build: Add a GHA Linter #79
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| @@ -4,3 +4,5 @@ | |||
| .git | |||
| .github | |||
| misc | |||
| ^\.github$ | |||
| .lintr | |||
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lintr is the R linting library and the file .lintr is its configuration.
| @@ -0,0 +1,32 @@ | |||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |||
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This file is autogenerated by using the tool usethis::use_github_action("lint-project")
| linters: linters_with_defaults( | ||
| line_length_linter(120), | ||
| commented_code_linter = NULL, | ||
| object_usage_linter = NULL |
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This last one is useful, but there is a bug in the way lintr works where it views internal functions and references to them as undeclared globals. I have too many internal functions to ignore each line, so disabling this for now. We could circumvent this by installing the package before linting, but that would requiring installing seurat and hdf5r which takes forever to install.
See here for more information
| executable_path = NULL, | ||
| force = FALSE | ||
| ) { | ||
| h5path, |
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code was auto formatted with styler
| cmd_msg <- sprintf('running command: "%s"', paste(c(executable_path, args), collapse=" ")) | ||
| logMsg(cmd_msg) | ||
| cmd_msg <- sprintf('running command: "%s"', paste(c(executable_path, args), collapse = " ")) | ||
| log_msg(cmd_msg) |
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updated the name to log_msg to satisfy the linter.
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| #' validation error with link to 10x support | ||
| #' @noRd | ||
| validation_err <- function(msg, name) { | ||
| sprintf("\nIt looks like the formatting of your %s does not match the required formatting for LoupeR. For further information, please see the documentation: 10xgen.com/louper\n\n%s", name, msg) | ||
| sprintf( | ||
| paste( |
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Use paste to fix lines that are too long
Used
stylerto auto format the code. Usedlintrto catch linting errors. No code change should follow.Fixes #77