Add gha for rsharp #1444
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Add gha for rsharp #1444
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+ remove Appveyor files + remove docs/ (will be build on gh-pages) + update badges
Will not push to gh-pages during PR, only when merged + remove unused action
#Conflicts: # appveyor-nightly.yml # appveyor.yml
…ctions # Conflicts: # docs/dev/LICENSE-text.html # docs/dev/articles/create-individual.html # docs/dev/articles/create-run-population.html # docs/dev/articles/create-run-population_files/figure-html/getOutputValues-1.png # docs/dev/articles/create-run-population_files/figure-html/getOutputValuesForIndividual-1.png # docs/dev/articles/data-combined-plotting.html # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-10-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-12-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-13-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-3-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-4-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-5-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-6-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-7-1.png # docs/dev/articles/data-combined-plotting_files/figure-html/unnamed-chunk-8-1.png # docs/dev/articles/data-combined.html # docs/dev/articles/data-combined_files/figure-html/unnamed-chunk-10-1.png # docs/dev/articles/data-combined_files/figure-html/unnamed-chunk-11-1.png # docs/dev/articles/data-combined_files/figure-html/unnamed-chunk-12-1.png # docs/dev/articles/data-combined_files/figure-html/unnamed-chunk-6-1.png # docs/dev/articles/data-combined_files/figure-html/unnamed-chunk-7-1.png # docs/dev/articles/efficient-calculations.html # docs/dev/articles/index.html # docs/dev/articles/load-get.html # docs/dev/articles/observed-data.html # docs/dev/articles/ospsuite.html # docs/dev/articles/pk-analysis.html # docs/dev/articles/run-simulation.html # docs/dev/articles/sensitivity-analysis.html # docs/dev/articles/set-values.html # docs/dev/articles/table-parameters.html # docs/dev/articles/unit-conversion.html # docs/dev/authors.html # docs/dev/deps/bootstrap-5.3.1/bootstrap.min.css # docs/dev/index.html # docs/dev/news/index.html # docs/dev/pkgdown.js # docs/dev/pkgdown.yml # docs/dev/reference/AgingData.html # docs/dev/reference/AllMatchingMethod.html # docs/dev/reference/AllPathsInMethod.html # docs/dev/reference/ApiConfig.html # docs/dev/reference/Application.html # docs/dev/reference/Cache.html # docs/dev/reference/CompareBy.html # docs/dev/reference/Container.html # docs/dev/reference/DataAggregationMethods.html # docs/dev/reference/DataColumn.html # docs/dev/reference/DataCombined.html # docs/dev/reference/DataErrorType.html # docs/dev/reference/DataImporterConfiguration.html # docs/dev/reference/DataRepository.html # docs/dev/reference/DataSet.html # docs/dev/reference/DefaultPlotConfiguration.html # docs/dev/reference/DotNetWrapper.html # docs/dev/reference/Entity.html # docs/dev/reference/Formula.html # docs/dev/reference/Gender.html # docs/dev/reference/HumanPopulation.html # docs/dev/reference/IndividualCharacteristics.html # docs/dev/reference/Interval.html # docs/dev/reference/Molecule.html # docs/dev/reference/MoleculeOntogeny.html # docs/dev/reference/MoleculeParameter.html # docs/dev/reference/ObjectBase.html # docs/dev/reference/OutputSchema.html # docs/dev/reference/OutputSelections.html # docs/dev/reference/PKParameter.html # docs/dev/reference/PKParameterSensitivity.html # docs/dev/reference/Parameter.html # docs/dev/reference/ParameterRange.html # docs/dev/reference/Population.html # docs/dev/reference/PopulationCharacteristics.html # docs/dev/reference/Quantity.html # docs/dev/reference/QuantityPKParameter.html # docs/dev/reference/QuantitySelection.html # docs/dev/reference/Rplot002.png # docs/dev/reference/Rplot003.png # docs/dev/reference/SensitivityAnalysis.html # docs/dev/reference/SensitivityAnalysisResults.html # docs/dev/reference/SensitivityAnalysisRunOptions.html # docs/dev/reference/Simulation.html # docs/dev/reference/SimulationBatch.html # docs/dev/reference/SimulationBatchOptions.html # docs/dev/reference/SimulationBatchRunValues.html # docs/dev/reference/SimulationPKAnalyses.html # docs/dev/reference/SimulationResults.html # docs/dev/reference/SimulationRunOptions.html # docs/dev/reference/SimulationSettings.html # docs/dev/reference/SnapshotParameter.html # docs/dev/reference/SolverSettings.html # docs/dev/reference/Species.html # docs/dev/reference/StandardContainer.html # docs/dev/reference/StandardOntogeny.html # docs/dev/reference/StandardPKParameter.html # docs/dev/reference/StandardPath.html # docs/dev/reference/UserDefinedPKParameter.html # docs/dev/reference/ValuePoint.html # docs/dev/reference/addOutputInterval.html # docs/dev/reference/addOutputs.html # docs/dev/reference/addUserDefinedPKParameter.html # docs/dev/reference/allAvailableDimensions.html # docs/dev/reference/allPKParameterNames.html # docs/dev/reference/calculatePKAnalyses.html # docs/dev/reference/calculateResiduals.html # docs/dev/reference/clearMemory.html # docs/dev/reference/clearOutputIntervals.html # docs/dev/reference/clearOutputs.html # docs/dev/reference/convertUnits.html # docs/dev/reference/createDistributions.html # docs/dev/reference/createImporterConfigurationForFile.html # docs/dev/reference/createIndividual.html # docs/dev/reference/createIndividualCharacteristics.html # docs/dev/reference/createPopulation.html # docs/dev/reference/createPopulationCharacteristics.html # docs/dev/reference/createSimulationBatch.html # docs/dev/reference/dataSetToDataFrame.html # docs/dev/reference/dot-ImporterErrorTypeToDataSetErrorType.html # docs/dev/reference/dot-addMissingGroupings.html # docs/dev/reference/dot-cleanVectorArgs.html # docs/dev/reference/dot-convertGeneralToSpecificPlotConfiguration.html # docs/dev/reference/dot-createAxesLabels.html # docs/dev/reference/dot-encodeUnit.html # docs/dev/reference/dot-expandPath.html # docs/dev/reference/dot-extractAggregatedSimulatedData.html # docs/dev/reference/dot-extractMostFrequentUnit.html # docs/dev/reference/dot-extractResidualsToTibble.html # docs/dev/reference/dot-geoRange.html # docs/dev/reference/dot-getAllEntitiesMatching.html # docs/dev/reference/dot-getAllEntityPathsIn.html # docs/dev/reference/dot-getConcurrentSimulationRunnerResults.html # docs/dev/reference/dot-getDimensionsEnum.html # docs/dev/reference/dot-getEntity.html # docs/dev/reference/dot-getNetTask.html # docs/dev/reference/dot-getNetTaskFromCache.html # docs/dev/reference/dot-getOspDimensions.html # docs/dev/reference/dot-getOspUnits.html # docs/dev/reference/dot-getPathToPKSimInstallDir.html # docs/dev/reference/dot-getPathToPKSimInstallDirFromFileSystem.html # docs/dev/reference/dot-getPathToPKSimInstallDirFromRegistry.html # docs/dev/reference/dot-getPropertyValue.html # docs/dev/reference/dot-getPropertyValues.html # docs/dev/reference/dot-getQuantityDisplayPaths.html # docs/dev/reference/dot-getUnitsEnum.html # docs/dev/reference/dot-initPackage.html # docs/dev/reference/dot-loadDataRepositoryFromPKML.html # docs/dev/reference/dot-makeDataFrameColumn.html # docs/dev/reference/dot-netEnumName.html # docs/dev/reference/dot-normRange.html # docs/dev/reference/dot-parameterValueListFrom.html # docs/dev/reference/dot-parseDimensionsXML.html # docs/dev/reference/dot-removeEmptyDataFrame.html # docs/dev/reference/dot-removeUnpairableDatasets.html # docs/dev/reference/dot-savePKAnalysesToCSV.html # docs/dev/reference/dot-savePopulationToCSV.html # docs/dev/reference/dot-saveResultsToCSV.html # docs/dev/reference/dot-saveSensitivityAnalysisResultsToCSV.html # docs/dev/reference/dot-scaleQuantityValues.html # docs/dev/reference/dot-setQuantityValues.html # docs/dev/reference/dot-toObjectType.html # docs/dev/reference/dot-unitConverter.html # docs/dev/reference/dot-validateHasUnit.html # docs/dev/reference/dot-validateScalarDataCombined.html # docs/dev/reference/exportIndividualSimulations.html # docs/dev/reference/exportPKAnalysesToCSV.html # docs/dev/reference/exportPopulationToCSV.html # docs/dev/reference/exportResultsToCSV.html # docs/dev/reference/exportSensitivityAnalysisResultsToCSV.html # docs/dev/reference/getAllContainerPathsIn.html # docs/dev/reference/getAllContainersMatching.html # docs/dev/reference/getAllMoleculePathsIn.html # docs/dev/reference/getAllMoleculesMatching.html # docs/dev/reference/getAllObserverPathsIn.html # docs/dev/reference/getAllParameterPathsIn.html # docs/dev/reference/getAllParametersForSensitivityAnalysisMatching.html # docs/dev/reference/getAllParametersMatching.html # docs/dev/reference/getAllQuantitiesMatching.html # docs/dev/reference/getAllQuantityPathsIn.html # docs/dev/reference/getAllStateVariableParametersPaths.html # docs/dev/reference/getAllStateVariablesPaths.html # docs/dev/reference/getBaseUnit.html # docs/dev/reference/getContainer.html # docs/dev/reference/getDimensionByName.html # docs/dev/reference/getDimensionForUnit.html # docs/dev/reference/getMolecule.html # docs/dev/reference/getOSPSuiteSetting.html # docs/dev/reference/getOutputValues.html # docs/dev/reference/getParameter.html # docs/dev/reference/getParameterDisplayPaths.html # docs/dev/reference/getQuantity.html # docs/dev/reference/getQuantityValuesByPath.html # docs/dev/reference/getSimulationTree.html # docs/dev/reference/getStandardMoleculeParameters.html # docs/dev/reference/getUnitsForDimension.html # docs/dev/reference/hasDimension.html # docs/dev/reference/hasUnit.html # docs/dev/reference/importPKAnalysesFromCSV.html # docs/dev/reference/importResultsFromCSV.html # docs/dev/reference/importSensitivityAnalysisResultsFromCSV.html # docs/dev/reference/index.html # docs/dev/reference/initPKSim.html # docs/dev/reference/isExplicitFormulaByPath.html # docs/dev/reference/loadAgingDataFromCSV.html # docs/dev/reference/loadDataImporterConfiguration.html # docs/dev/reference/loadDataSetFromPKML.html # docs/dev/reference/loadDataSetsFromExcel.html # docs/dev/reference/loadPopulation.html # docs/dev/reference/loadSimulation.html # docs/dev/reference/messages.html # docs/dev/reference/ospDimensions.html # docs/dev/reference/ospUnits.html # docs/dev/reference/ospsuiteSettingNames.html # docs/dev/reference/ospsuite_deprecated.html # docs/dev/reference/pkAnalysesToDataFrame.html # docs/dev/reference/pkParameterByName.html # docs/dev/reference/plotIndividualTimeProfile-1.png # docs/dev/reference/plotIndividualTimeProfile.html # docs/dev/reference/plotObservedVsSimulated-1.png # docs/dev/reference/plotObservedVsSimulated.html # docs/dev/reference/plotPopulationTimeProfile-1.png # docs/dev/reference/plotPopulationTimeProfile-2.png # docs/dev/reference/plotPopulationTimeProfile-3.png # docs/dev/reference/plotPopulationTimeProfile.html # docs/dev/reference/plotResidualsVsSimulated-1.png # docs/dev/reference/plotResidualsVsSimulated.html # docs/dev/reference/plotResidualsVsTime-1.png # docs/dev/reference/plotResidualsVsTime.html # docs/dev/reference/populationToDataFrame.html # docs/dev/reference/potentialVariableParameterPathsFor.html # docs/dev/reference/reexports.html # docs/dev/reference/removeAllUserDefinedPKParameters.html # docs/dev/reference/removeSimulationFromCache.html # docs/dev/reference/resetSimulationCache.html # docs/dev/reference/runSensitivityAnalysis.html # docs/dev/reference/runSimulation.html # docs/dev/reference/runSimulationBatches.html # docs/dev/reference/runSimulations.html # docs/dev/reference/saveDataSetToPKML.html # docs/dev/reference/saveSimulation.html # docs/dev/reference/scaleParameterValues.html # docs/dev/reference/setMoleculeInitialValues.html # docs/dev/reference/setMoleculeScaleDivisors.html # docs/dev/reference/setMoleculeValuesByPath.html # docs/dev/reference/setOutputInterval.html # docs/dev/reference/setOutputs.html # docs/dev/reference/setParameterValues.html # docs/dev/reference/setParameterValuesByPath.html # docs/dev/reference/setQuantityValuesByPath.html # docs/dev/reference/simulationResultsToDataFrame.html # docs/dev/reference/splitPopulationFile.html # docs/dev/reference/toBaseUnit.html # docs/dev/reference/toDisplayUnit.html # docs/dev/reference/toPathArray.html # docs/dev/reference/toPathString.html # docs/dev/reference/toUnit.html # docs/dev/reference/uniqueEntities.html # docs/dev/reference/updatePKParameter.html # docs/dev/reference/validateDimension.html # docs/dev/reference/validateUnit.html # docs/dev/search.json # docs/dev/sitemap.xml
#Conflicts: # appveyor-nightly.yml # appveyor.yml
+ refactor all jobs in one main workflow
+ rename to "bump..."
#Conflicts: # .github/workflows/bump-dev-version.yaml # .github/workflows/main-workflow.yaml
Merge branch 'implement-github-actions' into add-GHA-for-rsharp # Conflicts: # .gitignore # DESCRIPTION # appveyor-nightly.yml # appveyor.yml # rakefile.rb
+ remove extra packages since they are listed in DESCRIPTION as remotes field
+ remove trigger on "develop" branch
Merge commit 'bf57d506286d57a245d30fd1b2194056bca8c945' #Conflicts: # .github/workflows/main-workflow.yaml # DESCRIPTION
+ upload built package + install PKSim + runs only on windows and linux
…Pharmacology/OSPSuite-R into add-GHA-for-rsharp
Closed
Yuri05
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Jul 23, 2024
* Added authors to _pkgdown.yml * - Exchange rClr for rSharp as dependency * Docs * Replace all calls to rClr by calls to rShapr * Replace `clrLoadAssembly` by `loadAssembly` * - Replace `rClrCallStatic` by `callStatic` - Run docs * `getEnumNames` Docs * Use correct package reference in test * - Remove enc2utf, as conversion is done in rSharp * Moved some wrappers to NetObject in rSharp * Loading package works * .wrapProperty * Replace all clrGet * Replace all clrSet * Replace clrCall * Replace clrNew * DotNetWrapper expects a NetObject and not a pointer. * Remove ref * Fix all initilialize * Remove direct pointers * Styler * Documentation * Correct calling of private print methods * Prepend '.' to wrapPropertyReadOnly * Prepend '.' to throwPropertyISREadONly * Fix test for dotNetWrapper * Fix clrGetType to getType * use NPOI for .NET Core * Fix .wrapProperty * Fix print calls in DataCombined * Update snapshots for the use with the latest TLF * Remove unnecessary libs * Docs * Adjust README.Rmd Adjust install_dependencies.R * Remove appveyor for R 3.6 * Skip individual and simulation tests Update snapshots * Moved a test using