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Version 10.0 #631

Merged
merged 79 commits into from
Oct 13, 2021
Merged

Version 10.0 #631

merged 79 commits into from
Oct 13, 2021

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msevestre
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msevestre and others added 30 commits December 14, 2020 13:43
* Fixes #446 ensure that object ids are resetted

* Fixes #446 ensure that object ids are resetted

* Do not use develop to ensure we can use the latest build\

* Fixes issue with pksim setup tmp

* Comment out tests until PKSim is ready

* Comment out tests until PKSim is ready

* Fixes #451 output schema error in messages

* Also fixes #452

* Also fixes #452

* Fixes #446 ensure that object ids are reset and fixes #457

* Fixes #446 ensure that object ids are reset and fixes #457

* add tests back to the suite for individual and population

* Fixes #456

* Fixes #450

* Fixes #445 error when setting readonly props

* Update ospsuite.core
#463)


* Fixes #462 
* Do not create new quantity objects if utilities-simulation-results if quantites are passed.

* - Review fixes
- Run styler

* Fix tests
Co-authored-by: Yuri05 <Yuri05@github.com>
* - Using any(x == value) instead of (value %in% x)
- unlist(x, use.names = FALSE)

* Styler
* Fixes #444 batch simulation

* Fixes #444 batch simulation

* Fixes Add test commented out

* Update core

* Update example

* Update example

* Run styler
* Ensure that PK-Sim is installed from develop

* WIP #475 reactivate linux build

* WIP #475 reactivate linux build

* WIP #475 reactivate linux build

* WIP #475 reactivate linux build

* Fixes #475 reactivate linux build
* Fixes #467 Disable "Windows-only" tests if running under Linux

* Fixes #467 Disable "Windows-only" tests if running under Linux

* Fixes #467 Disable "Windows-only" tests if running under Linux

* Removed temporary DIR output

Co-authored-by: Yuri05 <Yuri05@github.com>
* WIP #476

* WIP #476

* Update version of ospsuite.R

* Fixes #476 mutants!
* Fixes #423 export population to csv

* Fixes #472
* Fixes #436 calculate pk fail

* Also Fixes #439 and #440
* Fixes #473 usability issue

* Fixes #473 usability issue

* Fixes #473 usability issue

* Fixes #422
* WIP #295 population calculation aging

* Fixes #295 population calculation aging

* Fixes #295 population calculation aging
* Fixes #417 document update

* Fixes #483 make sure package name is dynamic./ Also rename packageVersion to suiteVersion
* WIP #486 expose data repository

* Cache columns

* Ensures that the AllButBaseGrid method is a get

* WIP #486 expose data repository

* Fixes #486 expose data repository

* Fixes #486 expose data repository

* Update test file to support multiple data type

* Update example

* Update example

* Fixes #488

* Fixes #486 expose data repository
* Added methods for working with enums.

* Add tests for enum

* Typo

* Updated documentation.

* Dont run example with enum

* Update docs (again)
* Fixes #493 units for dimensions

* Make sure variable has the right case
* Fixes #496 expose enum

* Also update warnings
* create getUnitsEnum and getDimensionsEnum functions

* Fixes #478

* tests of dimensions and units enums
* Add utilities-dimensions.R

* Add utilities-dimensions.R

* merge develop..still code needs to be reviewed

* Some more updates

* Remove existsDimension from export

* Added tests
Moved methods to utilities-units
Using core methods

* Styler

* Remove obsolete error messages

* - Extend toUnit to convert from non-base unit

* Add molWeightUnit to toBaseUnit

* Styler

* Manual update

* Rebase on develop to avoid weird conflicts

* Rebase on develop to avoid weird conflicts

* Rebase on develop to avoid weird conflicts

* Fixes issue with missing parameter

* Fixes weird tests failing

Co-authored-by: Michael Sevestre <michael@design2code.ca>
* Fixes #503 debug output

* Adds the correct namespace
* Methods for concurrent running of simulations.

* Dimensions utilities

* -WIP

* Implement runSimulationsConcurrently

* Remov obsolete code

* Run styler

* Build options

* Docu update

* Project change
* Update utilities-units.R

* Update utilities-units.R
* Methods for concurrent running of simulations.

