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Shapr 1.0.0 #401

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wants to merge 175 commits into from
Closed

Shapr 1.0.0 #401

wants to merge 175 commits into from

Commits on May 6, 2024

  1. future testing added

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Commits on May 30, 2024

  1. init covergence

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  2. man

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Commits on May 31, 2024

  1. more work. seems to work all right now

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  2. starting to put the non-adaptive method into the same loop. Not done!

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Commits on Jun 4, 2024

  1. make tests for non-adaptive approach work out

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  2. tests still pass on this

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  3. work on the way to iter list

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  4. more work

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  5. where i am now. something is off, crashing in compute_vS

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Commits on Jun 7, 2024

  1. move to iter_list and more cleanup

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  2. div + .Rd

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  3. cleanup

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  4. .

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Commits on Jun 11, 2024

  1. [skip actions] rename and fix create_s_batch

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  2. remove all iteration relevant internals outside of iter_list

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  3. [skip actions] forgot reverting. Non-adaptive shap value tests works

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Commits on Aug 1, 2024

  1. real data sim for NSM2024 (to be deleted)

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Commits on Aug 2, 2024

  1. various minor edits

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  2. fix basic error in forecast with paried_shap_sampling

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  3. +adaptive

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  4. create_S_batch_new

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  5. get old functions back to make forecast work

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  6. adding approach to X

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  7. man ++

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  8. Revert "create_S_batch_new" 

    This reverts commit d140325.
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  9. add sample_freq=NA to exact method

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  10. shapley values are correct at this stage

    @martinju
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  11. make setup tests pass

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  12. .

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  13. accept regression snaps

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  14. fix regression_separates req to call shapley_setup before setup_approach

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  15. all tests good, except two vaeacs

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  16. set seed again before shapley_setup to fix failing vaeac test

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  17. fixed last failing test

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  18. fixing checks NSE + documentation (not properly)

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  19. exporting weight_matrix

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Commits on Aug 3, 2024

  1. upgraded all packages locally. Might be an issue with fit_times()

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  2. deletes fit_times for regression_surrogate to pass tests

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  3. styler

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  4. lintr

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  5. .

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Commits on Aug 5, 2024

  1. apply name changes to test files

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  2. rename regular output name

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  3. adding setup adaptive ++

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  4. update regular tests

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Commits on Aug 6, 2024

  1. bugfix, improve printing and init adaptive tests

    @martinju
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  2. update test files

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  3. div

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  4. remove timing arg and add hidden testing arg

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  5. fixing broken testing objects after updates

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  6. update tests with testing = TRUE, and remove timing = FALSE

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Commits on Aug 7, 2024

  1. rds files

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  2. styler

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  3. [skip actions] .

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  4. move functions to appropriate files

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  5. [skip actions] doc + temporary and hiddenly adding unique_sampling

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Commits on Aug 8, 2024

  1. add timing + experiment with improved bootstrapping code

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  2. [skip actions] fix non-unique sampling

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Commits on Aug 9, 2024

  1. init moving to max_n_combinations

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  2. add feature_samples to iter_list in setup for convenience

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  3. simplifying explain view + improve max_n_combinations sets and checks

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  4. man

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  5. Merge commit '2e7e86450686f61d6f4c7f63ac87c5857ff0094e' into convergence

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  6. .

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  7. [skip actions] remaining stuff of max_n_combinations. Works, i think 

    Fix tests later
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  8. [skip actions] remaining stuff of max_n_combinations. Works, i think 

    Fix tests later
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  9. new bootstrap introduced with tests

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  10. making tests work

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Commits on Aug 10, 2024

  1. tests OK

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  2. some more ok tests. Forecast dont work as of now

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  3. apply the feature_combination stuff also to groups

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  4. Not 100% sure this actually works as it should 

