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Version 7.1.0
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Version 7.1.0
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msevestre authored May 30, 2017
2 parents f75c2b2 + 116deb0 commit ac4622b
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3 changes: 3 additions & 0 deletions .gitmodules
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Expand Up @@ -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
2 changes: 2 additions & 0 deletions OSPSuite.Core.sln
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Expand Up @@ -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
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -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).
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44 changes: 44 additions & 0 deletions appveyor-coverage.yml
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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
15 changes: 14 additions & 1 deletion appveyor.yml
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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:
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9 changes: 2 additions & 7 deletions copy_to_mobi.bat
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@@ -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
9 changes: 2 additions & 7 deletions copy_to_pksim.bat
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@@ -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
47 changes: 47 additions & 0 deletions rakefile.rb
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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

1 change: 1 addition & 0 deletions scripts
Submodule scripts added at 1f7603
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7 changes: 4 additions & 3 deletions src/OSPSuite.Assets/OSPSuite.Assets.csproj
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Expand Up @@ -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" />
Expand Down Expand Up @@ -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" />
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62 changes: 37 additions & 25 deletions src/OSPSuite.Assets/UIConstants.cs
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Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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";
Expand Down Expand Up @@ -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?";
Expand Down Expand Up @@ -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}";
}
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion src/OSPSuite.Assets/packages.config
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@@ -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>
10 changes: 10 additions & 0 deletions src/OSPSuite.Core/Batch/BatchOutputValues.cs
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@@ -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; }
}
}
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