* Dimensions utilities

* -WIP

* Implement runSimulationsConcurrently

* Remov obsolete code

* Run styler

* Build options

* Docu update

* Project change

* SimulationBatch is OSPSuite.R.Services.SettingsForConcurrentRunSimulationBatch

* Working on concurrent batch runner

* Added function to run simulation batches concurrently

* Add example for concurrent batch runner

* Update dll version to match those used by PKSim

* Missing comment in examples

* Update example

* Update docu again...

* Dontrun example

* Reversed change of isOfType behavior when checking an empty list()

* Update comment regarding dispose

* Update binaries

* Address review comments.

* Rename SettingsForConcurrentRunSimulationBatch to ConcurrentRunSimulationBatch in comments.

Co-authored-by: Michael Sevestre <michael@design2code.ca>
* Fixes #515

* Rename enforceIsList to toList
* Using low-level rCrl methods in getOutputValues

* Depends rClr

* Using .NET methods to get output results and set output quantities.

* Update packages version

* Update package version number two...

* Update dependencies

* Do not state namespace for internal method.

* Add setQuantityValuesByPath

* - addOutputs does not return quantities any more
- Argument 'withMetaData' in 'getOutputValues' renamed to 'addMetaData'

* Styler

* Message for paths with wildcards updated

* Revert changes in calling function hierarchy

* All arguments in one line

* Ensures that we are now working with single path

* Renaming methods

Co-authored-by: Michael Sevestre <michael@design2code.ca>
* Add getAllStateVariablesPaths

* Remove unnecessary ospsuite imports

* - Using getAllMoleculePathsIn instead of getAllEntityPathsIn
-
* Update core

* Revert centOS
Co-authored-by: Yuri05 <Yuri05@github.com>
msevestre and others added 5 commits September 14, 2021 14:26
Merging. Please review
Enables intellisense in ospUnits lists such as Concentration (Mass)
* Fixing tests using ospUnits

* Using other units
* Fixes #621 minimum r version

* Check if it works with 3.5

* Check if it works with 3.5

* Check if it works with 3.5

* Check if it works with 3.5

* Check if it works with 3.5

* try same stuff with v4

* Bump version to 3.6 and download rclr from github. Also remove tools folder
@msevestre msevestre self-assigned this Sep 30, 2021
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* - Added method setMoleculeValuesByPath
- setParameterValues, setParameterValuesByPaths, setMoleculeValues, setMoleculeValuesByPaths accept units
- Added tests for units-argument

* Update documentation

* Fixes wrong signature

* Remove copy paste...

* `stopIfNotFound` argument always last

Co-authored-by: Michael Sevestre <michael@design2code.ca>
@github-pages github-pages bot temporarily deployed to github-pages October 1, 2021 13:09 Inactive
@github-pages github-pages bot temporarily deployed to github-pages October 1, 2021 13:14 Inactive
* Fixes #626 Error in validateIsOfType

* Fixes #626 Error in validateIsOfType

* Fixes #625 check that the value is indeed numeric

* Fixes #625 check that the value is indeed numeric
@github-pages github-pages bot temporarily deployed to github-pages October 1, 2021 13:42 Inactive
@github-pages github-pages bot temporarily deployed to github-pages October 1, 2021 13:54 Inactive
* Fixes #635 reorder vignettes

* Fixes #635 reorder vignettes
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@github-pages github-pages bot temporarily deployed to github-pages October 1, 2021 16:32 Inactive
* Update dlls

* Also sets the version by hand in description so that the version is updated

* Also sets the version by hand in description so that the version is updated
@github-pages github-pages bot temporarily deployed to github-pages October 4, 2021 22:03 Inactive
* Update dlls

* Also sets the version by hand in description so that the version is updated

* Also sets the version by hand in description so that the version is updated

* Try to get that build going
@github-pages github-pages bot temporarily deployed to github-pages October 5, 2021 00:15 Inactive
* Update core

* Update core

* Update dll
@github-pages github-pages bot temporarily deployed to github-pages October 6, 2021 22:15 Inactive
@msevestre msevestre marked this pull request as ready for review October 13, 2021 13:21
@msevestre msevestre merged commit 0ec56c6 into main Oct 13, 2021
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7 participants