russHyde

# An issue with the lintr pre-commit hook is that packages are not fully loaded
# prior to linting, so you can get lots of object-usage lints when an object from
# your dev packages namespace is used.
#
# The following ensures your dev package is loaded before linting the changed
# files within it. It requires {lintr} to be installed in your dev environment.
# This differs from most pre-commit hooks (which usually run in a hook-specific
# renv environment)
#
# All available hooks: https://pre-commit.com/hooks.html

russHyde

[alias]                                                                                                                                                                                                            
	biff = "!f() { \                                                                                                                                                                                           
  # all changes since branch/hash $2 separated from branch/hash $1 \                                                                                                                                               
  old=${1:-main}; new=${2:-HEAD}; base=$(git merge-base ${old} ${new}); \                                                                                                                                          
  git diff ${base} ${new}; \                                                                                                                                                           

russHyde

# Run the test file multiple times, break when it fails to pass
TEST_PATTERN="xxx"
for i in {1..10}; do
  npx jest ${TEST_PATTERN} --silent --runInBand;
  if [[ "$?" != 0 ]]; then echo "Failed after $i attempts" && break; fi;
done

russHyde

# compare the object-usage lints obtained before/after a given PR
# the PR is always compared against master

library(magrittr)
library(dplyr)
library(purrr)
library(tibble)

# In lintr directory

russHyde

# My rscript template assumes all command line arguments are in option-form
# `Rscript <script_name> --logical_option --some_flag some_value --some_other_flag some_other_value`
#
# When you want to pass a variable number of files into your script, the option-form doesn't work well
# so it's better to use trailing arguments
# `Rscript <script_name> --some_option --flag with_value trailing1 trailing2 trailing3 ...`
#
# optparse works well in the latter case:

library(magrittr)

russHyde

# My title

```{r}
tables <- list(a = iris[1:10, ], b = iris[11:20, ])
```

```{r}
#' When makinig an Rmarkdown, this function will print all the data.frames
#' in a list
#'

russHyde

linters: with_defaults(
  # By using the `with_defaults` function in .lintr to set up the linters for your package / project,
  # you are telling {lintr}: start with this named-list of linters (given in the argument `default`,
  # see below) and modify any that I specify.
  # Here, that means you want to use the list `default_linters`, but modify that list.
  #
  # See `names(lintr::default_linters)` for the contents of the `default_linters` used here.
  #
  # You could alternatively
  #

russHyde

#!/usr/bin/env Rscript

###############################################################################

# Package names for non-test dependencies
pkgs <- c(
  # CRAN
  "magrittr",
  "optparse",
  # Bioconductor