Reintegrate OSMOSES into develop #2045

msevestre · 2023-06-23T14:24:58Z

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* 1749 default scaling when changing output * Revert "1749 default scaling when changing output" This reverts commit 584d5ab. * 1749 default scaling when changing output Signed-off-by: georgeDaskalakis <37107428+georgeDaskalakis@users.noreply.github.com> * add missing space Signed-off-by: georgeDaskalakis <37107428+georgeDaskalakis@users.noreply.github.com> Co-authored-by: Michael Sevestre <michael@design2code.ca>

* Fixes #1748 output mapping wrong namespace * Fixes #1748 output mapping wrong namespace

* 1749 default scaling when changing output * Revert "1749 default scaling when changing output" This reverts commit 584d5ab. * initial implementation * correcting test

* 1749 default scaling when changing output * Revert "1749 default scaling when changing output" This reverts commit 584d5ab. * 1752 fixed * correcting unit test * corrections

* correcting build * exception fixed

* Ensure that WeightedObservedData is also in domain * Fixes #1772 ensure that output mapping are exported * Fixes tests * Fixes tests also that was hard coding number of pk parameters"

* Fixes #791 Crash when simulation doesn't have results * add a test

* duplicate deviation lines fixed * correcting tests * Update PredictedVsObservedChartService.cs Co-authored-by: Michael Sevestre <michael@design2code.ca>

…or naming, and remove hard core query in a loop (#1776)

#1784) * Fixes #1783 Crash when exporting population simulation pk analyses to csv * update test

* initial implementation * code review change * test corrected

* adding interface member * correcting initialization * adding clear to outputMappings

* grouping fixed in code * adding comment

… not work as expected (#1996) * Add tests to reproduce the bug * Fixes #1995 setting the value should also create the formula underneath * Fixes #1995. Setting a value for discrete resets the percentile

…1998) * Fixes #1997 Building blocks of cloned module do not have parent module set * add a test

# Conflicts: # src/OSPSuite.Assets/UIConstants.cs # src/OSPSuite.Infrastructure.Import/Core/DataFormat/AbstractColumnsDataFormat.cs # src/OSPSuite.Infrastructure.Import/Core/DataSource.cs # src/OSPSuite.Infrastructure.Import/Core/DataSourceFileReaders/ExcelDataSourceFile.cs # src/OSPSuite.Infrastructure.Import/Core/InvalidObservedDataFileException.cs # src/OSPSuite.Infrastructure.Import/Services/Importer.cs # tests/OSPSuite.Infrastructure.Tests/Import/DataSourceSpecs.cs

* Renamed molecule start values to initial conditions * renamed parameter start values * rename some variables * PR feedback * PR feedback

* Fixes #2002 Remove StartValueBase and IStartValue temporary code * Remove StartValueBuildingBlock abstractions * Remove StartValue abstractions in xml serializers * PR feedback

…2007) * Fixes #2006 Require that applications specify their local directory * spacing * adding the null case * null check

#2009) * Fixes #2008 Double-click on a module opens "Add building blocks" dialogue * pr feedback

* Fixes Create building blocks with default names * add some tests

#2018) * Fixes #2017 Move Initial Conditions relating to an expression profile into the expression profile object * Add removeInitialCondition * PR feedback * PR feedback

#2027) * Fixes #2022 Add common interface to indicate a building block contains initial conditions * PR feedback * PR feedback * PR feedback

…2031) * Fixes #2030 Weird "differences" when applying an expression profile * PR feedback

#2029) * Fixes #2028 "Initial concentration" overwritten to 0 when creating a simulation from module from PK-Sim 11.2 * comment and test

…tions folders (#2039)

…ock (#2042) * Fixes #2041 Create initial conditions for ExpressionProfileBuildingBlock * PR feedback

msevestre · 2023-06-23T14:26:07Z

appveyor.yml

-  assembly_version: '$(ospsuite_version).$(build_number)'
-  file_version: '$(ospsuite_version).$(build_number)'
-  informational_version: '$(ospsuite_version).$(build_number)'
+  version: '12.0.$(build_number)'


we should undo this

I think we don't need any of these changes in appveyor.yml, just bump the environment var

rwmcintosh and others added 30 commits November 28, 2022 12:55

Create OSMOSES branch

ce31243

remove older nupkg files for each deploy

05fe2ff

update build-scripts

1497e9f

automatically update applications with -m -p arguments

85bf3c5

add batch files for rake tasks

c062872

fixed (#1740)

79df3bc

description corrected (#1742)

e7b645e

Fixes #1746 Create typed way to use quantile extension methods (#1747)

d1c969e

Fixes #1744 default dimension for QuantityPKParameter (#1745)

12939aa

1748 output mapping wrong namespace (#1756)

fed6391

* Fixes #1748 output mapping wrong namespace * Fixes #1748 output mapping wrong namespace

1743 transferring mappings from simulation to PI (#1755)

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* 1749 default scaling when changing output * Revert "1749 default scaling when changing output" This reverts commit 584d5ab. * initial implementation * correcting test

1752 deviation lines in legend (#1754)

ee61568

* 1749 default scaling when changing output * Revert "1749 default scaling when changing output" This reverts commit 584d5ab. * 1752 fixed * correcting unit test * corrections

correcting build (#1760)

0954593

1761 closing Residuals vs Time exception fixed (#1762)

6e50444

* correcting build * exception fixed

Fixes #1764 refresh mapped observed data (#1766)

