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Merged
merged 102 commits into from
Jun 14, 2022
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4d0e44a
New file
kenmawer May 24, 2022
71425ee
Merge pull request #1 from kenmawer/km-test-df_mat_mul
kenmawer May 24, 2022
881be88
New test
kenmawer May 24, 2022
0f2fb31
Updated descriptor
kenmawer May 24, 2022
f5ab890
Updated test
kenmawer May 25, 2022
d3a8d9c
Merge pull request #2 from kenmawer/km-test-assign_arg_list
kenmawer May 25, 2022
05e688f
Merge branch 'cmu-delphi:main' into main
kenmawer May 25, 2022
2597b90
Template for new lag function.
kenmawer May 25, 2022
3457ee5
Replaced ahead with lags of negative numbers.
kenmawer May 25, 2022
a4ff33d
Merge pull request #3 from kenmawer/km-issue_22_unite
kenmawer May 25, 2022
93503d4
Documented changes.
kenmawer May 25, 2022
ea3a197
Merge pull request #4 from kenmawer/km-issue_22_unite
kenmawer May 25, 2022
139616b
Updates on code
kenmawer May 26, 2022
0168875
I still get an error
kenmawer May 26, 2022
5004176
Merge pull request #5 from kenmawer/km-issue_22_unite
kenmawer May 26, 2022
a62be17
Renamed a subclass.
kenmawer May 26, 2022
5527bcb
Merge pull request #6 from kenmawer/km-issue_22_unite
kenmawer May 26, 2022
beb7a37
Reall needs fixing as I somehow managed to break this.
kenmawer May 26, 2022
f3d182e
Fixed issue of "step" duplicating.
kenmawer May 26, 2022
e5aeaf1
Update
kenmawer May 26, 2022
7fa5163
Added epi_ahead
kenmawer May 27, 2022
e5e7737
Fixed epi_lag
kenmawer May 27, 2022
7912dd3
Fixed recipe
kenmawer May 27, 2022
492234b
Merge pull request #7 from kenmawer/km-issue_22_fix
kenmawer May 27, 2022
fe1d6fe
Pulled from origin main.
kenmawer May 27, 2022
6741d65
Updated changes and broken syntax.
kenmawer May 27, 2022
3df6009
Merge pull request #8 from kenmawer/km-issue_22_unite
kenmawer May 27, 2022
11f56e7
Copy-pasted internal
kenmawer May 27, 2022
82a885f
Updated recipe
kenmawer May 27, 2022
4996530
It's still working!
kenmawer May 27, 2022
1ace3d7
Updated main step funcction.
kenmawer May 27, 2022
f2220b2
Partially finished with one function.
kenmawer May 27, 2022
861f8cf
Refactored epi_lag
kenmawer May 30, 2022
894247d
Code that finally works.
kenmawer May 30, 2022
be6c421
Removed extra function.
kenmawer May 30, 2022
cbb4fe5
Merge pull request #9 from kenmawer/km-issue_22_unite_v2
kenmawer May 30, 2022
5d3546f
Added code stub for testing epi_shift_internal.
kenmawer May 30, 2022
f05ec0c
Note that having lag and ahead as negative values is odd behaviour.
kenmawer May 31, 2022
03a2b14
Added error checking
kenmawer May 31, 2022
6a43444
Merge pull request #10 from kenmawer/km-issue_22_tests
kenmawer May 31, 2022
67980e0
Updated library due to failing test.
kenmawer Jun 1, 2022
183e268
Merge pull request #11 from kenmawer/km-issue_22_tests
kenmawer Jun 1, 2022
a9beed5
Removed library loading.
kenmawer Jun 1, 2022
eb9771c
Re-added packages.
kenmawer Jun 1, 2022
6654a6c
Merge pull request #12 from kenmawer/km-issue_22_tests
kenmawer Jun 1, 2022
3001b69
Updated test as to not use covidcast and delphi.epidata.
kenmawer Jun 1, 2022
ca8e971
Merge pull request #13 from kenmawer/km-issue_22_tests
kenmawer Jun 1, 2022
500c158
Used specific libraries rather than tidymodels.
kenmawer Jun 1, 2022
1d14e9a
Merge pull request #14 from kenmawer/km-issue_22_tests
kenmawer Jun 1, 2022
ea9aff0
Fix error of packages not being found on GitHub.
kenmawer Jun 1, 2022
892562d
Merge pull request #15 from kenmawer/km-issue_22_tests
kenmawer Jun 1, 2022
bf141f4
Updated as install.packages causes errors on GitHub.
kenmawer Jun 2, 2022
844e4bd
Merge pull request #16 from kenmawer/km-issue_22_tests
kenmawer Jun 2, 2022
0f4f6fe
Changed format as to use :: rather than load packages.
kenmawer Jun 2, 2022
dd25021
Merge pull request #17 from kenmawer/km-issue_22_tests
kenmawer Jun 2, 2022
20f8bac
Updated description.
kenmawer Jun 2, 2022
da4b1ac
Merge pull request #18 from kenmawer/km-issue_22_tests
kenmawer Jun 2, 2022
1c5c1c0
pp function won't run, so that needs to be fixed.
kenmawer Jun 2, 2022
0233cd5
Merge pull request #19 from kenmawer/km-issue_23
kenmawer Jun 2, 2022
722815e
Put some work into it.
kenmawer Jun 2, 2022
4459f02
Updated description to be better.
kenmawer Jun 3, 2022
d00631f
Documented changes.
kenmawer Jun 3, 2022
877edb7
Merge pull request #20 from kenmawer/km-issue_27
kenmawer Jun 3, 2022
45a241c
Updated incorrect code.
kenmawer Jun 3, 2022
f229b46
Added testing template.
kenmawer Jun 3, 2022
e42dd5d
Fixed misplaced file
kenmawer Jun 3, 2022
e60abfd
Renamed misnamed test
kenmawer Jun 3, 2022
45c5ab6
Finished test
kenmawer Jun 3, 2022
0961ecd
Merge pull request #21 from kenmawer/km-issue_27
kenmawer Jun 3, 2022
6b7862f
Polished test.
kenmawer Jun 3, 2022
c2da965
Merge pull request #22 from kenmawer/km-issue_27
kenmawer Jun 3, 2022
e5ac2fb
New test added
kenmawer Jun 3, 2022
63b1bfc
Merge pull request #23 from kenmawer/km-test-grab_names
kenmawer Jun 3, 2022
11addec
Name replacement.
kenmawer Jun 6, 2022
338f277
Issue documented.
kenmawer Jun 6, 2022
0eff8e6
Merge pull request #24 from kenmawer/km-issue_27
kenmawer Jun 6, 2022
e373b49
Removed unnecessary export of step_epi_shift
kenmawer Jun 6, 2022
f29ae48
Made test names more specific.
kenmawer Jun 6, 2022
54ca1f5
Changed name to step_epi_naomit
kenmawer Jun 6, 2022
878eb71
Merge pull request #25 from kenmawer/km-issue_27
kenmawer Jun 6, 2022
00f3755
Merged namespace
kenmawer Jun 6, 2022
fce1153
Merge pull request #26 from kenmawer/km-issue_22_v3
kenmawer Jun 6, 2022
3326893
Fixed butchered NAMESPACE.
kenmawer Jun 6, 2022
53425e8
Merge pull request #27 from kenmawer/km-issue_22_v3
kenmawer Jun 6, 2022
11b8a95
Deleted placeholder I made when creating file.
kenmawer Jun 6, 2022
3c0bd3c
Merge pull request #28 from kenmawer/km-test-grab_names
kenmawer Jun 6, 2022
fa1a476
Added assign_arg_list test for testing.
kenmawer Jun 6, 2022
efc4e06
Updated df_mat_mul
kenmawer Jun 6, 2022
c4948a5
Merge pull request #29 from kenmawer/km-pr_34_rectify_tests
kenmawer Jun 6, 2022
28ae5d3
Added test for checking for a mismatched test.
kenmawer Jun 7, 2022
d73d9e2
Added comments on why we need to do certain tests that way.
kenmawer Jun 7, 2022
0dbfc2e
Merge pull request #30 from kenmawer/km-pr_34_rectify_tests
kenmawer Jun 7, 2022
f272839
Committed changes that should be updated.
kenmawer Jun 7, 2022
6fa4a5f
Removed randomness.
kenmawer Jun 7, 2022
5464bd1
Merge pull request #31 from kenmawer/km-pr_34_rectify_tests
kenmawer Jun 7, 2022
910dd19
Merge branch 'main' into main
kenmawer Jun 7, 2022
6092075
add codeowners
dajmcdon Jun 7, 2022
168e91a
Rewrite main history to earlier
dajmcdon Jun 8, 2022
a68e901
Merge pull request #44 from cmu-delphi/working-main
dajmcdon Jun 8, 2022
18cc390
Add frosting to CI
dshemetov Jun 13, 2022
7da1d5b
Fix subtle but evil as_tibble.epi_df bug, fix tests
dshemetov Jun 14, 2022
1ea32d2
Merge remote-tracking branch 'origin/main' into ds/frosting-ci
dshemetov Jun 14, 2022
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1 change: 1 addition & 0 deletions .github/CODEOWNERS
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
* @dajmcdon
4 changes: 2 additions & 2 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
on:
push:
branches: [main, master]
branches: [main, frosting]
pull_request:
branches: [main, master]
branches: [main, frosting]

