, Version=2.0.0.5, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\..\packages\OSPSuite.Utility.2.0.0.5\lib\net45\OSPSuite.Utility.dll</HintPath>
+      <Private>True</Private>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -71,8 +72,8 @@
   </ItemGroup>
   <ItemGroup>
     <None Include="Icons\Absorption.ico" />
-    <None Include="packages.config" />
     <None Include="OSPSuite.Assets.nuspec" />
+    <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
     <None Include="Icons\AgingPopulationSimulation.ico" />

src/OSPSuite.Assets/UIConstants.cs

@@ -193,7 +193,7 @@ public static string ReallyDeleteAllObservedData(IEnumerable<string> anythingNot
 
       public static string CloneObjectBase(string entityType, string name)
       {
-         return "New name for the cloned {0} '{1}'".FormatWith(entityType, name);
+         return $"New name for the cloned {entityType} '{name}'";
       }
 
       public static string ContactSupport(string forumUrl)
@@ -203,17 +203,17 @@ public static string ContactSupport(string forumUrl)
 
       public static string CreatedOn(string creationDate)
       {
-         return "Created on {0}".FormatWith(creationDate);
+         return $"Created on {creationDate}";
       }
 
       public static string ClonedOn(string creationDate, string clonedFrom)
       {
-         return "Cloned from '{0}' on {1}".FormatWith(clonedFrom, creationDate);
+         return $"Cloned from '{clonedFrom}' on {creationDate}";
       }
 
       public static string ConfiguredOn(string creationDate)
       {
-         return "Configured on {0}".FormatWith(creationDate);
+         return $"Configured on {creationDate}";
       }
 
       public static string ChartFingerprintDataFrom(string projectName, string simulationName, string dateString)
@@ -241,30 +241,42 @@ public static string DoYouWantToDeleteDirectory(string newDirectoryName)
          return $"Do you want to delete the directory '{newDirectoryName}' and continue?";
       }
 
+      public static void AppendListItem(string listItem, StringBuilder sb)
+      {
+         sb.Append($"<li>{listItem}</li>");
+      }
+
+      public static void AppendLine(string lineToAppend, StringBuilder sb)
+      {
+         sb.Append($"<p>{lineToAppend}</p>");
+      }
+
       public static string ExceptionViewDescription(string issueTrackerUrl)
       {
          var sb = new StringBuilder();
-         sb.AppendLine("oops...something went terribly wrong.");
-         sb.AppendLine();
-         sb.AppendLine("To best address the error, please enter an issue in our issue tracker:");
-         sb.AppendLine($"    1 - Visit <b>{issueTrackerUrl}</b> or click on the link below");
-         sb.AppendLine("    2 - Click on the <b>New Issue</b> button");
-         sb.AppendLine("    3 - Describe the steps you took prior to the problem emerging");
-         sb.AppendLine($"    4 - Copy the information below by using the <b>{CopyToClipboard}</b> button and paste it in the issue description");
-         sb.AppendLine("    5 - if possible, attach your project file to the issue (do not attach confidential information)");
-         sb.AppendLine();
-         sb.AppendLine("Note: A GitHub account is required to create an issue");
+         AppendLine("oops...something went terribly wrong.", sb);
+         AppendLine(string.Empty, sb);
+         AppendLine("To best address the error, please enter an issue in our issue tracker:", sb);
+         sb.Append("<ol>");
+         AppendListItem($"Visit <b>{issueTrackerUrl}</b> or click on the link below", sb);
+         AppendListItem("Click on the <b>New Issue</b> button", sb);
+         AppendListItem("Describe the steps you took prior to the problem emerging", sb);
+         AppendListItem($"Copy the information below by using the <b>{CopyToClipboard}</b> button and paste it in the issue description", sb);
+         AppendListItem("if possible, attach your project file to the issue (do not attach confidential information)", sb);
+         sb.Append("</ol>");
+         AppendLine(string.Empty, sb);
+         AppendLine("Note: A GitHub account is required to create an issue", sb);
          return sb.ToString();
       }
 
       public static string EnterNameEntityCaption(string type)
       {
-         return "Enter name for {0}".FormatWith(type, type);
+         return $"Enter name for {type}";
       }
 
       public static string RenameEntityCaption(string type, string name)
       {
-         return "New name for {0} '{1}'".FormatWith(type, name);
+         return $"New name for {type} '{name}'";
       }
 
       public static class Importer
@@ -294,7 +306,7 @@ public static class Importer
          public static readonly string TheUnitInformationMustBeEnteredOrConfirmed = "The unit information must be entered or confirmed.";
          public static readonly string TheMetaDataInformationMustBeEnteredOrConfirmed = "The meta data must be entered or confirmed.";
 
