Version 12.0

Merge pull request #2415 from Open-Systems-Pharmacology/develop

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,40 @@
+Fixes #
+
+# Description
+
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+## Type of change
+
+Please mark relevant options with an `x` in the brackets.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires documentation changes (link at least one [user](https://github.com/Open-Systems-Pharmacology/docs) or [developer](https://github.com/Open-Systems-Pharmacology/developer-docs) documentation issue):
+- [ ] Algorithm update - updates algorithm documentation/questions/answers etc.
+- [ ] Other (please describe):
+
+# How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
+
+- [ ] Integration tests
+- [ ] Unit tests
+- [ ] Manual tests 
+- [ ] No tests required
+
+# Reviewer checklist
+
+Mark everything that needs to be checked before merging the PR.
+
+- [ ] Check if the code is well documented
+- [ ] Check if the behavior is what is expected
+- [ ] Check if the code is well tested
+- [ ] Check if the code is readable and well formatted
+- [ ] Additional checks (document below if any)
+- [ ] Check if documentation update issue(s) are created if the option `This change requires a documentation update` above is selected
+
+# Screenshots (if appropriate):
+
+# Questions (if appropriate):

.gitignore

@@ -1,6 +1,8 @@
 ## Ignore Visual Studio temporary files, build results, and
 ## files generated by popular Visual Studio add-ons.
 
+.NCrunch_OSPSuite.Core/
+
 # User-specific files
 *.suo
 *.user
@@ -259,4 +261,6 @@ paket-files/
 /src/OSPSuite.Core/include
 /tests/OSPSuite.Core.Tests/include
 
-licenses.licx
+licenses.licx
+*.DotSettings
+/OSPSuite.Core.v3.ncrunchsolution

SolutionInfo.cs

@@ -7,6 +7,7 @@
 [assembly: AssemblyCopyright("Copyright © 2017 - present - Open Systems Pharmacology Community")]
 [assembly: ComVisible(false)]
 [assembly: InternalsVisibleTo("OSPSuite.Core.Tests")]
+[assembly: InternalsVisibleTo("OSPSuite.HelperForTests")]
 [assembly: InternalsVisibleTo("OSPSuite.UI.Tests")]
 [assembly: InternalsVisibleTo("OSPSuite.Presentation.Tests")]
 [assembly: InternalsVisibleTo("OSPSuite.R.Tests")]

appveyor.yml

@@ -1,18 +1,18 @@
 configuration: Debug
-image: Visual Studio 2019
+image: Visual Studio 2022
 
 version: '{build}'
 
 init:
-- ps: Update-AppveyorBuild -Version "$($env:ospsuite_nightly_version).$($env:appveyor_build_version)"
+- ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
 
 dotnet_csproj:
   patch: true
   file: '**\*.csproj'
-  version: '$(ospsuite_nightly_version).$(build_number)'
-  assembly_version: '$(ospsuite_nightly_version).$(build_number)'
-  file_version: '$(ospsuite_nightly_version).$(build_number)'
-  informational_version: '$(ospsuite_nightly_version).$(build_number)'
+  version: '$(ospsuite_version).$(build_number)'
+  assembly_version: '$(ospsuite_version).$(build_number)'
+  file_version: '$(ospsuite_version).$(build_number)'
+  informational_version: '$(ospsuite_version).$(build_number)'
 
 before_build:
   - nuget sources add -name bddhelper -source https://ci.appveyor.com/nuget/ospsuite-bddhelper 
@@ -30,7 +30,6 @@ build:
   publish_nuget: true
   verbosity: minimal
   publish_nuget_symbols: true
-  use_snupkg_format: true
   project: OSPSuite.Core.sln
 
 skip_branch_with_pr: true
@@ -49,7 +48,7 @@ skip_commits:
 
 branches:
   only:
-    - hotfix/11.3
+    - develop
 
 test:
   assemblies:

