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Reintegrate OSMOSES into develop (#2045)
* Create OSMOSES branch * remove older nupkg files for each deploy * update build-scripts * automatically update applications with -m -p arguments * add batch files for rake tasks * fixed (#1740) * description corrected (#1742) * Fixes #1746 Create typed way to use quantile extension methods (#1747) * Fixes #1744 default dimension for QuantityPKParameter (#1745) * 1749 default scaling when changing output (#1751) * 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 <[email protected]> * add missing space Signed-off-by: georgeDaskalakis <[email protected]> Co-authored-by: Michael Sevestre <[email protected]> * 1748 output mapping wrong namespace (#1756) * Fixes #1748 output mapping wrong namespace * Fixes #1748 output mapping wrong namespace * 1743 transferring mappings from simulation to PI (#1755) * 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) * 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) * 1761 closing Residuals vs Time exception fixed (#1762) * correcting build * exception fixed * Fixes #1764 refresh mapped observed data (#1766) * Move output mappings also int he wrong namespace * 1772 ensure that output mapping are exported (#1775) * 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) * Fixes #791 Crash when simulation doesn't have results * add a test * 1769 duplicate deviation lines (#1770) * duplicate deviation lines fixed * correcting tests * Update PredictedVsObservedChartService.cs Co-authored-by: Michael Sevestre <[email protected]> * Fixes some code update to remove unused method, abide to convention for naming, and remove hard core query in a loop (#1776) * Swap simulations (#1777) * Fixes #1783 Crash when exporting population simulation pk analyses to… (#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) * initial implementation * code review change * test corrected * Fixes #1785 Inconsistent curve naming * add comment for why we are removing the simulation name * 1787 adding features to simulation comparisons (#1790) * adding interface member * correcting initialization * adding clear to outputMappings * Fixes #1792 Deviation and Identity columns are not named in data browser * PR requested change * 1781 grouping fixed in code (#1782) * grouping fixed in code * adding comment * 1763 delete observed data entry (#1765) * initial test * removing commented out code * adding none entry to the dropbox * just a try * implementing check for used data * correcting unit tests * correcting build * temp * removing redundant parameter * new DTO for none entry * adding unit tests * corrections * removing empty lines * code review changes * moving the observed data deletion to the task * cleaning up * change * update for none_entry * update for test to not know about IList Co-authored-by: Michael Sevestre <[email protected]> * Fixes #1780 Clone of chart does not clone deviation lines (#1791) * Fixes #1780 Clone of chart does not clone deviation lines * add a comment for count exception * update for PR * Fixes #1794 residuals vs time plot not refreshing * Fixes #1794 Residuals vs. Time plot: no refresh * PR changes * 1796 serializer for residual vs time chart missing (#1797) * Fixes #1796 and also #1789 * Fixes #1796 and also #1789 * Fixes #1798 missing identity line (#1799) * WIP #1798 * WIP #1798 * WIP #1798 * Fixes #1798 missing identity line Co-authored-by: Robert McIntosh <[email protected]> * Fixes improve codre resilience (#1800) * fixed (#1808) * issue fixed (#1805) * 1802 inconsistent dimension fixed (#1803) * inconsistent dimension fixed * removing redundant function * updating develop merge * Expression profile in core (#1814) * temp * fixing build * changing the namespace naming * adding the serializer initial implementation * trying to update expression profile * updating the serializer * temporarily hard coding the icon name * expanding ExpressionParameter * ExpressionParameter serializer test * second try * third try * fourth try * fifth try * sixth try * removing abstract identifier * adding ExpressionParameter empty constructor * skipping formulas with value only * Create OSMOSES branch * remove older nupkg files for each deploy * update build-scripts * automatically update applications with -m -p arguments * add batch files for rake tasks * working import/export * resharper * building * building * building * adding tests for ExpressionProfileBuildingBlock * corecting appveyor.yml * adding serialization test * adding tests for expressionParameter * correcting appveyor * Serialize expression type. * moved constants to Core location * consolidating assets in Core * comparison of expression profile building block properties * adding objectType * code review changes * adding name * changing PKSimVersion type * correcting build * PR comments Co-authored-by: Robert McIntosh <[email protected]> * build