Merge pull request swcarpentry#323 from swcarpentry/fix-ref-links

[fix swcarpentry#322] Fix reference links and upgrade to latest version of styles
tanash1983 · Jul 13, 2020 · 97c367b · 97c367b
2 parents e4ff6d4 + 5f31492
commit 97c367b
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diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,25 @@
+root = true
+
+[*]
+charset = utf-8
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+indent_size = 2
+indent_style = space
+max_line_length = 100  # Please keep this in sync with bin/lesson_check.py!
+
+[*.r]
+max_line_length = 80
+
+[*.py]
+indent_size = 4
+indent_style = space
+max_line_length = 79
+
+[*.sh]
+end_of_line = lf
+
+[Makefile]
+indent_style = tab
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -0,0 +1,2 @@
+github: [carpentries, swcarpentry, datacarpentry, librarycarpentry]
+custom: ["https://carpentries.wedid.it"]
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,9 +1,21 @@
-Please delete the text below before submitting your contribution. 
+<details>
+<summary><strong>Instructions</strong></summary>
 
----
+Thanks for contributing! :heart:
 
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+If this contribution is for instructor training, please email the link to this contribution to
+checkout@carpentries.org so we can record your progress. You've completed your contribution
+step for instructor checkout by submitting this contribution!
 
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
+If this issue is about a specific episode within a lesson, please provide its link or filename.
 
----
+Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
+respond to your contribution. Although not all contributions can be incorporated into the lesson
+materials, we appreciate your time and effort to improve the curriculum. If you have any questions
+about the lesson maintenance process or would like to volunteer your time as a contribution
+reviewer, please contact The Carpentries Team at team@carpentries.org.
+
+You may delete these instructions from your comment.
+
+\- The Carpentries
+</details>
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,9 +1,19 @@
-Please delete the text below before submitting your contribution. 
+<details>
+<summary><strong>Instructions</strong></summary>
 
----
+Thanks for contributing! :heart:
 
-Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+If this contribution is for instructor training, please email the link to this contribution to
+checkout@carpentries.org so we can record your progress. You've completed your contribution
+step for instructor checkout by submitting this contribution!
 
-Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  
+Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
+respond to your contribution. Although not all contributions can be incorporated into the lesson
+materials, we appreciate your time and effort to improve the curriculum. If you have any questions
+about the lesson maintenance process or would like to volunteer your time as a contribution
+reviewer, please contact The Carpentries Team at team@carpentries.org.
 
----
+You may delete these instructions from your comment.
+
+\- The Carpentries
+</details>
diff --git a/.gitignore b/.gitignore
@@ -3,9 +3,14 @@
 .DS_Store
 .ipynb_checkpoints
 .sass-cache
+.jekyll-cache/
 __pycache__
 _site
 .Rproj.user
 .Rhistory
 .RData
-
+.bundle/
+.vendor/
+.docker-vendor/
+Gemfile.lock
+.*history
diff --git a/Gemfile b/Gemfile
@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Synchronize with https://pages.github.com/versions
+ruby '>=2.5.8'
+
+gem 'github-pages', group: :jekyll_plugins
diff --git a/LICENSE.md b/LICENSE.md
@@ -5,7 +5,7 @@ root: .
 ---
 ## Instructional Material
 
-All Software Carpentry and Data Carpentry instructional material is
+All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
 made available under the [Creative Commons Attribution
 license][cc-by-human]. The following is a human-readable summary of
 (and not a substitute for) the [full legal text of the CC BY 4.0

diff --git a/Makefile b/Makefile
@@ -1,39 +1,72 @@
+# Use /bin/bash instead of /bin/sh
+export SHELL = /bin/bash
+
 ## ========================================
 ## Commands for both workshop and lesson websites.
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL=jekyll
-JEKYLL_VERSION=3.7.3
+JEKYLL=bundle install --path .vendor/bundle && bundle update && bundle exec jekyll
 PARSER=bin/markdown_ast.rb
 DST=_site
 
+# Check Python 3 is installed and determine if it's called via python3 or python
+# (https://stackoverflow.com/a/4933395)
+PYTHON3_EXE := $(shell which python3 2>/dev/null)
+ifneq (, $(PYTHON3_EXE))
+  ifeq (,$(findstring Microsoft/WindowsApps/python3,$(subst \,/,$(PYTHON3_EXE))))
+    PYTHON := python3
+  endif
+endif
+
+ifeq (,$(PYTHON))
+  PYTHON_EXE := $(shell which python 2>/dev/null)
+  ifneq (, $(PYTHON_EXE))
+    PYTHON_VERSION_FULL := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
+    PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION_FULL})
+    ifneq (3, ${PYTHON_VERSION_MAJOR})
+      $(error "Your system does not appear to have Python 3 installed.")
+    endif
+    PYTHON := python
+  else
+      $(error "Your system does not appear to have any Python installed.")
+  endif
+endif
+
+
 # Controls
 .PHONY : commands clean files
-.NOTPARALLEL:
-all : commands
 