mobi_nuget.bat

@@ -0,0 +1,4 @@
+@echo off
+cls
+rake create_local_nuget[m] 
+pause

nuget_to_both.bat

@@ -0,0 +1,4 @@
+@echo off
+cls
+rake create_local_nuget[m,p] 
+pause

pksim_nuget.bat

@@ -0,0 +1,4 @@
+@echo off
+cls
+rake create_local_nuget[p] 
+pause

rakefile.rb

@@ -25,33 +25,68 @@
 
 	Coverage.cover(filter, targetProjects)
 end
-
-  task :copy_to_pksim do
-	copy_to_app '../PK-Sim/src/PKSim/bin/Debug/net472'
+
+task :create_local_nuget, [:arg1, :arg2, :arg3] do |t, args|
+  FileUtils.rm_f Dir.glob("./nuget_repo/*.nupkg")
+  versionId = "12.0.0-" + generate_code(5)
+  puts("Your version is " + versionId.red)
+  system("dotnet", "pack", "-p:PackageVersion="+ versionId, "--configuration", "Debug", "--output", "nuget_repo", "--no-build") 
+  if args.to_hash.values.include? "m"
+    update_mobi(versionId)
   end
-
-  task :copy_to_mobi do
-	copy_to_app '../MoBi/src/MoBi/bin/Debug/net472'
+  if args.to_hash.values.include? "p"
+    update_pksim(versionId)
   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(tests_dir, 'OSPSuite.Starter', 'bin', 'Debug', "net472")
-
-	copy_dependencies source_dir,  app_target_path do
-	  copy_file 'OSPSuite.*.dll'
-	  copy_file 'OSPSuite.*.pdb'
-	end
-
+end
+
+private
+def find_token(file, regex)
+  file_content = str = IO.read(file)
+  matches = file_content.match(regex)
+
+  if(matches.nil?)
+    return nil
   end
-
-  def solution_dir
-	File.dirname(__FILE__)
+  return matches[1]
+end
+
+def update_mobi(versionId)
+  puts("updating MoBi")
+  token = find_token("../MoBi/src/MoBi/MoBi.csproj", /<PackageReference Include="OSPSuite.Core" Version="(.*)"/)
+  if(token.nil?)
+    return
   end
-
-  def tests_dir
-	File.join(solution_dir, 'tests')
+
+  glob = Dir.glob('../MoBi/**/*.csproj')
+  glob.each do |file|
+    Utils.replace_tokens({token => versionId}, file)
+  end
+
+end
+
+def update_pksim(versionId)
+  puts("updating PKSim")
+  token = find_token("../PK-Sim/src/PKSim/PKSim.csproj", /<PackageReference Include="OSPSuite.Core" Version="(.*)"/)
+  if(token.nil?)
+    return
+  end
+
+  glob = Dir.glob('../PK-Sim/**/*.csproj')
+  glob.each do |file|
+    Utils.replace_tokens({token => versionId}, file)
   end
+end
+
+def generate_code(number)
+  charset = Array('A'..'Z') + Array('a'..'z')
+  Array.new(number) { charset.sample }.join
+end
+
+def solution_dir
+  File.dirname(__FILE__)
+end
+
+def tests_dir
+  File.join(solution_dir, 'tests')
+end
 

