hpc-carpentry · mikerenfro · Mar 5, 2021 · Mar 5, 2021 · Mar 5, 2021 · Mar 5, 2021
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
@@ -20,7 +20,7 @@ jobs:
         pip3 install codespell
     - name: Check spelling
       run: |
-        codespell --skip="assets,*.svg,bin" --quiet-level=2  -L "rouge,dropse,namd,hist"
+        codespell --skip="assets,.bundle,_site,*.svg,*.txt,.vendor" --quiet-level=2  -L "dropse,hart,hist,namd,rouge"
 
   check_lesson_and_build_default:
     runs-on: ubuntu-latest

diff --git a/Makefile b/Makefile
@@ -97,7 +97,7 @@ workshop-check :
 ## III. Commands specific to lesson websites
 ## =================================================
 
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme spellcheck
 
 # RMarkdown files
 RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
@@ -137,6 +137,9 @@ lesson-check : lesson-fixme
 lesson-check-all :
 	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
 
+spellcheck:
+	codespell --skip="assets,.bundle,_site,*.svg,*.txt,.vendor" --quiet-level=2  -L "dropse,hart,hist,namd,rouge"
+
 ## * unittest         : run unit tests on checking tools
 unittest :
 	@${PYTHON} bin/test_lesson_check.py

diff --git a/_config.yml b/_config.yml
@@ -25,14 +25,14 @@ episode_order:
   - 04-dicts
   - 05-functions
   - 06-parallel
-  - 11-snakemake-intro
-  - 12-snakefiles
-  - 13-wildcards
-  - 14-patterns
-  - 15-snakemake-python
-  - 16-resources
-  - 17-cluster
-  - 18-final-notes
+  - 07-snakemake-intro
+  - 08-snakefiles
+  - 09-wildcards
+  - 10-patterns
+  - 11-snakemake-python
+  - 12-resources
+  - 13-cluster
+  - 14-final-notes
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).

diff --git a/_episodes/11-snakemake-intro.md → _episodes/07-snakemake-intro.md b/_episodes/11-snakemake-intro.md → _episodes/07-snakemake-intro.md
diff --git a/_episodes/12-snakefiles.md → _episodes/08-snakefiles.md b/_episodes/12-snakefiles.md → _episodes/08-snakefiles.md
diff --git a/_episodes/13-wildcards.md → _episodes/09-wildcards.md b/_episodes/13-wildcards.md → _episodes/09-wildcards.md
diff --git a/_episodes/14-patterns.md → _episodes/10-patterns.md b/_episodes/14-patterns.md → _episodes/10-patterns.md
diff --git a/_episodes/15-snakemake-python.md → _episodes/11-snakemake-python.md b/_episodes/15-snakemake-python.md → _episodes/11-snakemake-python.md
diff --git a/_episodes/16-resources.md → _episodes/12-resources.md b/_episodes/16-resources.md → _episodes/12-resources.md
diff --git a/_episodes/17-cluster.md → _episodes/13-cluster.md b/_episodes/17-cluster.md → _episodes/13-cluster.md
diff --git a/_episodes/18-final-notes.md → _episodes/14-final-notes.md b/_episodes/18-final-notes.md → _episodes/14-final-notes.md
diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
@@ -13,7 +13,7 @@ generate_md_episodes <- function() {
   required_pkgs <- unique(c(
     ## Packages for episodes
     requirements:::req_dir("_episodes_rmd"),
-    ## Pacakges for tools
+    ## Packages for tools
     requirements:::req_dir("bin")
   ))
 

diff --git a/bin/repo_check.py b/bin/repo_check.py
@@ -145,7 +145,7 @@ def check_labels(reporter, repo_url):
     for name in sorted(overlap):
         reporter.check(EXPECTED[name].lower() == actual[name].lower(),
                        None,
-                       'Color mis-match for label {0} in {1}: expected {2}, found {3}',
+                       'Color mismatch for label {0} in {1}: expected {2}, found {3}',
                        name, repo_url, EXPECTED[name], actual[name])
 
 

diff --git a/files/snakemake-lesson/books/LICENSE_TEXTS.md b/files/snakemake-lesson/books/LICENSE_TEXTS.md
@@ -220,7 +220,7 @@ opportunities to fix the problem.
 1.F.4.  Except for the limited right of replacement or refund set forth
 in paragraph 1.F.3, this work is provided to you 'AS-IS' WITH NO OTHER
 WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO
-WARRANTIES OF MERCHANTIBILITY OR FITNESS FOR ANY PURPOSE.
+WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PURPOSE.
 
 1.F.5.  Some states do not allow disclaimers of certain implied
 warranties or the exclusion or limitation of certain types of damages.