Merge branch gh-pages of carpentries/styles

Conflicts:
	aio.md

Author: maxim-belkin

.github/FUNDING.yml

@@ -0,0 +1,2 @@
+github: [carpentries, swcarpentry, datacarpentry, librarycarpentry]
+custom: ["https://carpentries.wedid.it"]

.gitignore

@@ -4,9 +4,13 @@
 .DS_Store
 .ipynb_checkpoints
 .sass-cache
+.jekyll-cache/
 __pycache__
 _site
 .Rproj.user
 .Rhistory
 .RData
-
+.bundle/
+.vendor/
+.docker-vendor/
+Gemfile.lock

.travis.yml

@@ -1,3 +1,4 @@
+# Travis CI is only used to check the lesson and is not involved in its deployment
 dist: xenial  # Ubuntu 16.04 (required for python 3.7)
 language: python
 python: 3.7
@@ -7,15 +8,15 @@ branches:
   - /.*/
 before_install:
   - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-  - echo "deb https://cran.rstudio.com/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
+  - echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" | sudo tee -a /etc/apt/sources.list
   - sudo apt-get update -y
   - sudo apt-get install -y r-base
   - sudo Rscript -e "install.packages('knitr', repos = 'https://', dependencies = TRUE)"
   - sudo Rscript -e "install.packages('stringr', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
   - sudo Rscript -e "install.packages('checkpoint', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
   - sudo Rscript -e "install.packages('ggplot2', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
   - rvm default
-  - gem install json kramdown jekyll
+  - gem install json kramdown jekyll bundler
 install:
   - pip install pyyaml
 script:

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 '>=2.5.3'
+
+gem 'github-pages', group: :jekyll_plugins

Makefile

@@ -1,39 +1,70 @@
+# 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_VERSION=3.8.5
+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 run --rm -it --volume ${PWD}:/srv/jekyll \
+           --volume=${PWD}/.docker-vendor/bundle:/usr/local/bundle \
+           -p 127.0.0.1:4000:4000 \
+           jekyll/jekyll:${JEKYLL_VERSION} \
+           bin/run-make-docker-serve.sh
+
+## * repo-check       : check repository settings
 repo-check :
-	@bin/repo_check.py -s .
+	@${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 +73,26 @@ clean :
 	@find . -name '*~' -exec rm {} \;
 	@find . -name '*.pyc' -exec rm {} \;
 
-## clean-rmd        : clean intermediate R files (that need to be committed to the repo).
+## * 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
 
@@ -85,37 +120,39 @@ 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}
 
 _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)

README.md

@@ -1,13 +1,41 @@
 [![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/)
 [![Slack Status](https://img.shields.io/badge/Slack_Channel-dc--ecology--py-E01563.svg)](https://swcarpentry.slack.com/messages/C9X44HCDS)
 
-
 ## Data Carpentry Python Lessons with Ecological Data
 
 This repository contains the Data Carpentry Python material based on ecological
 data. Please see our [contribution guidelines](CONTRIBUTING.md) for information
 on how to contribute updates, bug fixes, or other corrections.
 
-### Maintainers
+## Contributing
+
+We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
+questions, concerns, or experience any difficulties along the way.
+
+We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
+the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
+how to write new episodes.
+
+Please see the current list of [issues][FIXME] for ideas for contributing to this
+repository. For making your contribution, we use the GitHub flow, which is
+nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git
+by Scott Chacon.
+Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first%20issue-gold.svg). This indicates that the maintainers will welcome a pull request fixing this issue.
+
+
+## Maintainer(s)
+
+Current maintainers of this lesson are
+
+* [Maxim Belkin](maxim-belkin)
+
+## Authors
+
+A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
+
+## Citation
+
+To cite this lesson, please consult with [CITATION](CITATION)
 
-- Maxim Belkin ([@maxim-belkin](https://github.com/maxim-belkin))
+[lesson-example]: https://carpentries.github.io/lesson-example
+[maxim-belkin]: https://github.com/maxim-belkin

_config.yml

@@ -12,6 +12,10 @@ carpentry: "dc"
 # Overall title for pages.
 title: "Data Analysis and Visualization in Python for Ecologists"
 
