danchaltiel/autoimport

A toolbox to automatically generate @importFrom roxygen tags from R files.

autoimport's Issues

"never remove" list

A list of terms that should never get removed, like cli::qty for instance

`autoimport()` tries to include R6 public methods as `@importFrom`

Current situation

I've run autoimport() on the code in https://github.com/mlverse/tabnet
and I get some unexpected insertion of R6 public methods as Roxygen #' @importFrom

Before autoimport()

• the following code chunk uses view and transpose as public methods of the torch R6 object rho
  https://github.com/mlverse/tabnet/blob/7186ba6048a6818283d05fb86c2af6ead862173b/R/sparsemax.R#L2-L10

• idem for gather
  https://github.com/mlverse/tabnet/blob/7186ba6048a6818283d05fb86c2af6ead862173b/R/sparsemax.R#L19

• idem for clone and squeeze
  https://github.com/mlverse/tabnet/blob/7186ba6048a6818283d05fb86c2af6ead862173b/R/sparsemax.R#L41-L44

After autoimport()

- autoimport() add erroneously import from functions from exotic libraries, messing up the NAMESPACE file and DESCRIPTION file

Reproducible example

# git clone https://github.com/mlverse/tabnet
# cd tabnet
library(autoimport)
library(tidyverse)
autoimport(files = "R/sparsemax.R")

Fails if any file is empty

Either empty .R file or empty NAMESPACE

`autoimport()` is doubling the very first line of a file, the function name when function has no Roxygen skeleton

Current situation

Being inspired by the presentation at RR_2023 Avignon, I've run autoimport() on the code in https://github.com/mlverse/tabnet
I'm impressed by the user interface but I get the following issue on few files where the first line of code in the file is the function definition (i.e. function without Roxygen skeleton )

Before autoimport()

file R/pretraining.R is starting with the following lines :

train_batch_un <- function(network, optimizer, batch, config) {
  # forward pass

After autoimport()

file R/pretraining.R is starting with the following lines :

train_batch_un <- function(network, optimizer, batch, config) {
#' @importFrom torch nn_utils_clip_grad_norm_
train_batch_un <- function(network, optimizer, batch, config) {
  # forward pass

where we can see the function definition line is doubled around the Roxygen @importFrom statement

see https://github.com/mlverse/tabnet/blob/9890314421526b2244433ea1f168078fd8feb447/R/dials.R#L1-L3
see https://github.com/mlverse/tabnet/blob/9890314421526b2244433ea1f168078fd8feb447/R/package.R#L1-L3
see https://github.com/mlverse/tabnet/blob/9890314421526b2244433ea1f168078fd8feb447/R/pretraining.R#L1-L3

Reproducible example

# git clone https://github.com/mlverse/tabnet
# cd tabnet
library(autoimport)
autoimport(files = "R/dials.R")
#> Error: './NAMESPACE' does not exist in current working directory ('/tmp/RtmpXgZklI/reprex-301dcf3b5c6d89-pure-tayra').

