From: Greg Wilson <gvwilson@third-bit.com>
Date: Sat, 25 Jun 2016 14:24:34 +0000 (-0400)
Subject: Only cleaning intermediate R files on demand.
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/5217736aeb4b2e9f76a8cecf4d127a094a901281

Only cleaning intermediate R files on demand.

1.  Splitting commands to clean intermediate R files into separate target.  These files must be committed to the repo, so they shouldn't be deleted under normal circumstances.
2.  Modifying intermediate file generation to create fig/rmd-* rather than fig/swc-rmd-*, since this template is used by other carpentries (not just SWC).
---

diff --git a/Makefile b/Makefile
index c8011dd..7b1b1b9 100644
--- a/Makefile
+++ b/Makefile
@@ -35,8 +35,11 @@ clean :
 	@find . -name .DS_Store -exec rm {} \;
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
+
+## clean-rmd      : clean intermediate R files (that need to be committed to the repo).
+clear-rmd :
 	@rm -rf ${RMD_DST}
-	@rm -rf fig/swc-rmd-*
+	@rm -rf fig/rmd-*
 
 ## ----------------------------------------
 ## Commands specific to workshop websites.
diff --git a/bin/chunk-options.R b/bin/chunk-options.R
index 1890d32..5836973 100644
--- a/bin/chunk-options.R
+++ b/bin/chunk-options.R
@@ -8,18 +8,20 @@ library("knitr")
 
 fix_fig_path <- function(pth) file.path("..", pth)
 
-## We use the swc-rmd- prefix for the figures generated by the lssons
-## so they can be easily identified and deleted by `make clean`.  The
+## We use the rmd- prefix for the figures generated by the lssons so
+## they can be easily identified and deleted by `make clean-rmd`.  The
 ## working directory when the lessons are generated is the root so the
 ## figures need to be saved in fig/, but when the site is generated,
 ## the episodes will be one level down. We fix the path using the
 ## `fig.process` option.
+
 opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
-               fig.align = "center", fig.path = "fig/swc-rmd-",
+               fig.align = "center", fig.path = "fig/rmd-",
                fig.process = fix_fig_path)
 
 # The hooks below add html tags to the code chunks and their output so that they
 # are properly formatted when the site is built.
+
 hook_in <- function(x, options) {
   stringr::str_c("\n\n~~~\n",
                  paste0(x, collapse="\n"),