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Project-based Workflow #651

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Project-based Workflow #651

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Commits on Apr 18, 2024

  1. Rename createDefaultProjectConfiguration to createProjectConfiguratio… 

    …n without inducing breaking changes

+ usethis::use_package("lifecycle")
+ update tests accordingly
+ add test for deprecation
    @Felixmil
    Felixmil committed Apr 18, 2024
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  2. Harmonize Excel configuration files (#633)

    @Felixmil
    Felixmil committed Apr 18, 2024
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  3. renamed the Parameters folder to Configurations (#631)

    @Felixmil
    Felixmil committed Apr 18, 2024
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  4. Created helpers for frequently used paths/ProjectConfiguration in tests

    @Felixmil
    Felixmil committed Apr 18, 2024
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  5. fix devtools::document() errors 

    + devtools::document()
    @Felixmil
    Felixmil committed Apr 18, 2024
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  6. skip some test on CI (instead of CRAN)

    @Felixmil
    Felixmil committed Apr 18, 2024
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  7. Update NEWS 

    + remove names of internal collaborators
    @Felixmil
    Felixmil committed Apr 18, 2024
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  8. Merge remote-tracking branch 'origin/new-project-structure' into para… 

    …msFile-to-modelParamsFile

# Conflicts:
#	NEWS.md
#	R/project-configuration.R
#	inst/extdata/examples/TestProject/Configurations/Populations.xlsx
#	inst/extdata/examples/TestProject/ProjectConfiguration.xlsx
#	tests/testthat/test-utilities-population.R
    @Felixmil
    Felixmil committed Apr 18, 2024
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  9. enable GitHub actions when making PR in any branch

    @Felixmil
    Felixmil committed Apr 18, 2024
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  10. remove snapshot for projectConfiguration as it contains absolute path… 

    … that depends on environment
    @Felixmil
    Felixmil committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. start working on project definition

    @Felixmil
    Felixmil committed Apr 19, 2024
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  2. Add populationsCSV path in projectConfiguration 

    + use projectConfiguration$populationsCSV to locate population CSV files to read
+ add test to make sure all test scenarios can be properly created
    @Felixmil
    Felixmil committed Apr 19, 2024
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  3. Fix "Indiv" to "Indiv1" to prevent warnings

    @Felixmil
    Felixmil committed Apr 19, 2024
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  4. Merge remote-tracking branch 'origin/new-project-structure' into para… 

    …msFile-to-modelParamsFile

# Conflicts:
#	NEWS.md
    @Felixmil
    Felixmil committed Apr 19, 2024
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  5. devtools::document()

    @Felixmil
    Felixmil committed Apr 19, 2024
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  6. Update test expectation

    @Felixmil
    Felixmil committed Apr 19, 2024
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  7. Merge branch 'paramsFile-to-modelParamsFile' into implement-project

    @Felixmil
    Felixmil committed Apr 19, 2024
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Commits on May 6, 2024

  1. Add Project object that contains all esqlabsR workflow components (co… 

    …nfigurations, scenarios, simulationResults)

+ tests
    @Felixmil
    Felixmil committed May 6, 2024
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  2. Improve projectConfiguration print method

    @Felixmil
    Felixmil committed May 6, 2024
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  3. style pkg

    @Felixmil
    Felixmil committed May 6, 2024
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  4. keep inactivated scenarios status when changing configurations

    @Felixmil
    Felixmil committed May 6, 2024
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Commits on May 15, 2024

  1. ignore excel temporary files

    @Felixmil
    Felixmil committed May 15, 2024
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  2. Merge branch 'new-project-structure' into implement-project 

    # Conflicts:
#	R/project-configuration.R
#	R/scenario.R
#	R/utilities-project-configuration.R
#	inst/extdata/examples/TestProject/ProjectConfiguration.xlsx
#	man/ExportConfiguration.Rd
#	man/ProjectConfiguration.Rd
#	tests/testthat/helpers.R
#	tests/testthat/test-utilities-population.R
#	tests/testthat/test-utilities-project-configuration.R
#	tests/testthat/test-utilities-scenarios.R
    @Felixmil
    Felixmil committed May 15, 2024
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Commits on May 16, 2024

