Merge pull request #431 from cmu-delphi/ds/r6-clean

wip feat: replace R6 `epi_archive` with S3 implementation

DESCRIPTION

@@ -39,7 +39,6 @@ Imports:
     lubridate,
     magrittr,
     purrr,
-    R6,
     rlang,
     slider,
     tibble,
@@ -50,12 +49,12 @@ Imports:
     vctrs
 Suggests:
     covidcast,
+    devtools,
     epidatr,
     knitr,
     outbreaks,
     rmarkdown,
     testthat (>= 3.1.5),
-    waldo (>= 0.3.1),
     withr
 VignetteBuilder:
     knitr

NAMESPACE

@@ -9,10 +9,14 @@ S3method(as_epi_df,tbl_ts)
 S3method(as_tibble,epi_df)
 S3method(as_tsibble,epi_df)
 S3method(autoplot,epi_df)
+S3method(clone,epi_archive)
+S3method(clone,grouped_epi_archive)
 S3method(dplyr_col_modify,col_modify_recorder_df)
 S3method(dplyr_col_modify,epi_df)
 S3method(dplyr_reconstruct,epi_df)
 S3method(dplyr_row_slice,epi_df)
+S3method(epix_slide,epi_archive)
+S3method(epix_slide,grouped_epi_archive)
 S3method(epix_truncate_versions_after,epi_archive)
 S3method(epix_truncate_versions_after,grouped_epi_archive)
 S3method(group_by,epi_archive)
@@ -27,7 +31,9 @@ S3method(key_colnames,epi_archive)
 S3method(key_colnames,epi_df)
 S3method(next_after,Date)
 S3method(next_after,integer)
+S3method(print,epi_archive)
 S3method(print,epi_df)
+S3method(print,grouped_epi_archive)
 S3method(select,epi_df)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
@@ -40,37 +46,38 @@ export(as_epi_archive)
 export(as_epi_df)
 export(as_tsibble)
 export(autoplot)
+export(clone)
 export(detect_outlr)
 export(detect_outlr_rm)
 export(detect_outlr_stl)
-export(epi_archive)
 export(epi_cor)
 export(epi_slide)
 export(epi_slide_mean)
 export(epi_slide_opt)
 export(epi_slide_sum)
 export(epix_as_of)
+export(epix_fill_through_version)
 export(epix_merge)
 export(epix_slide)
 export(epix_truncate_versions_after)
 export(filter)
 export(group_by)
 export(group_modify)
 export(growth_rate)
-export(is_epi_archive)
 export(is_epi_df)
 export(is_grouped_epi_archive)
 export(key_colnames)
 export(max_version_with_row_in)
 export(mutate)
+export(new_epi_archive)
 export(new_epi_df)
 export(next_after)
 export(relocate)
 export(rename)
 export(slice)
 export(ungroup)
 export(unnest)
-importFrom(R6,R6Class)
+export(validate_epi_archive)
 importFrom(checkmate,anyInfinite)
 importFrom(checkmate,anyMissing)
 importFrom(checkmate,assert)
@@ -86,12 +93,16 @@ importFrom(checkmate,assert_scalar)
 importFrom(checkmate,checkInt)
 importFrom(checkmate,check_atomic)
 importFrom(checkmate,check_data_frame)
+importFrom(checkmate,check_names)
+importFrom(checkmate,expect_class)
 importFrom(checkmate,test_set_equal)
 importFrom(checkmate,test_subset)
 importFrom(checkmate,vname)
+importFrom(cli,cat_line)
 importFrom(cli,cli_abort)
-importFrom(cli,cli_inform)
+importFrom(cli,cli_vec)
 importFrom(cli,cli_warn)
+importFrom(cli,format_message)
 importFrom(data.table,":=")
 importFrom(data.table,address)
 importFrom(data.table,as.data.table)
@@ -111,12 +122,15 @@ importFrom(dplyr,bind_rows)
 importFrom(dplyr,dplyr_col_modify)
 importFrom(dplyr,dplyr_reconstruct)
 importFrom(dplyr,dplyr_row_slice)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_drop_default)
 importFrom(dplyr,group_modify)
 importFrom(dplyr,group_vars)
 importFrom(dplyr,groups)
+importFrom(dplyr,if_all)
+importFrom(dplyr,if_any)
 importFrom(dplyr,mutate)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
@@ -133,12 +147,14 @@ importFrom(purrr,map)
 importFrom(purrr,map_lgl)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
+importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,arg_match)
 importFrom(rlang,as_label)
 importFrom(rlang,caller_arg)
 importFrom(rlang,caller_env)
+importFrom(rlang,check_dots_empty)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,env)

NEWS.md

@@ -32,6 +32,15 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 ## Breaking changes
 
 - Switched `epi_df`'s `other_keys` default from `NULL` to `character(0)`; PR #390
+- Refactored `epi_archive` to use S3 instead of R6 for its object model. The
+  functionality stay the same, but it will break the member function interface.
+  For migration, you can usually just convert `epi_archive$merge(...)` to
+  `epi_archive <- epi_archive %>% epix_merge(...)` (and the same for
+  `fill_through_version` and `truncate_after_version`) and
+  `epi_archive$slide(...)` to `epi_archive %>% epix_slide(...)` (and the same
+  for `as_of`, `group_by`, `slide`, etc.) (#340). In some limited situations,
+  such as if you have a helper function that calls `epi_archive$merge` etc. on
+  one of its arguments, then you may need to more carefully refactor them.
 
 # epiprocess 0.7.0