src/OSPSuite.Assets.Images/ApplicationIcons.cs

@@ -113,7 +113,7 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon ExpertParameters = AddNamedIcon("Parameters", "ExpertParameters");
       public static readonly ApplicationIcon PopulationExportToCSV = AddNamedIcon("PopulationExportToCSV");
       public static readonly ApplicationIcon ExportToPDF = AddNamedIcon("PDF", "ExportToPDF");
-      public static readonly ApplicationIcon ExtendParameterStartValues = AddNamedIcon("ExtendParameterStartValues");
+      public static readonly ApplicationIcon ExtendParameterValues = AddNamedIcon("ExtendParameterValues");
       public static readonly ApplicationIcon ExtracellularMembrane = AddNamedIcon("ExtracellularMembrane");
       public static readonly ApplicationIcon Fat = AddNamedIcon("Fat");
       public static readonly ApplicationIcon Favorites = AddNamedIcon("Favorites");
@@ -138,8 +138,8 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon HumanGreen = AddNamedIcon("HumanGreen");
       public static readonly ApplicationIcon HumanRed = AddNamedIcon("HumanRed");
       public static readonly ApplicationIcon Import = AddNamedIcon("ObservedData", "Import");
-      public static readonly ApplicationIcon MoleculeStartValuesImport = AddNamedIcon("MoleculeStartValuesImport");
-      public static readonly ApplicationIcon ParameterStartValuesImport = AddNamedIcon("ParameterStartValuesImport");
+      public static readonly ApplicationIcon InitialConditionsImport = AddNamedIcon("InitialConditionsImport");
+      public static readonly ApplicationIcon ParameterValuesImport = AddNamedIcon("ParameterValuesImport");
       public static readonly ApplicationIcon ImportPopulation = AddNamedIcon("ImportPopulation");
       public static readonly ApplicationIcon PopulationSimulationLoad = AddNamedIcon("PopulationSimulationLoad");
       public static readonly ApplicationIcon ResultsImportFromCSV = AddNamedIcon("ResultsImportFromCSV", IconNames.RESULTS_IMPORT_FROM_CSV);
@@ -216,10 +216,10 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon MoleculeFolder = AddNamedIcon("MoleculeFolder");
       public static readonly ApplicationIcon MoleculeGreen = AddNamedIcon("MoleculeGreen");
       public static readonly ApplicationIcon MoleculeRed = AddNamedIcon("MoleculeRed");
-      public static readonly ApplicationIcon MoleculeStartValues = AddNamedIcon("MoleculeStartValues", IconNames.MOLECULE_START_VALUES);
-      public static readonly ApplicationIcon MoleculeStartValuesFolder = AddNamedIcon("MoleculeStartValuesFolder");
-      public static readonly ApplicationIcon MoleculeStartValuesGreen = AddNamedIcon("MoleculeStartValuesGreen");
-      public static readonly ApplicationIcon MoleculeStartValuesRed = AddNamedIcon("MoleculeStartValuesRed");
+      public static readonly ApplicationIcon InitialConditions = AddNamedIcon("InitialConditions", IconNames.INITIAL_CONDITIONS);
+      public static readonly ApplicationIcon InitialConditionsFolder = AddNamedIcon("InitialConditionsFolder");
+      public static readonly ApplicationIcon InitialConditionsGreen = AddNamedIcon("InitialConditionsGreen");
+      public static readonly ApplicationIcon InitialConditionsRed = AddNamedIcon("InitialConditionsRed");
       public static readonly ApplicationIcon Monkey = AddNamedIcon("Monkey");
       public static readonly ApplicationIcon MonkeyGreen = AddNamedIcon("MonkeyGreen");
       public static readonly ApplicationIcon MonkeyRed = AddNamedIcon("MonkeyRed");
@@ -257,10 +257,10 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon ParameterDistribution = AddNamedIcon("Histogram", "ParameterDistribution");
       public static readonly ApplicationIcon Parameters = AddNamedIcon("Parameters");
       public static readonly ApplicationIcon ParametersError = AddNamedIcon("ParametersError");
-      public static readonly ApplicationIcon ParameterStartValueGreen = AddNamedIcon("ParameterStartValuesGreen");
-      public static readonly ApplicationIcon ParameterStartValues = AddNamedIcon("ParameterStartValues", IconNames.PARAMETER_START_VALUES);
-      public static readonly ApplicationIcon ParameterStartValuesFolder = AddNamedIcon("ParameterStartValuesFolder");
-      public static readonly ApplicationIcon ParameterStartValuesRed = AddNamedIcon("ParameterStartValuesRed");
+      public static readonly ApplicationIcon ParameterValueGreen = AddNamedIcon("ParameterValuesGreen");
+      public static readonly ApplicationIcon ParameterValues = AddNamedIcon("ParameterValues", IconNames.PARAMETER_VALUES);
+      public static readonly ApplicationIcon ParameterValuesFolder = AddNamedIcon("ParameterValuesFolder");
+      public static readonly ApplicationIcon ParameterValuesRed = AddNamedIcon("ParameterValuesRed");
       public static readonly ApplicationIcon PassiveTransport = AddNamedIcon("PassiveTransport", IconNames.PASSIVE_TRANSPORT);
       public static readonly ApplicationIcon PassiveTransportFolder = AddNamedIcon("PassiveTransportFolder");
       public static readonly ApplicationIcon PassiveTransportGreen = AddNamedIcon("PassiveTransportGreen");
@@ -403,13 +403,13 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon SaveFormulation = AddNamedIcon("FormulationSave");