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Move output mappings also int he wrong namespace

b331c3e

1772 ensure that output mapping are exported (#1775)

a2f7aad

* Ensure that WeightedObservedData is also in domain * Fixes #1772 ensure that output mapping are exported * Fixes tests * Fixes tests also that was hard coding number of pk parameters"

Fixes #1773 Crash when simulation doesn't have results (#1774)

5e8d31b

* Fixes #791 Crash when simulation doesn't have results * add a test

1769 duplicate deviation lines (#1770)

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* duplicate deviation lines fixed * correcting tests * Update PredictedVsObservedChartService.cs Co-authored-by: Michael Sevestre <michael@design2code.ca>

Fixes some code update to remove unused method, abide to convention f…

efdd866

…or naming, and remove hard core query in a loop (#1776)

Swap simulations (#1777)

7924bf2

Fixes #1783 Crash when exporting population simulation pk analyses to… (

4fab196

#1784) * Fixes #1783 Crash when exporting population simulation pk analyses to csv * update test

1767 return empty plot when observed data without nonZero values (#1768)

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* initial implementation * code review change * test corrected

Fixes #1785 Inconsistent curve naming

a84e89d

add comment for why we are removing the simulation name

c4851b9

1787 adding features to simulation comparisons (#1790)

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* adding interface member * correcting initialization * adding clear to outputMappings

Fixes #1792 Deviation and Identity columns are not named in data browser

fbe7cf8

PR requested change

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1781 grouping fixed in code (#1782)

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* grouping fixed in code * adding comment

rwmcintosh and others added 22 commits April 28, 2023 12:06

Fixes #1993 Remove PKSim Folders icons (#1994)

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1995 setting the value of a discrete distribution mean parameter does…

54ac464

… not work as expected (#1996) * Add tests to reproduce the bug * Fixes #1995 setting the value should also create the formula underneath * Fixes #1995. Setting a value for discrete resets the percentile

1997 building blocks of cloned module do not have parent module set (#…

aa9922d

…1998) * Fixes #1997 Building blocks of cloned module do not have parent module set * add a test

Fixes #1999 rename msv and psv (#2000)

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* Renamed molecule start values to initial conditions * renamed parameter start values * rename some variables * PR feedback * PR feedback

2002 remove StartValue abstractions (#2003)

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* Fixes #2002 Remove StartValueBase and IStartValue temporary code * Remove StartValueBuildingBlock abstractions * Remove StartValue abstractions in xml serializers * PR feedback

Fixes #2006 Require that applications specify their local directory (#…

f8d7b0d

…2007) * Fixes #2006 Require that applications specify their local directory * spacing * adding the null case * null check

Fixes #2008 Double-click on a module opens "Add building blocks" dial… (

ac4e4ff

#2009) * Fixes #2008 Double-click on a module opens "Add building blocks" dialogue * pr feedback

Fixes #2010 create building blocks with default names (#2011)

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* Fixes Create building blocks with default names * add some tests

Fixes #2013 Cannot rename a simulation (#2014)

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Fixes #2015 Small expression display caption changes (#2016)

051bcda

Fixes #2017 Move Initial Conditions relating to an expression profile… (

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#2018) * Fixes #2017 Move Initial Conditions relating to an expression profile into the expression profile object * Add removeInitialCondition * PR feedback * PR feedback

Fixes #2020 building block are not cloned (#2021)

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Fixes #2025 unhandled exception (#2026)

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Fixes #2022 Add common interface to indicate a building block contain… (

d60f0cd

#2027) * Fixes #2022 Add common interface to indicate a building block contains initial conditions * PR feedback * PR feedback * PR feedback

Fixes #2030 Weird "differences" when applying an expression profile (#…

5b61b0d

…2031) * Fixes #2030 Weird "differences" when applying an expression profile * PR feedback

Fixes #2028 "Initial concentration" overwritten to 0 when creating a … (

d4c875e

#2029) * Fixes #2028 "Initial concentration" overwritten to 0 when creating a simulation from module from PK-Sim 11.2 * comment and test

Fixes #2032 Create DisplayName property of building block (#2033)

e6f92a9

Fixes #2036 add distributed table formula to core (#2037)

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Make sure expression profile values are updated BEFORE indiviudal values

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Fixes #2038 Double click to expand parameter values and initial condi…

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…tions folders (#2039)

Fixes #2041 Create initial conditions for ExpressionProfileBuildingBl…

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…ock (#2042) * Fixes #2041 Create initial conditions for ExpressionProfileBuildingBlock * PR feedback

msevestre requested review from rwmcintosh and Yuri05 June 23, 2023 14:25

msevestre commented Jun 23, 2023

View reviewed changes

rwmcintosh approved these changes Jun 23, 2023

View reviewed changes

msevestre added 2 commits June 23, 2023 10:30

Undo changes in appveyor.yml

3e85fb3

Undo changes in appveyor.yml

ef28c4c

msevestre merged commit 3c18ced into develop Jun 23, 2023

msevestre deleted the OSMOSES branch June 23, 2023 14:44

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Reintegrate OSMOSES into develop #2045

Reintegrate OSMOSES into develop #2045

msevestre commented Jun 23, 2023

msevestre Jun 23, 2023

rwmcintosh Jun 23, 2023

Reintegrate OSMOSES into develop #2045

Reintegrate OSMOSES into develop #2045

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msevestre commented Jun 23, 2023

msevestre Jun 23, 2023

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