+# Life cycle stage of the lesson
+# possible values: "pre-alpha", "alpha", "beta", "stable"
+life_cycle: "stable"
+
 #------------------------------------------------------------
 # Generic settings (should not need to change).
 #------------------------------------------------------------
@@ -28,26 +32,29 @@ repository: <USERNAME>/<PROJECT>
 email: "[email protected]"
 
 # Sites.
-amy_site: "https://amy.software-carpentry.org/workshops"
+amy_site: "https://amy.carpentries.org/workshops"
 carpentries_github: "https://github.com/carpentries"
 carpentries_pages: "https://carpentries.github.io"
 carpentries_site: "https://carpentries.org/"
-dc_site: "http://datacarpentry.org"
+dc_site: "https://datacarpentry.org"
 example_repo: "https://github.com/carpentries/lesson-example"
 example_site: "https://carpentries.github.io/lesson-example"
-lc_site: "https://librarycarpentry.github.io/"
+lc_site: "https://librarycarpentry.org/"
 swc_github: "https://github.com/swcarpentry"
 swc_pages: "https://swcarpentry.github.io"
 swc_site: "https://software-carpentry.org"
 template_repo: "https://github.com/carpentries/styles"
 training_site: "https://carpentries.github.io/instructor-training"
 workshop_repo: "https://github.com/carpentries/workshop-template"
 workshop_site: "https://carpentries.github.io/workshop-template"
+cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
 
 # 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"
+pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="
+post_survey: "https://carpentries.typeform.com/to/UgVdRQ?slug="
+instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
+instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="
+
 
 # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am)
 start_time: 0
@@ -84,6 +91,8 @@ exclude:
   - Makefile
   - bin/
   - .Rproj.user/
+  - .vendor/
+  - .docker-vendor/
 
 # Turn on built-in syntax highlighting.
 highlighter: rouge

_extras/figures.md

@@ -3,11 +3,17 @@ title: Figures
 ---
 
 {% include base_path.html %}
+{% include manual_episode_order.html %}
 
 <script>
   window.onload = function() {
     var lesson_episodes = [
-    {% for episode in site.episodes %}
+    {% for lesson_episode in lesson_episodes %}
+      {% if site.episode_order %}
+        {% assign episode = site.episodes | where: "slug", lesson_episode | first %}
+      {% else %}
+        {% assign episode = lesson_episode %}
+      {% endif %}
     "{{ episode.url }}"{% unless forloop.last %},{% endunless %}
     {% endfor %}
     ];
@@ -58,10 +64,15 @@ title: Figures
     }
   }
 </script>
-{% comment %}
-Create anchor for each one of the episodes.
-{% endcomment %}
-{% for episode in site.episodes %}
+
+{% comment %} Create anchor for each one of the episodes.  {% endcomment %}
+
+{% for lesson_episode in lesson_episodes %}
+  {% if site.episode_order %}
+    {% assign episode = site.episodes | where: "slug", lesson_episode | first %}
+  {% else %}
+    {% assign episode = lesson_episode %}
+  {% endif %}
 <article id="{{ episode.url }}" class="figures"></article>
 {% endfor %}
 

_includes/aio-script.md

@@ -0,0 +1,25 @@
+{% comment %}
+As a maintainer, you don't need to edit this file.
+If you notice that something doesn't work, please
+open an issue: https://github.com/carpentries/styles/issues/new
+{% endcomment %}
+
+{% include manual_episode_order.html %}
+
+{% for lesson_episode in lesson_episodes %}
+
+{% if site.episode_order %}
+  {% assign e = site.episodes | where: "slug", lesson_episode | first %}
+{% else %}
+  {% assign e = lesson_episode %}
+{% endif %}
+
+<h1 id="{{ e.title | slugify }}" class="maintitle">{{ e.title }}</h1>
+
+{% include episode_overview.html teaching_time=e.teaching exercise_time=e.exercises episode_questions=e.questions episode_objectives=e.objectives %}
+
+{{ e.content }}
+
+{% include episode_keypoints.html episode_keypoints=e.keypoints %}
+<hr />
+{% endfor %}