population creation from simulation-results test * Update snapshots. All tests passing locally under Windows * Delete "install-packages.R" * Update documentation * Move vignettes that use PK-Sim functions to WIP folder * Fixed author roles Fixed minor docs problems Excluded vignettes about individuals and populations from pkgdown * Fix role * unzip rSharp archive before installing it * correct typo * delete and ignore tests/testthat/*.pdf * Tweak test to avoid writing file in package directory * update c++ libs (#1415) temporarily disable failing tests Co-authored-by: Yuri05 <Yuri05@github.com> * Temporarily disable vignettes building for nightly builds (#1418) Co-authored-by: Yuri05 <Yuri05@github.com> * Temporary fix vignette (#1419) * Temporarily disable vignettes building for nightly builds * Temporarily disable vignettes building for nightly builds --------- Co-authored-by: Yuri05 <Yuri05@github.com> * Fix packages.ubuntu22.config (#1420) Co-authored-by: Yuri05 <Yuri05@github.com> * fix weird appveyor build dir change (#1421) Co-authored-by: Yuri05 <Yuri05@github.com> * next try (#1423) * next try * next try * disable code coverage * Update appveyor-nightly.yml --------- Co-authored-by: Yuri05 <Yuri05@github.com> * Restrict branch rsharp (#1427) * restrict branch to rSharp * restrict branch to rSharp --------- Co-authored-by: Yuri05 <Yuri05@github.com> * does this prevent branch building for PR on develop? * Styler * Add script to update core files * update core files * fix unzip path * fix path + remove zip file after * Update initPKSIM function to always target "lib" folder + devtools::document() * Overwrite unziped files + preserve file datetime from the zip file (for better diff detection) * Add gha for rsharp (#1444) - Add github action to update Core files (OSPS and PKSim in `inst/lib`) - Update github actions to work with rSharp - Update github actions to run RCMD on linux - Update github actions to run pkgdown and test-coverage on linux machines (use default r-lib actions) * Enable articles about individuals and populations in pkgdown * Update NEWS * Remove install_dependencies.R * 🤖 Update Core Files. * Update readme section about loading the workspace * Update README * Move excluded vignettes back to folder * Remove packages.config * Fix individual-characteristics.R * Fix utilities-population * Enable some skipped tests * Styler * Fix population vignette failing * Pksim installation vignette (#1456) * usethis::use_vignette("PKSim-installation") + reference vignette in _pkgdown.yml + write vignette content * add mention to the core files update script * 🤖 Update Core Files. * Increment version number to 12.1.0 * 🤖 Update Core Files. * add LD_LIBRARY_PATH variable * temporarly ignore vignettes building and check * idem * dynamically load shared object files * restore vignettes building * prepend PKSim dependent vignettes with _ to ignore them * Better/clearer binary initialization * 🤖 Update Core Files. * Move vignettes to draft folder to prevent RCMDCheck test on them * update pkgdown structure * add devtools as suggests (for dev) * Remove test skip conditions * Restore vignettes * run update_core_files.R * styler::style_pkg() * add alt text for osp logo --------- Co-authored-by: Robert McIntosh <261477+rwmcintosh@users.noreply.github.com> Co-authored-by: Felix MIL <felix.mil@esqlabs.com> Co-authored-by: Juri Solodenko <Yuri05@users.noreply.github.com> Co-authored-by: Yuri05 <Yuri05@github.com> Co-authored-by: Felix MIL <34234913+Felixmil@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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