       public static readonly ApplicationIcon MoleculeError = AddNamedIcon("MoleculeError");
       public static readonly ApplicationIcon SaveMolecule = AddNamedIcon("MoleculeSave");
-      public static readonly ApplicationIcon AddMoleculeStartValues = AddNamedIcon("MoleculeStartValuesAdd");
-      public static readonly ApplicationIcon MoleculeStartValuesLoad = AddNamedIcon("MoleculeStartValuesLoad");
-      public static readonly ApplicationIcon SaveMoleculeStartValues = AddNamedIcon("MoleculeStartValuesSave");
+      public static readonly ApplicationIcon AddInitialConditions = AddNamedIcon("InitialConditionsAdd");
+      public static readonly ApplicationIcon InitialConditionsLoad = AddNamedIcon("InitialConditionsLoad");
+      public static readonly ApplicationIcon SaveInitialConditions = AddNamedIcon("InitialConditionsSave");
       public static readonly ApplicationIcon SaveObserver = AddNamedIcon("ObserverSave");
-      public static readonly ApplicationIcon AddParameterStartValues = AddNamedIcon("ParameterStartValuesAdd");
-      public static readonly ApplicationIcon ParameterStartValuesLoad = AddNamedIcon("ParameterStartValuesLoad");
-      public static readonly ApplicationIcon SaveParameterStartValues = AddNamedIcon("ParameterStartValuesSave");
+      public static readonly ApplicationIcon AddParameterValues = AddNamedIcon("ParameterValuesAdd");
+      public static readonly ApplicationIcon ParameterValuesLoad = AddNamedIcon("ParameterValuesLoad");
+      public static readonly ApplicationIcon SaveParameterValues = AddNamedIcon("ParameterValuesSave");
       public static readonly ApplicationIcon SaveReaction = AddNamedIcon("ReactionSave");
       public static readonly ApplicationIcon SaveSpatialStructure = AddNamedIcon("SpatialStructureSave");
       public static readonly ApplicationIcon ParameterIdentificationFolder = AddNamedIcon("ParameterIdentificationFolder");
@@ -434,7 +434,7 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon CovarianceAnalysisRed = AddNamedIcon("CovarianceAnalysisRed");
       public static readonly ApplicationIcon DeleteSelected = AddNamedIcon("DeleteSelected");
       public static readonly ApplicationIcon DeleteSourceNotDefined = AddNamedIcon("DeleteSourceNotDefined");
-      public static readonly ApplicationIcon ExtendMoleculeStartValues = AddNamedIcon("ExtendMoleculeStartValues");
+      public static readonly ApplicationIcon ExtendInitialConditions = AddNamedIcon("ExtendInitialConditions");
       public static readonly ApplicationIcon MoleculeObserver = AddNamedIcon("MoleculeObserver");
       public static readonly ApplicationIcon OutputSelection = AddNamedIcon("OutputSelection");
       public static readonly ApplicationIcon PreviewOriginData = AddNamedIcon("PreviewOriginData");
@@ -493,6 +493,23 @@ public static class ApplicationIcons
       public static readonly ApplicationIcon ExpressionProfileFolder = AddNamedIcon("ExpressionProfileFolder");
       public static readonly ApplicationIcon OSPSuite = AddNamedIcon("OSPSuite");
       public static readonly ApplicationIcon RedCross = AddNamedIcon("RedCross");
+      public static readonly ApplicationIcon ModuleExplorer = AddNamedIcon("ModuleExplorer");
+      public static readonly ApplicationIcon ModulesFolder = AddNamedIcon("ModulesFolder");
+      public static readonly ApplicationIcon Module = AddNamedIcon("Module");
+      public static readonly ApplicationIcon Neighborhood = AddNamedIcon( "Neighborhood");
+      public static readonly ApplicationIcon Neighbor = AddNamedIcon("Neighbor");
+      public static readonly ApplicationIcon TransporterRed = AddNamedIcon("TransporterRed", "TransporterRed");
+      public static readonly ApplicationIcon TransporterGreen = AddNamedIcon("TransporterGreen", "TransporterGreen");
+      public static readonly ApplicationIcon EnzymeRed = AddNamedIcon("EnzymeRed", "EnzymeRed");
+      public static readonly ApplicationIcon EnzymeGreen = AddNamedIcon("EnzymeGreen", "EnzymeGreen");
+      public static readonly ApplicationIcon ProteinRed = AddNamedIcon("ProteinRed", "ProteinRed");
+      public static readonly ApplicationIcon ProteinGreen = AddNamedIcon("ProteinGreen", "ProteinGreen");
+      public static readonly ApplicationIcon ModuleGreen = AddNamedIcon("ModuleGreen");
+      public static readonly ApplicationIcon ModuleRed = AddNamedIcon("ModuleRed");
+      public static readonly ApplicationIcon PKSimModule = AddNamedIcon("PKSimModule");
+      public static readonly ApplicationIcon PKSimModuleGreen = AddNamedIcon("PKSimModuleGreen");
+      public static readonly ApplicationIcon PKSimModuleRed = AddNamedIcon("PKSimModuleRed");
+
 
       // All icons should go at the end of the preceding list, before this delimiting icon - EmptyIcon
       private static ApplicationIcon createEmptyIcon() => new ApplicationIcon((SvgImage) null);
@@ -530,7 +547,7 @@ public static ApplicationIcon AddNamedIcon(string resName, string iconName = nul
       {
          var name = (iconName ?? resName).ToUpperInvariant();
          var iconAsBytes = getIcon(resName);
-
+         
          var appIcon = new ApplicationIcon(iconAsBytes)
          {
             IconName = name,