    Nope, the bootstrapping uses features and n_features, so not using the groups. Can I make it generally applicable? with coal+ n_per_coal or so everywhere?  Discuss this with Lars.
Also add a test where the groups corresponds to one feature each as a sanity check of wethter i can identical results.
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Commits on Aug 12, 2024

  1. add and fix group tests

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Commits on Aug 16, 2024

  1. new

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  2. adaptive OK

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  3. all tests pass

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  4. styler

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  5. man

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  6. fix checks

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  7. Disable rcpp approx solve warnings

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  8. temporary fix forecast (not adaptive yet)

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  9. tests

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  10. combinations -> coalitions and merging all features/groups-code

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Commits on Aug 19, 2024

  1. add features to coalition table for both features and groups

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  2. bugfix groups + some plot test updates

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  3. more fixing

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  4. adaptive tests

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  5. remaining tests

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Commits on Aug 20, 2024

  1. forcast tests (something is up with forecast grouping, though)

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  2. [skip actions] style

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Commits on Aug 21, 2024

  1. adding reweighting strategy on all cond

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Commits on Aug 23, 2024

  1. [skip actions] add reweighting strategies + non-unique paired sampling 

    + scripts
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  2. n_samples -> n_MC_samples

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  3. tests OK

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Commits on Sep 5, 2024

  1. fix iterative with paired sampling

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  2. update tests after bootstrap change + .Rprofile for smoother testing

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Commits on Sep 6, 2024

  1. add intermediate saving

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  2. working version of continue training

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  3. moves prev_shapr_object handling to setup and add validity test 

    NEXT: Briefly tests that it works and add testthat tests
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  4. working

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  5. [skip actions] Working 

    What remains is adding testthat tests
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Commits on Sep 9, 2024

  1. man + testthat

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  2. new adaptive output testfiles

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Commits on Sep 10, 2024

  1. Fix cutting of coalition list per horizon in ```shapley_setup_forecas… 

    …t```
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Commits on Sep 11, 2024

  1. Merge remote-tracking branch 'jonlachmann/convergence' into convergence

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  2. update OK forecast test files

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  3. extra forecast test file update

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Commits on Sep 19, 2024

  1. add max_batch_size og min_n_batches

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  2. apply the new n_batches settings in practice 

    Next is delete any traces of n_batches from setup and usage of internal$parameters$b_batches
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Commits on Sep 26, 2024

  1. remove all traces of n_batches in the older code

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  2. adaptive tests ok

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  3. more tests

    @martinju
    martinju committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. adding checks for adaptive argument formats

    @martinju
    martinju committed Sep 27, 2024
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  2. update tests

    @martinju
    martinju committed Sep 27, 2024
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  3. regression

    @martinju
    martinju committed Sep 27, 2024
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  4. temporary disabling the forecast tests

    @martinju
    martinju committed Sep 27, 2024
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  5. new test files

    @martinju
    martinju committed Sep 27, 2024
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  6. move reweighting and set new defaults

    @martinju
    martinju committed Sep 27, 2024
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  7. moving towards new defaults

    @martinju
    martinju committed Sep 27, 2024
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  8. adpative-output at least OK 

    Continue checking the other tests after update
    @martinju
    martinju committed Sep 27, 2024
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Commits on Sep 28, 2024

  1. [skip tests] new test files

    @martinju
    martinju committed Sep 28, 2024
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Commits on Sep 30, 2024

  1. [skip actions] other tests ok

    @martinju
    martinju committed Sep 30, 2024
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  2. Merge remote-tracking branch 'origin/convergence' into convergence

    @martinju
    martinju committed Sep 30, 2024
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  3. [skip actions] .

    @martinju
    martinju committed Sep 30, 2024
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  4. [skip actions] documenting explain

    @martinju
    martinju committed Sep 30, 2024
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  5. more documentation

    @martinju
    martinju committed Sep 30, 2024
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  6. .