-    
+
          public class ToolTips
          {
             public static readonly string NamingPattern = "Set a pattern for renaming imported data";
@@ -442,12 +454,12 @@ public static string ExportRelatedItemToFileFilter(string defaultFileExtension)
 
          public static string CreatedAtBy(string formattedDate, string by)
          {
-            return "Created on {0} by {1}".FormatWith(formattedDate, by);
+            return $"Created on {formattedDate} by {by}";
          }
 
          public static string UpdatedAtBy(string formattedDate, string by)
          {
-            return "Last updated on {0} by {1}".FormatWith(formattedDate, by);
+            return $"Last updated on {formattedDate} by {by}";
          }
 
          public static readonly string ReallyDeleteMultipleRelatedItems = "Really delete Related Items?";
@@ -1284,7 +1296,7 @@ public static class MPFit
          public static readonly string InitialConstraintsInconsistent = "Initial constraints inconsistent";
          public static readonly string NotEnoughDegreesOfFreedom = "Not enough degrees of freedom";
          public static readonly string ErrorObjectiveFunction = "Error in objective function: {0}";
-         public static readonly string UnknownStatus = "Unknown status: {0}";
+         public static string UnknownStatus(string status) => $"Unknown status: {status}";
          public static readonly string GeneralInputError = "General input error";
          public static string OptimizationFailed(string error) => $"Levenberg-Marquardt optimization failed: {error}";
       }
@@ -1370,22 +1382,22 @@ public static string ValueGreaterThanMinSizeInPixelAndLessThanMaxSizeIsRequiredO
 
       public static string ValueSmallerThanMax(string parameterName, string value, string unit)
       {
-         return "Value for {0} should be less than or equal to {1} {2}".FormatWith(parameterName, value, unit);
+         return $"Value for {parameterName} should be less than or equal to {value} {unit}";
       }
 
       public static string ValueBiggerThanMin(string parameterName, string value, string unit)
       {
-         return "Value for {0} should be greater than or equal to {1} {2}".FormatWith(parameterName, value, unit);
+         return $"Value for {parameterName} should be greater than or equal to {value} {unit}";
       }
 
       public static string ValueStrictBiggerThanMin(string parameterName, string value, string unit)
       {
-         return "Value for {0} should be strictly greater than {1} {2}".FormatWith(parameterName, value, unit);
+         return $"Value for {parameterName} should be strictly greater than {value} {unit}";
       }
 
       public static string ValueStrictSmallerThanMax(string parameterName, string value, string unit)
       {
-         return "Value for {0} should be strictly less than {1} {2}".FormatWith(parameterName, value, unit);
+         return $"Value for {parameterName} should be strictly less than {value} {unit}";
       }
 
       public static string StartValueDefinedForNonPhysicalContainer(string moleculeName, string containerPath)
@@ -1606,7 +1618,7 @@ public static class Command
 
       public static string CreateProjectDescription(string version)
       {
-         return "Project started with version {0}".FormatWith(version);
+         return $"Project started with version {version}";
       }
 
       public static string SetMetaDataAddedCommandDescripton(string name, string value)

src/OSPSuite.Assets/packages.config

@@ -1,4 +1,4 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="OSPSuite.Utility" version="2.0.0.1" targetFramework="net452" />
+  <package id="OSPSuite.Utility" version="2.0.0.5" targetFramework="net452" />
 </packages>

src/OSPSuite.Core/Batch/BatchOutputValues.cs

@@ -0,0 +1,10 @@
+namespace OSPSuite.Core.Batch
+{
+   public class BatchOutputValues
+   {
+      public string Path { get; set; }
+      public float[] Values { get; set; }
+      public string Dimension { get; set; }
+      public double ComparisonThreshold { get; set; }
+   }
+}