  1. Add an optional path argument to save ProjectCOnfiguration 

    + add related test
    @Felixmil
    Felixmil committed May 16, 2024
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  2. Add test for Project 

    Small fixes
    @Felixmil
    Felixmil committed May 16, 2024
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Commits on May 29, 2024

  1. rename file and relocate functions

    @Felixmil
    Felixmil committed May 29, 2024
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  2. Rename files and add "-legacy" to older versions (temporary)

    @Felixmil
    Felixmil committed May 29, 2024
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  3. style + document

    @Felixmil
    Felixmil committed May 29, 2024
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  4. replace function with latest name

    @Felixmil
    Felixmil committed May 29, 2024
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Commits on May 30, 2024

  1. Better user feedback on simulation results

    @Felixmil
    Felixmil committed May 30, 2024
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  2. Add documentation

    @Felixmil
    Felixmil committed May 30, 2024
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  3. Add simulationTime objects 

    + test
+ documentation
    @Felixmil
    Felixmil committed May 30, 2024
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Commits on May 31, 2024

  1. Rename time and timeUnit to simulationTime and simulationTimeUnit 

    + add method for nice printing of simulationTime objects
    @Felixmil
    Felixmil committed May 31, 2024
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  2. Apply simulationTime output intervals to simulation 

    + scenario$configuration is now a copy of configurations$scenarios
+ rename scenarioConfigurationData argument to scenarioConfiguration
    @Felixmil
    Felixmil committed May 31, 2024
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Commits on Jun 5, 2024

  1. Add OutputPaths 

    + replace purrr:map(names(... by purrr:imap(...
    @Felixmil
    Felixmil committed Jun 5, 2024
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Commits on Jun 6, 2024

  1. Add simulationTimeUnit validation

    @Felixmil
    Felixmil committed Jun 6, 2024
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  2. Add steadyState simulation run

    @Felixmil
    Felixmil committed Jun 6, 2024
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  3. Add pretty printing method for individuals

    @Felixmil
    Felixmil committed Jun 6, 2024
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  4. Rename validation function

    @Felixmil
    Felixmil committed Jun 6, 2024
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Commits on Jun 11, 2024

  1. Rename ModelParameter to SimulationParameter

    @Felixmil
    Felixmil committed Jun 11, 2024
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  2. Add Population object and pop simulation capabilities 

    + refactor and document
+ remove legacy code that was re-implemented in new framework
+ relocate "utils" function in appropriate files
    @Felixmil
    Felixmil committed Jun 11, 2024
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  3. devtools::document()

    @Felixmil
    Felixmil committed Jun 11, 2024
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  4. minor fix and optimizations 

    +devtools::document()
    @Felixmil
    Felixmil committed Jun 11, 2024
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Commits on Jul 30, 2024

  1. merge branch main into implement-project

    @Felixmil
    Felixmil committed Jul 30, 2024
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  2. git merge 

    Merge branch 'new-project-structure' into implement-project

# Conflicts:
#	R/SimulationParameter.R
#	R/utilities-individual.R
#	R/utilities-project-configuration.R
#	R/utilities-scenarios.R
#	R/zzz.R
    @Felixmil
    Felixmil committed Jul 30, 2024
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  3. Merge branch 'new-project-structure' into implement-project

    @Felixmil
    Felixmil authored Jul 30, 2024
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Commits on Aug 28, 2024

  1. Merge branch 'new-project-structure' into implement-project 

    # Conflicts:
#	R/project-configuration.R
    @Felixmil
    Felixmil committed Aug 28, 2024
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  2. Merge branch 'implement-project' of https://github.com/esqLABS/esqlabsR… 

    … into implement-project
    @Felixmil
    Felixmil committed Aug 28, 2024
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Commits on Sep 17, 2024

  1. Update project.R

    @AKostiv8
    AKostiv8 committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. Prevent user from modifying scenarios directly

    @Felixmil
    Felixmil committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Refactor repeated error messages

    @Felixmil
    Felixmil committed Sep 19, 2024
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Commits on Oct 1, 2024

  1. config validation

    @AKostiv8
    AKostiv8 committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Feedback implemented