name: R-CMD-check

Expand Down
3 changes: 3 additions & 0 deletions R/epi_recipe.R
Original file line number Diff line number Diff line change
Expand Up @@ -408,5 +408,8 @@ kill_levels <- function(x, keys) {
#' @export
as_tibble.epi_df <- function(x, ...) {
# so that downstream calls to as_tibble don't clobber our metadata
# this avoids infinite recursion inside dplyr::dplyr_col_modify
# TODO: this needs a different approach, long-term
class(x) <- class(x)[class(x) != "grouped_df"]
return(x)
}
2 changes: 0 additions & 2 deletions tests/testthat/test-frosting.R
Original file line number Diff line number Diff line change
Expand Up @@ -36,5 +36,3 @@ test_that("prediction works without any postprocessor", {
expect_equal(tail(p$time_value, 1), as.Date("2021-12-31"))
expect_equal(unique(p$geo_value), c("ak", "ca", "ny"))
})


8 changes: 2 additions & 6 deletions tests/testthat/test-layer_predict.R
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ test_that("predict layer works alone", {
expect_equal(ncol(p), 3L)
expect_s3_class(p, "epi_df")
expect_equal(nrow(p), 108L)
expect_named(p, c("geo_value", "time_value", ".pred"))
expect_named(p, c("time_value", "geo_value", ".pred"))

})

Expand All @@ -32,9 +32,5 @@ test_that("prediction with interval works", {
expect_equal(ncol(p), 4L)
expect_s3_class(p, "epi_df")
expect_equal(nrow(p), 108L)
expect_named(p, c("geo_value", "time_value", ".pred_lower", ".pred_upper"))



expect_named(p, c("time_value", "geo_value", ".pred_lower", ".pred_upper"))
})