the osmoses branch (#1818) * increment build version (#1820) * Fixes #1825 Refactor StartValues vs PathWithValueEntity (#1824) * Fixes #818 Refactor StartValues vs PathWithValueEntity * PR feedback * Remove IMoleculeStartValue and IParameterStartValue interfaces * remove interfaces * Fixes #1828 create expression profiles from PKSim (#1830) * Fixes #1357 individual building block for mobi (#1831) * wip on creating a individual building block in core * PR feedback * PR feedback * reverse scripts submodule changes * Adding ValueOrigin and CalculationMethodCache * Fixes #1832 individual serialization (#1847) * Fixes #1832 individual serialization * PR feedback * Fixes #1855 Individual Management (#1856) * Fixes #1855 Individual Management * PR Feedback * #1866 view and presenter for individual (#1867) * Fixes #1833 Comparison of cloned expression profile (#1869) * Fixes #1833 Comparison of cloned expression profile * fix typo * Fixes #1870 implement individual comparison (#1871) * Fixes #1870 Implement individual comparison * move to separate files * rename * PR feedback * Fixes #1878 Rename error description incorrect when renaming building block (#1879) * Fixes #1876 Comparison of MSV BBs - list "Molecule name" and "Path" se… (#1877) * Fixes #835 Comparison of MSV BBs - list "Molecule name" and "Path" separately * Add explanations for indexing and offset magic numbers * PR feedback * Fixes #1884 Create domain object for Module (#1885) * Fixes #1887 Create placeholder ApplicationIcons for Modules (#1889) * Fixes #1887 Create placeholder ApplicationIcons for Modules * PR Feedback * PR feedback * Fixes #1890 create placeholder icon for new module ribbon button (#1893) * Fixes #1890 Create placeholder icon for 'New Module' Ribbon button * adding folder icons * Fixes #1894 Some user interface changes based on demo (#1895) * Fixes #822 Module Serialization (#1896) * Fixes #1897 Implement module registration (#1898) * Fixes #603 extension of formula reference (#1899) * 603 plug function to model constructor (#1900) * Fixes #693 plug the function into model construction * Fixes #693 plug the function into model construction * 837 sum formula parent (#1901) * Fixes #837 sum formula parent * Fixes #837 sum formula parent * Fixes #837 sum formula parent * PR feedback * Remove interface for object path making stuff just too complicated fo… (#1905) * Remove interface for object path making stuff just too complicated for nothing * Fixing tests * Fixes #1904 parent * Fixes #1904 * Fixes #1903 Resolve commands with dynamic container instead of static (#1906) * Fixes #1907 Imported expression profile is not populated from the database (#1908) * Fixes #1912 Rename class ExpressionParameterUpdate (#1913) * missing from #1912 null checks (#1914) * reverse the removal of extension methods (#1915) * Fixes #1918 (#1919) * Fixes #1909 Gridview dark mode is hard to use (#1917) * Fixes #1909 Gridview dark mode is hard to use * pr feedback * Fixes #1920 create neighborhood builder with path instead of container: (#1922) * Fixes #1920 create neighborhood builder with path instead of container: * Fixes #1920 create neighborhood builder with path instead of container * add icons * add icons * update to diagram (#1923) * Add neighbor icons * Some typo fixing * 1928 do not export psv (#1929) Co-authored-by: georgeDaskalakis <[email protected]> Co-authored-by: Robert McIntosh <[email protected]> Co-authored-by: Juri Solodenko <[email protected]> Co-authored-by: Yuri05 <[email protected]> * Fixes #1933 readonly cells are not easily readable (#1935) * Fixes #1934 create simulation configuration (#1936) * Fixes #1934 create simulation configuration * Also add conversion * Make helper properties virtual * Make helper properties virtual * Make helper properties virtual * Simulation Configuration only returns one * Add missing serialization * Add missing serialization * Fixes #1939 logic update do not override formula with constant (#1940) * Add missing itnerfaces to OriginDataItem (#1941) * Fixes #1943 Open access to project conversion for simulation xml (#1944) * 1945 proposal for parameters in individual (#1950) * WIP #1945. Write tests firt * WIP #1945. Write tests firt * Fixes #1945 * REmove empty test file * Unify model and config in a ModelConfiguration * Also update NUnit * Some tests concurrency issue? * Update config * 1954 remove pk sim project and add extension properties (#1955) * Fixes 1954-remove-pk-sim-project-and-add-extension-properties * Fixes 1954-remove-pk-sim-project-and-add-extension-properties * 1953 ensures that the simulation configuration supports multiple modules) (#1956) * Fixes 1954-remove-pk-sim-project-and-add-extension-properties * Fixes 1954-remove-pk-sim-project-and-add-extension-properties * WIP #1953 * WIP #1953 * Fixes #1953 ensures that the simulation xx * Fixes #1953 ensures that the simulation xx * Add setter for module configuration * 1963 only export species independent parameters to spatial structure (#1964) * Fixes #1963 Change order of validation * WIP #1963 * Fixes #1963 only export species independent * #1963 Add easy access method to get entity by path as string * Adding functionalities to module (#1966) * implemented * adding building block functionality * resharper * Fixes #1967 add origin (#1968) * Fixes #1967 add origin * Fixes #1967 add origin * Apply the meta data also for existing parameter (#1969) * #1970 add merger function to simulation configuration. Actual mer… (#1971) * WIP #1970 add merger function to simulation configuration. Actual merge not done yet * Fixes #1970 add merge function to simulation configuraiton * Fixes #1970 add merge function to simulation configuration * Remove virtual * Fixes #1970 add simulation builder (#1973) * Fixes #1970 add simulation builder * Fixes #1970 add simulation builder * Fixes #1976 remove some domain interfaces (#1977) * Fixes #1976 remove some domain interfaces * Fixes missing tests * Fixes missing tests * Add missing IProcessBuilder interface * 1972 how are we going to merge spatial structure (#1978) * Add some tests first * WIP #1972 * Fixes #1972 how are we going to merge spatial structure * Fixes #1972 how are we going to merge spatial structure * Fixes #1972 how are we going to merge spatial structure * Small update * Fixes #1979 Changes required for creating simulation in MoBi (#1980) Co-authored-by: Michael Sevestre <[email protected]> * Fixes #1981 Cloning module crashes (#1982) * Fixes #1983 Module icon is missing in Module explorer (#1984) * Fixes #1985 ignore neighborhood nto defined (#1986) * Fixes #1987 add reference to module in building blocks (#1988) * Fixes #1989 Implement clone of SimulationConfiguration (#1990) * Fixes #1989 Implement clone of SimulationConfiguration * remove spaces * Fixes #1991 curve binder refresh performance (#1992) * We are frequently looking up the index of basegrid values so that we can use the index to get y value. In the refresh, we can avoid searching the list over and over by using the index in the first place * remove commented code * some more refactoring * Revert "some more refactoring" This reverts commit 42fcc65. * Revert "remove commented code" This reverts commit 4e4ff11. * Revert "We are frequently looking up the index of basegrid values so that we can use the index to get y value." This reverts commit 0eae16f. * What about a step where we use indexing if we can, otherwise use GetValue which we know will interpolate * modify AddRElatedVAluesToRow * Check if basegrids are the same object rather than if they have the same values * typo * Fixes #1993 Remove PKSim Folders icons (#1994) * 1995 setting the value of a discrete distribution mean parameter does 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 (#1998) * Fixes #1997 Building blocks of cloned module do not have parent module set * add a test * Fixes #1999 rename msv and psv (#2000) * Renamed molecule start values to initial conditions * renamed parameter start values * rename some variables * PR feedback * PR feedback * 2002 remove StartValue abstractions (#2003) * 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 (#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… (#2009) * Fixes #2008 Double-click on a module opens "Add building blocks" dialogue * pr feedback * Fixes #2010 create building blocks with default names (#2011) * Fixes Create building blocks with default names * add some tests * Fixes #2013 Cannot rename a simulation (#2014) * Fixes #2015 Small expression display caption changes (#2016) * Fixes #2017 Move Initial Conditions relating to an expression profile… (#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) * Fixes #2025 unhandled exception (#2026) * Fixes #2022 Add common interface to indicate a building block contain… (#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 (#2031) * Fixes #2030 Weird "differences" when applying an expression profile * PR feedback * Fixes #2028 "Initial concentration" overwritten to 0 when creating a … (#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) * Fixes #2036 add distributed table formula to core (#2037) * Make sure expression profile values are updated BEFORE indiviudal values * Fixes #2038 Double click to expand parameter values and initial conditions folders (#2039) * Fixes #2041 Create initial conditions for ExpressionProfileBuildingBlock (#2042) * Fixes #2041 Create initial conditions for ExpressionProfileBuildingBlock * PR feedback * Undo changes in appveyor.yml * Undo changes in appveyor.yml --------- Signed-off-by: georgeDaskalakis <[email protected]> Co-authored-by: Robert McIntosh <[email protected]> Co-authored-by: georgeDaskalakis <[email protected]> Co-authored-by: Juri Solodenko <[email protected]> Co-authored-by: Yuri05 <[email protected]>
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