    @AKostiv8
    AKostiv8 committed Oct 2, 2024
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  2. Update project.R

    @AKostiv8
    AKostiv8 committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Project status tests

    @AKostiv8
    AKostiv8 committed Oct 3, 2024
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Commits on Oct 7, 2024

  1. Test adjustment to the new project structure.

    @AKostiv8
    AKostiv8 committed Oct 7, 2024
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  2. update time param warning

    @AKostiv8
    AKostiv8 committed Oct 7, 2024
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Commits on Oct 10, 2024

  1. Merge commit '7d4271027aff77abe19c41cf1749106570fce118' 

    #Conflicts:
#	R/utilities-population.R
    @Felixmil
    Felixmil committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. replace deprecated function

    @Felixmil
    Felixmil committed Oct 11, 2024
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  2. pull from main

    @Felixmil
    Felixmil committed Oct 11, 2024
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  3. Update path to where results are stored now

    @Felixmil
    Felixmil committed Oct 11, 2024
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  4. Remove embeded shiny apps

    @Felixmil
    Felixmil committed Oct 11, 2024
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  5. Update plots test for new project structure

    @Felixmil
    Felixmil committed Oct 11, 2024
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  6. remove/relocate outdated test

    @Felixmil
    Felixmil committed Oct 11, 2024
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  7. update snaps

    @Felixmil
    Felixmil committed Oct 11, 2024
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Commits on Oct 14, 2024

  1. shiny app remove

    @AKostiv8
    AKostiv8 committed Oct 14, 2024
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  2. shiny app remove

    @AKostiv8
    AKostiv8 committed Oct 14, 2024
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  3. conflicts resolved

    @AKostiv8
    AKostiv8 committed Oct 14, 2024
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  4. Rename / Comment out of date tests

    @Felixmil
    Felixmil committed Oct 14, 2024
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  5. remove shiny app launching script

    @Felixmil
    Felixmil committed Oct 14, 2024
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  6. merge from main

    @Felixmil
    Felixmil committed Oct 14, 2024
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  7. devtools::documen()

    @Felixmil
    Felixmil committed Oct 14, 2024
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  8. merge new-project-structure into branch 

    Merge branch 'new-project-structure' into implement-project

# Conflicts:
#	R/utilities-project-configuration.R
#	man/ProjectConfiguration.Rd
#	tests/testthat/helpers.R
#	tests/testthat/test-project-configuration.R
#	tests/testthat/test-utilities-population.R
#	tests/testthat/test-utilities-scenarios.R
    @Felixmil
    Felixmil committed Oct 14, 2024
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  9. Merge branch 'individual-validation-demo' into implement-project

    @AKostiv8
    AKostiv8 committed Oct 14, 2024
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  10. Merge branch 'implement-project' of https://github.com/esqLABS/esqlabsR… 

    … into implement-project
    @AKostiv8
    AKostiv8 committed Oct 14, 2024
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  11. Revert "Validation object & individual modification validation" (#726)

    @AKostiv8
    AKostiv8 authored Oct 14, 2024
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  12. update snapshot after updating packages

    @Felixmil
    Felixmil committed Oct 14, 2024
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  13. Merge branch 'implement-project' of https://github.com/esqLABS/esqlabsR… 

    … into implement-project
    @Felixmil
    Felixmil committed Oct 14, 2024
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  14. fix code examples in documentation

    @Felixmil
    Felixmil committed Oct 14, 2024
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  15. fix path to Example Project Configuration File

    @Felixmil
    Felixmil committed Oct 14, 2024
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  16. remove old test files 

    + update time unit error regex
    @Felixmil
    Felixmil committed Oct 14, 2024
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  17. fix exampleProject

    @Felixmil
    Felixmil committed Oct 14, 2024
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  18. Move some objects to Internal

    @Felixmil
    Felixmil committed Oct 14, 2024
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  19. disable vignettes (temporary)

    @Felixmil
    Felixmil committed Oct 14, 2024
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  20. restore original build options

    @Felixmil
    Felixmil committed Oct 14, 2024
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  21. remove unsuported character in doc

    @Felixmil
    Felixmil committed Oct 14, 2024
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