initial steps towards dc template

.gitignore

@@ -1,3 +1,4 @@
 _site
 .DS_Store
-_config.yml
+_config.yml
+.Rproj.user

CONDUCT.md

@@ -0,0 +1,45 @@
+---
+layout: page
+title: "Contributor Code of Conduct"
+permalink: /conduct/
+---
+As contributors and maintainers of this project,
+we pledge to respect all people who contribute through reporting issues,
+posting feature requests,
+updating documentation,
+submitting pull requests or patches,
+and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone,
+regardless of level of experience,
+gender,
+gender identity and expression,
+sexual orientation,
+disability,
+personal appearance,
+body size,
+race,
+ethnicity,
+age,
+or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery,
+derogatory comments or personal attacks,
+trolling,
+public or private harassment,
+insults,
+or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to our [Code of Conduct][coc].
+Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+
+
+- [Software and Data Carpentry Code of Conduct][coc]
+- [Code of Conduct Reporting Guide][coc-reporting]
+
+{% include links.md %}

Gemfile

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+source 'https://rubygems.org'
+gem 'github-pages', group: :jekyll_plugins

Makefile

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+## ========================================
+## Commands for both workshop and lesson websites.
+
+# Settings
+MAKEFILES=Makefile $(wildcard *.mk)
+JEKYLL=jekyll
+PARSER=bin/markdown_ast.rb
+DST=_site
+
+# Controls
+.PHONY : commands clean files
+.NOTPARALLEL:
+all : commands
+
+## commands         : show all commands.
+commands :
+	@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
+
+## serve            : run a local server.
+serve : lesson-md
+	${JEKYLL} serve
+
+## site             : build files but do not run a server.
+site : lesson-md
+	${JEKYLL} build
+
+# repo-check        : check repository settings.
+repo-check :
+	@bin/repo_check.py -s .
+
+## clean            : clean up junk files.
+clean :
+	@rm -rf ${DST}
+	@rm -rf .sass-cache
+	@rm -rf bin/__pycache__
+	@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/rmd-*
+
+## ----------------------------------------
+## Commands specific to workshop websites.
+
+.PHONY : workshop-check
+
+## workshop-check   : check workshop homepage.
+workshop-check :
+	@bin/workshop_check.py .
+
+## ----------------------------------------
+## Commands specific to lesson websites.
+
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+
+# RMarkdown files
+RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
+RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
+
+# Lesson source files in the order they appear in the navigation menu.
+MARKDOWN_SRC = \
+  index.md \
+  CONDUCT.md \
+  setup.md \
+  $(sort $(wildcard _episodes/*.md)) \
+  reference.md \
+  $(sort $(wildcard _extras/*.md)) \
+  LICENSE.md
+
+# Generated lesson files in the order they appear in the navigation menu.
+HTML_DST = \
+  ${DST}/index.html \
+  ${DST}/conduct/index.html \
+  ${DST}/setup/index.html \
+  $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \
+  ${DST}/reference/index.html \
+  $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
+  ${DST}/license/index.html
+
+## 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}
+
+## lesson-check     : validate lesson Markdown.
+lesson-check :
+	@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 :
+	@bin/lesson_check.py -s . -p ${PARSER} -l -w
+
+## lesson-figures   : re-generate inclusion displaying all figures.
+lesson-figures :
+	@bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
+
+## unittest         : run unit tests on checking tools.
+unittest :
+	python bin/test_lesson_check.py
+
+## 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 :
+	@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
+
+#-------------------------------------------------------------------------------
+# Include extra commands if available.
+#-------------------------------------------------------------------------------
+
+-include commands.mk

_config.yml

@@ -1,91 +1,73 @@
-title: 	NEON Raster Data in R 
-description: 	A set of lessons .
-#Comment out url when working locally to resolve base urls correctly ok
-#use this when pushing to git for live version
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
 
-url:      http://datacarpentry.org/NEON-R-Spatial-Raster
-baseurl:   http://datacarpentry.org/NEON-R-Spatial-Raster
+# Which carpentry is this ("swc", "dc", or "lc")?
+carpentry: "dc"
 
-#use this when working locally
-#just uncomment the first localhost.
-#url: http://localhost:4000
-#baseurl: http://localhost:4000
+# Overall title for pages.
+title: "Geospatial analysis with R"
 