^{Created on 2023-06-25 with reprex v2.0.2}

Session info

``` r R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices datasets utils methods base

other attached packages:
[1] tabnet_0.4.0.9000 testthat_3.1.9 shiny_1.7.4 bit_4.0.5 autoimport_0.0.1.9000
[6] recipes_1.0.6 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
[11] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[16] tidyverse_2.0.0 data.tree_1.0.0 data.table_1.14.8

loaded via a namespace (and not attached):
[1] remotes_2.4.2 rlang_1.1.1 magrittr_2.0.3 compiler_4.3.0 callr_3.7.3 vctrs_0.6.3
[7] profvis_0.3.8 pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1 backports_1.4.1 ellipsis_0.3.2
[13] utf8_1.2.3 promises_1.2.0.1 rmarkdown_2.22 prodlim_2023.03.31 sessioninfo_1.2.2 tzdb_0.4.0
[19] ps_1.7.5 torch_0.10.0 reprex_2.0.2 xfun_0.39 cachem_1.0.8 progress_1.2.2
[25] later_1.3.1 parallel_4.3.0 prettyunits_1.1.1 R6_2.5.1 stringi_1.7.12 parallelly_1.36.0
[31] pkgload_1.3.2 rpart_4.1.19 brio_1.1.3 Rcpp_1.0.10 knitr_1.43 future.apply_1.11.0
[37] usethis_2.2.1 httpuv_1.6.11 Matrix_1.5-4.1 splines_4.3.0 nnet_7.3-19 timechange_0.2.0
[43] tidyselect_1.2.0 yaml_2.3.7 rstudioapi_0.14 timeDate_4022.108 codetools_0.2-19 miniUI_0.1.1.1
[49] processx_3.8.1 listenv_0.9.0 pkgbuild_1.4.1 lattice_0.21-8 withr_2.5.0 evaluate_0.21
[55] desc_1.4.2 future_1.32.0 survival_3.5-5 urlchecker_1.0.1 diffviewer_0.1.1 pillar_1.9.0
[61] checkmate_2.2.0 generics_0.1.3 rprojroot_2.0.3 hms_1.1.3 munsell_0.5.0 scales_1.2.1
[67] coro_1.0.3 globals_0.16.2 xtable_1.8-4 bspm_0.5.1 class_7.3-22 glue_1.6.2
[73] clipr_0.8.0 tools_4.3.0 gower_1.0.1 fs_1.6.2 grid_4.3.0 ipred_0.9-14
[79] devtools_2.4.5 colorspace_2.1-0 cli_3.6.1 fansi_1.0.4 lava_1.7.2.1 gtable_0.3.3
[85] digest_0.6.31 htmlwidgets_1.6.2 memoise_2.0.1 htmltools_0.5.5 lifecycle_1.0.3 hardhat_1.3.0
[91] mime_0.12 bit64_4.0.5 MASS_7.3-60 ```

bug

Try with crosstable with this NAMESPACE file

# Generated by roxygen2: do not edit by hand

S3method(as_flextable,crosstable)
S3method(as_gt,crosstable)
S3method(as_gt,default)
S3method(compact,crosstable)
S3method(compact,data.frame)
S3method(compact,default)
S3method(ct_compact,crosstable)
S3method(ct_compact,data.frame)
S3method(ct_compact,default)
S3method(t,crosstable)
export("%>%")
export(N)
export(af)
export(all_of)
export(any_of)
export(apply_labels)
export(as_flextable)
export(as_gt)
export(as_workbook)
export(body_add_crosstable)
export(body_add_crosstable_footnote)
export(body_add_crosstable_list)
export(body_add_figure_legend)
export(body_add_flextable_list)
export(body_add_gg2)
export(body_add_glued)
export(body_add_img2)
export(body_add_list)
export(body_add_list_item)
export(body_add_normal)
export(body_add_table_legend)
export(body_add_table_list)
export(body_add_title)
export(body_replace_text_at_bkms)
export(clean_names_with_labels)
export(compact)
export(confint_numeric)
export(contains)
export(copy_label_from)
export(cross_summary)
export(cross_to_flextable)
export(crosstable)
export(crosstable_effect_args)
export(crosstable_options)
export(crosstable_peek_options)
export(crosstable_reset_options)
export(crosstable_test_args)
export(ct_compact)
export(ctf)
export(diff_mean_auto)
export(diff_mean_boot)
export(diff_mean_student)
export(diff_median)
export(diff_median_boot)
export(display_effect)
export(display_test)
export(docx_bookmarks2)
export(effect_odds_ratio)
export(effect_relative_risk)
export(effect_risk_difference)
export(effect_survival_coxph)
export(ends_with)
export(everything)
export(format_fixed)
export(generate_autofit_macro)
export(get_label)
export(get_percent_pattern)
export(import_labels)
export(is.compacted_crosstable)
export(is.crosstable)
export(is.multiby_crosstable)
export(is.transposed_crosstable)
export(matches)
