From 2a6ab3f104a18873588c8e3f4f476729f85e3efa Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Fri, 5 Mar 2021 14:19:09 -0500 Subject: [PATCH 1/3] fix spelling errors --- .github/workflows/test_and_build.yml | 2 +- bin/generate_md_episodes.R | 2 +- bin/repo_check.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index 430088a..f4380fa 100644 --- 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,books,.bundle,_site,*.svg,.vendor" --quiet-level=2 -L "rouge,dropse,namd,hist" check_lesson_and_build_default: runs-on: ubuntu-latest diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R index 0b4c69e..d71e0bf 100644 --- 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 index 9bf5c59..4528f0e 100755 --- 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]) From bfce41257052a80ed4caabc5d050432ae4c51858 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Fri, 5 Mar 2021 14:25:43 -0500 Subject: [PATCH 2/3] renumber episodes to close gap --- _config.yml | 16 ++++++++-------- ...-snakemake-intro.md => 07-snakemake-intro.md} | 0 _episodes/{12-snakefiles.md => 08-snakefiles.md} | 0 _episodes/{13-wildcards.md => 09-wildcards.md} | 0 _episodes/{14-patterns.md => 10-patterns.md} | 0 ...nakemake-python.md => 11-snakemake-python.md} | 0 _episodes/{16-resources.md => 12-resources.md} | 0 _episodes/{17-cluster.md => 13-cluster.md} | 0 .../{18-final-notes.md => 14-final-notes.md} | 0 9 files changed, 8 insertions(+), 8 deletions(-) rename _episodes/{11-snakemake-intro.md => 07-snakemake-intro.md} (100%) rename _episodes/{12-snakefiles.md => 08-snakefiles.md} (100%) rename _episodes/{13-wildcards.md => 09-wildcards.md} (100%) rename _episodes/{14-patterns.md => 10-patterns.md} (100%) rename _episodes/{15-snakemake-python.md => 11-snakemake-python.md} (100%) rename _episodes/{16-resources.md => 12-resources.md} (100%) rename _episodes/{17-cluster.md => 13-cluster.md} (100%) rename _episodes/{18-final-notes.md => 14-final-notes.md} (100%) diff --git a/_config.yml b/_config.yml index 4ff9d06..0f8e7c9 100644 --- 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 b/_episodes/07-snakemake-intro.md similarity index 100% rename from _episodes/11-snakemake-intro.md rename to _episodes/07-snakemake-intro.md diff --git a/_episodes/12-snakefiles.md b/_episodes/08-snakefiles.md similarity index 100% rename from _episodes/12-snakefiles.md rename to _episodes/08-snakefiles.md diff --git a/_episodes/13-wildcards.md b/_episodes/09-wildcards.md similarity index 100% rename from _episodes/13-wildcards.md rename to _episodes/09-wildcards.md diff --git a/_episodes/14-patterns.md b/_episodes/10-patterns.md similarity index 100% rename from _episodes/14-patterns.md rename to _episodes/10-patterns.md diff --git a/_episodes/15-snakemake-python.md b/_episodes/11-snakemake-python.md similarity index 100% rename from _episodes/15-snakemake-python.md rename to _episodes/11-snakemake-python.md diff --git a/_episodes/16-resources.md b/_episodes/12-resources.md similarity index 100% rename from _episodes/16-resources.md rename to _episodes/12-resources.md diff --git a/_episodes/17-cluster.md b/_episodes/13-cluster.md similarity index 100% rename from _episodes/17-cluster.md rename to _episodes/13-cluster.md diff --git a/_episodes/18-final-notes.md b/_episodes/14-final-notes.md similarity index 100% rename from _episodes/18-final-notes.md rename to _episodes/14-final-notes.md From 8ab555af6eb18e3aa5b62ea41b95b81f44d1d41c Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Fri, 5 Mar 2021 14:33:14 -0500 Subject: [PATCH 3/3] only skip book texts --- .github/workflows/test_and_build.yml | 2 +- Makefile | 5 ++++- files/snakemake-lesson/books/LICENSE_TEXTS.md | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index f4380fa..1622f07 100644 --- 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,books,.bundle,_site,*.svg,.vendor" --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 index 35aa8ad..b17bd49 100644 --- 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/files/snakemake-lesson/books/LICENSE_TEXTS.md b/files/snakemake-lesson/books/LICENSE_TEXTS.md index e338a30..2b65b36 100644 --- 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.