-## commands         : show all commands.
-commands :
-	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+# Default target
+.DEFAULT_GOAL := commands
 
-## docker-serve     : use docker to build the site
-docker-serve :
-	docker run --rm -it -v ${PWD}:/srv/jekyll -p 127.0.0.1:4000:4000 jekyll/jekyll:${JEKYLL_VERSION} make serve
+## I. Commands for both workshop and lesson websites
+## =================================================
 
-## serve            : run a local server.
+## * serve            : render website and run a local server
 serve : lesson-md
 	${JEKYLL} serve
 
-## site             : build files but do not run a server.
+## * site             : build website but do not run a server
 site : lesson-md
 	${JEKYLL} build
 
-# repo-check        : check repository settings.
+## * docker-serve     : use Docker to serve the site
+docker-serve :
+	docker pull carpentries/lesson-docker:latest
+	docker run --rm -it \
+		-v $${PWD}:/home/rstudio \
+		-p 4000:4000 \
+		-p 8787:8787 \
+		-e USERID=$$(id -u) \
+		-e GROUPID=$$(id -g) \
+		carpentries/lesson-docker:latest
+
+## * repo-check       : check repository settings
 repo-check :
-	@bin/repo_check.py -s .
+	@${PYTHON} bin/repo_check.py -s .
 
-## clean            : clean up junk files.
+## * clean            : clean up junk files
 clean :
 	@rm -rf ${DST}
 	@rm -rf .sass-cache
@@ -42,22 +75,26 @@ clean :
 	@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 :
+## * clean-rmd        : clean intermediate R files (that need to be committed to the repo)
+clean-rmd :
 	@rm -rf ${RMD_DST}
 	@rm -rf fig/rmd-*
 
-## ----------------------------------------
-## Commands specific to workshop websites.
+
+##
+## II. Commands specific to workshop websites
+## =================================================
 
 .PHONY : workshop-check
 
-## workshop-check   : check workshop homepage.
+## * workshop-check   : check workshop homepage
 workshop-check :
-	@bin/workshop_check.py .
+	@${PYTHON} bin/workshop_check.py .
 
-## ----------------------------------------
-## Commands specific to lesson websites.
+
+##
+## III. Commands specific to lesson websites
+## =================================================
 
 .PHONY : lesson-check lesson-md lesson-files lesson-fixme
 
@@ -85,38 +122,39 @@ HTML_DST = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
-## lesson-md        : convert Rmarkdown files to markdown
+## * lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-# Use of .NOTPARALLEL makes rule execute only once
-${RMD_DST} : ${RMD_SRC}
-	@bin/knit_lessons.sh ${RMD_SRC}
+_episodes/%.md: _episodes_rmd/%.Rmd
+	@bin/knit_lessons.sh $< $@
 
-## lesson-check     : validate lesson Markdown.
+# * lesson-check     : validate lesson Markdown
 lesson-check : lesson-fixme
-	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
+	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
-## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
+## * lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace
 lesson-check-all :
-	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
+	@${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive
 
-## unittest         : run unit tests on checking tools.
+## * unittest         : run unit tests on checking tools
 unittest :
-	@bin/test_lesson_check.py
+	@${PYTHON} bin/test_lesson_check.py
 
-## lesson-files     : show expected names of generated files for debugging.
+## * lesson-files     : show expected names of generated files for debugging
 lesson-files :
 	@echo 'RMD_SRC:' ${RMD_SRC}
 	@echo 'RMD_DST:' ${RMD_DST}
 	@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
 	@echo 'HTML_DST:' ${HTML_DST}
 
-## lesson-fixme     : show FIXME markers embedded in source files.
+## * lesson-fixme     : show FIXME markers embedded in source files
 lesson-fixme :
 	@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
 
-#-------------------------------------------------------------------------------
-# Include extra commands if available.
-#-------------------------------------------------------------------------------
+##
+## IV. Auxililary (plumbing) commands
+## =================================================
 
--include commands.mk
+## * commands         : show all commands.
+commands :
+	@sed -n -e '/^##/s|^##[[:space:]]*||p' $(MAKEFILE_LIST)
diff --git a/_config.yml b/_config.yml
@@ -29,7 +29,7 @@ repository: <USERNAME>/<PROJECT>
 email: "team@carpentries.org"
 
 # Sites.
-amy_site: "https://amy.software-carpentry.org/workshops"
+amy_site: "https://amy.software-carpentry.org/"
 carpentries_github: "https://github.com/carpentries"
 carpentries_pages: "https://carpentries.github.io"
 carpentries_site: "https://carpentries.org/"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		github: [carpentries, swcarpentry, datacarpentry, librarycarpentry]
		custom: ["https://carpentries.wedid.it"]