    @martinju
    martinju committed Sep 30, 2024
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  7. [skip actions] Slight restructure + update of main vignette 

    Not great, but something.
    @martinju
    martinju committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. checks for the adaptive argument

    @martinju
    martinju committed Oct 1, 2024
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  2. NSE warnings

    @martinju
    martinju committed Oct 1, 2024
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  3. test updates

    @martinju
    martinju committed Oct 1, 2024
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  4. man and zzz

    @martinju
    martinju committed Oct 1, 2024
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  5. man + tests

    @martinju
    martinju committed Oct 1, 2024
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  6. tmp

    @martinju
    martinju committed Oct 1, 2024
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  7. deal with cont estimation for non-adaptive

    @martinju
    martinju committed Oct 1, 2024
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  8. first vignette

    @martinju
    martinju committed Oct 1, 2024
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  9. vaeac also need X in setup

    @martinju
    martinju committed Oct 1, 2024
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  10. vaeac vignette works

    @martinju
    martinju committed Oct 1, 2024
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  11. [skip actions] init update of regression vignette

    @martinju
    martinju committed Oct 1, 2024
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  12. + regression

    @martinju
    martinju committed Oct 1, 2024
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  13. fix docs

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

  1. style

    @martinju
    martinju committed Oct 2, 2024
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  2. linting

    @martinju
    martinju committed Oct 2, 2024
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  3. fix man

    @martinju
    martinju committed Oct 2, 2024
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  4. fix vignette

    @martinju
    martinju committed Oct 2, 2024
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  5. remove (>= 3.0.0) for testthat for tesitng

    @martinju
    martinju committed Oct 2, 2024
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  6. Merge branch 'verbose' into convergence

    @martinju
    martinju committed Oct 2, 2024
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  7. Merge branch 'convergence' into verbose

    @martinju
    martinju committed Oct 2, 2024
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  8. replacing the old verbose syntax in vaeac and regresion

    @martinju
    martinju committed Oct 2, 2024
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  9. move everything to string verbose

    @martinju
    martinju committed Oct 2, 2024
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  10. playing around with cli progress

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

  1. more testing

    @martinju
    martinju committed Oct 3, 2024
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  2. more work

    @martinju
    martinju committed Oct 3, 2024
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  3. working OK for now

    @martinju
    martinju committed Oct 3, 2024
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  4. more work

    @martinju
    martinju committed Oct 3, 2024
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  5. separate regression done

    @martinju
    martinju committed Oct 3, 2024
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  6. also regression_surrogate done 

    vaeac + maybe messages/errors is now left
    @martinju
    martinju committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. fixed no testthat package?

    @martinju
    martinju committed Oct 4, 2024
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  2. consider myself done for now

    @martinju
    martinju committed Oct 4, 2024
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  3. vignettes

    @martinju
    martinju committed Oct 4, 2024
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  4. testfile updates

    @martinju
    martinju committed Oct 4, 2024
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  5. styler

    @martinju
    martinju committed Oct 4, 2024
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  6. lint and some checks

    @martinju
    martinju committed Oct 4, 2024
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  7. Merge branch 'verbose' into convergence

    @martinju
    martinju committed Oct 4, 2024
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  8. hoping to avoid the missing testthat package error on GHA

    @martinju
    martinju committed Oct 4, 2024
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Commits on Oct 5, 2024

  1. annabelles comments

    @martinju
    martinju committed Oct 5, 2024
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  2. update main vignette

    @martinju
    martinju committed Oct 5, 2024
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  3. rerun regression vignette

    @martinju
    martinju committed Oct 5, 2024
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  4. styler

    @martinju
    martinju committed Oct 5, 2024
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  5. clean out unused messages

    @martinju
    martinju committed Oct 5, 2024
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  6. minor bugfixing

    @martinju
    martinju committed Oct 5, 2024
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  7. man

    @martinju
    martinju committed Oct 5, 2024
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  8. tests

    @martinju
    martinju committed Oct 5, 2024
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  9. styler

    @martinju
    martinju committed Oct 5, 2024
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