export(meanCI)
export(meansd)
export(mediqr)
export(minmax)
export(moystd)
export(na)
export(narm)
export(nna)
export(peek)
export(pivot_crosstable)
export(plim)
export(remove_label)
export(remove_labels)
export(rename_dataframe_with_labels)
export(rename_with_labels)
export(save_labels)
export(set_label)
export(starts_with)
export(test_correlation_auto)
export(test_summarize_auto)
export(test_summarize_linear_contrasts)
export(test_survival_logrank)
export(test_tabular_auto)
export(to_flextable)
export(transpose_crosstable)
export(write_and_open)
importFrom(checkmate,assert)
importFrom(checkmate,assert_character)
importFrom(dplyr,recode)
importFrom(dplyr,rename)
importFrom(dplyr,summarise)
importFrom(flextable,hline_top)
importFrom(flextable,set_header_df)
importFrom(flextable,set_header_labels)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
importFrom(methods,formalArgs)
importFrom(officer,body_add_fpar)
importFrom(officer,body_add_img)
importFrom(purrr,safely)
importFrom(purrr,walk)
importFrom(rlang,":=")
importFrom(rlang,as_function)
importFrom(rlang,as_string)
importFrom(rlang,is_named)
importFrom(rlang,is_null)
importFrom(stats,cor.test)
importFrom(stats,fisher.test)
importFrom(stats,glm)
importFrom(stats,kruskal.test)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stringr,str_starts)
importFrom(stringr,str_subset)
importFrom(stringr,str_wrap)
importFrom(tibble,add_row)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tidyr,unite)
importFrom(tidyr,unpack)
importFrom(utils,browseURL)

TODO:

• warning bizarre,
• align vient de flextable mais n'est pas détecté,
• @importFrom error devrait donner une erreur

autoimport removes trailing comments

For instance, try this code:

f = function(){
  2
}

#dummy function
# don't remove me please

`autoimport()` unexpectidly removes some required `#' @importFrom `

Current situation

I've run autoimport() on the code in https://github.com/mlverse/tabnet
and I get some unexpected removal of existing and required Roxygen #' @importFrom

Before autoimport()

• file R/plot.R includes the following lines where importFrom in line 20 is used in line 45 of code:
  https://github.com/mlverse/tabnet/blob/7186ba6048a6818283d05fb86c2af6ead862173b/R/plot.R#L20-L45

• file R/parsnip.R includes the following lines where importFrom in line 302 is used in line 303 of the code:
  https://github.com/mlverse/tabnet/blob/7186ba6048a6818283d05fb86c2af6ead862173b/R/parsnip.R#L300-L307

After autoimport()

• file R/plot.R is missing the #' @importFrom rlang .data
  

• file R/parsnip.R is missing the #' @importFrom stats update
  

Reproducible example

# git clone https://github.com/mlverse/tabnet
# cd tabnet
library(autoimport)
library(tidyverse)
autoimport(files = "R/plot.R")
autoimport(files = "R/parsnip.R")

autoimport() is missing some extraction of explicit function in the code

Current situation
Being very inspired by the presentation at RR_2023 Avignon, I've run autoimport() on the code in https://github.com/mlverse/tabnet
I'm impressed by the user interface but the parsing is missing some explicit ::() statements in the code :

missing @ImportFrom have been manually added in a specific commit and can be seen in few locations like :

• mlverse/tabnet@3ec6b07#diff-4e36c4149b4e2837f4fef39996041c6f5e75ecade215313b3fa35bea595ba162R398
• mlverse/tabnet@3ec6b07#diff-1e36bd726e25b876564d0c896324fc80c919576e022f550168f4fbd57c265249R35
• mlverse/tabnet@3ec6b07#diff-1e36bd726e25b876564d0c896324fc80c919576e022f550168f4fbd57c265249R489
• mlverse/tabnet@3ec6b07#diff-1e36bd726e25b876564d0c896324fc80c919576e022f550168f4fbd57c265249R566

Reproducible example

# git clone https://github.com/mlverse/tabnet
# cd tabnet
library(autoimport)
autoimport(files = "R/tab-network.R")