[Bug]: flepiconfig Test Suite Currently Does Not Pass

[TimothyWillard]

Label

flepiconfig, quick issue

Priority Label

medium priority

Describe the bug/issue

The test suite for flepiconfig currently has two failures. Looks like this is a classic geoid vs subpop column naming issue. This is a blocker to integrating flepiconfig into our set of GitHub actions.

To Reproduce

To reproduce:

> getwd()
[1] "/Users/twillard/Desktop/GitHub/HopkinsIDD/flepiMoP/flepimop/R_packages/flepiconfig"
> devtools::test()
ℹ Testing flepiconfig

Attaching package: ‘testthat’

The following object is masked from ‘package:devtools’:

    test_file

✔ | F W  S  OK | Context
✖ | 1        0 | gen_npi
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-gen_npi.R:97:5): Interventions processing works
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., geoid = as.character(geoid))`: ℹ In argument: `geoid = as.character(geoid)`.
Caused by error:
! object 'geoid' not found
Backtrace:
     ▆
  1. ├─flepiconfig (local) generate_processed(...) at test-gen_npi.R:97:5
  2. │ └─flepiconfig:::load_geodata_file(filename = geodata_path) at test-gen_npi.R:13:5
  3. │   └─readr::read_csv(filename) %>% ... at flepiconfig/R/process_npi_list.R:25:5
  4. ├─dplyr::mutate(., geoid = as.character(geoid))
  5. ├─dplyr:::mutate.data.frame(., geoid = as.character(geoid))
  6. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │   ├─base::withCallingHandlers(...)
  8. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │     └─mask$eval_all_mutate(quo)
 10. │       └─dplyr (local) eval()
 11. └─base::.handleSimpleError(...)
 12.   └─dplyr (local) h(simpleError(msg, call))
 13.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✖ | 1        0 | print_config
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error ('test-print_config.R:73:5'): Config generation works
Error in `print_header(sim_name = "USA", sim_start_date = "2020-01-01",
    sim_end_date = "2021-08-07", dt = 0.25, nslots = 300, modeled_states = unique(interventions$USPS[!interventions$USPS %in%
        c("", "all") & !is.na(interventions$USPS)]), setup_name = "usa_inference_territories_statelevel",
    geodata = "geodata_territories_2019_statelevel.csv", mobility = "mobility_territories_2011-2015_statelevel.csv")`: unused arguments (dt = 0.25, modeled_states = unique(interventions$USPS[!interventions$USPS %in% c("", "all") & !is.na(interventions$USPS)]), geodata = "geodata_territories_2019_statelevel.csv", mobility = "mobility_territories_2011-2015_statelevel.csv")
Backtrace:
    ▆
 1. └─flepiconfig (local) generate_config() at test-print_config.R:73:5
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
── Failed tests ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error ('test-gen_npi.R:97:5'): Interventions processing works
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., geoid = as.character(geoid))`: ℹ In argument: `geoid = as.character(geoid)`.
Caused by error:
! object 'geoid' not found
Backtrace:
     ▆
  1. ├─flepiconfig (local) generate_processed(...) at test-gen_npi.R:97:5
  2. │ └─flepiconfig:::load_geodata_file(filename = geodata_path) at test-gen_npi.R:13:5
  3. │   └─readr::read_csv(filename) %>% ... at flepiconfig/R/process_npi_list.R:25:5
  4. ├─dplyr::mutate(., geoid = as.character(geoid))
  5. ├─dplyr:::mutate.data.frame(., geoid = as.character(geoid))
  6. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │   ├─base::withCallingHandlers(...)
  8. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │     └─mask$eval_all_mutate(quo)
 10. │       └─dplyr (local) eval()
 11. └─base::.handleSimpleError(...)
 12.   └─dplyr (local) h(simpleError(msg, call))
 13.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

Error ('test-print_config.R:73:5'): Config generation works
Error in `print_header(sim_name = "USA", sim_start_date = "2020-01-01",
    sim_end_date = "2021-08-07", dt = 0.25, nslots = 300, modeled_states = unique(interventions$USPS[!interventions$USPS %in%
        c("", "all") & !is.na(interventions$USPS)]), setup_name = "usa_inference_territories_statelevel",
    geodata = "geodata_territories_2019_statelevel.csv", mobility = "mobility_territories_2011-2015_statelevel.csv")`: unused arguments (dt = 0.25, modeled_states = unique(interventions$USPS[!interventions$USPS %in% c("", "all") & !is.na(interventions$USPS)]), geodata = "geodata_territories_2019_statelevel.csv", mobility = "mobility_territories_2011-2015_statelevel.csv")
Backtrace:
    ▆
 1. └─flepiconfig (local) generate_config() at test-print_config.R:73:5

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
Warning messages:
1: replacing previous import ‘foreach::when’ by ‘purrr::when’ when loading ‘flepicommon’
2: replacing previous import ‘foreach::accumulate’ by ‘purrr::accumulate’ when loading ‘flepicommon’
> q()
Save workspace image? [y/n/c]: n

Environment, if relevant

MacOS 14.6.1, R 4.3.3, Python 3.10.15, conda 24.5.0