-#we might not need comments here???
-disqus_shortname: 
+# Contact.  This *must* include the protocol: if it's an email
+# address, it must look like "mailto:lessons@software-carpentry.org",
+# or if it's a URL, "https://gitter.im/username/ProjectName".
+contact: "mailto:lessons@software-carpentry.org"
 
-# Social networking links are used in author-bio sidebar. Update and remove as you like.
+#------------------------------------------------------------
+# Generic settings (should not need to change).
+#------------------------------------------------------------
 
-# Owner/author information
-owner: 		
-  name: NEON / Data Carpentry Hackathon
-  avatar: profilePic.png
-  bio: "Devoted to open data and open source in science and education."
-  email: "neondataskills@neoninc.org"
-#  twitter: "leahawasser"
-  github: "data-lessons"
-#  youtube: " "
-# instagram:      " "
-# For Google Authorship https://plus.google.com/authorship
-# google_plus:    
+# What kind of thing is this ("workshop" or "lesson")?
+kind: "lesson"
 
-# Analytics and webmaster tools stuff goes here
-google_analytics:   
-#google_verify:      UQj93ERU9zgECodaaXgVpkjrFn9UrDMEzVamacSoQ8Y
-# https://ssl.bing.com/webmaster/configure/verify/ownership Option 2 content= goes here
-#bing_verify:        D81F4C18A6CB3018F64D7C827D953DFD
+# Magic to make URLs resolve both locally and on GitHub.
+# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+repository: datacarpentry/R-spatial-raster-vector-lesson
 
-# Links to include in top navigation
-# For external links add external: true
+# Sites.
+amy_site: "https://amy.software-carpentry.org/workshops"
+dc_site: "http://datacarpentry.org"
+swc_github: "https://github.com/swcarpentry"
+swc_site: "https://software-carpentry.org"
+swc_pages: "https://swcarpentry.github.io"
+lc_site: "http://librarycarpentry.github.io/"
+template_repo: "https://github.com/swcarpentry/styles"
+example_repo: "https://github.com/swcarpentry/lesson-example"
+example_site: "https://swcarpentry.github.com/lesson-example"
+workshop_repo: "https://github.com/swcarpentry/workshop-template"
+workshop_site: "https://swcarpentry.github.io/workshop-template"
+training_site: "https://swcarpentry.github.io/instructor-training"
 
-links:  
-  - title: Data Tutorials
-    url: /self-paced-tutorial/   
+# Surveys.
+pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
+post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
+training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"
 
-  - title: Tutorial Series
-    url: /tutorial-series/
-
-  - title: Events
-    url: /workshop-event/
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
+start_time: 0
 
-  - title: Science Videos
-    url: /science-video/ 
-
-  - title: About
-    url: /about/ 
-
-  - title: NEON Website
-    url: http://neonscience.org
-    external: true
-
-# http://en.wikipedia.org/wiki/List_of_tz_database_time_zones
-timezone:    America/Denver
-future:      true
-# turning off pygments for the time being
-#pygments:    true
-#highlighter: pygments
-markdown:    kramdown
-#markdown: redcarpet
-redcarpet:
-  extensions: ["no_intra_emphasis", "fenced_code_blocks", "autolink", "tables", "with_toc_data"]
+# Specify that things in the episodes collection should be output.
+collections:
+  episodes:
+    output: true
+    permalink: /:path/
+  extras:
+    output: true
 
+# Set the default layout for things in the episodes collection.
+defaults:
+  - values:
+      root: ..
+  - scope:
+      path: ""
+      type: episodes
+    values:
+      layout: episode
 
-# https://github.com/mojombo/jekyll/wiki/Permalinks
-permalink:   /:categories/:title/
+# Files and directories that are not to be copied.
+exclude:
+  - Makefile
+  - bin
 
-kramdown:
-  auto_ids: true
-  footnote_nr: 1
-  entity_output: as_char
-  toc_levels: 1..2
-  enable_coderay: false
-
-  coderay:
-    coderay_line_numbers: 
-    coderay_line_numbers_start: 1
-    coderay_tab_width: 4
-    coderay_bold_every: 10
-    coderay_css: class
-
-include: [".htaccess"]
-exclude: ["*.Rmd", "lib", "config.rb", "Capfile", "config", "log", "Rakefile", "Rakefile.rb", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules", "Gemfile", "Gemfile.lock", "LICENSE", "README.md"]
+# Turn off built-in syntax highlighting.
+highlighter: false