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Merge pull request #90 from LibraryCarpentry/upgrade-template
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‎.github/FUNDING.yml

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github: [carpentries, swcarpentry, datacarpentry, librarycarpentry]
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custom: ["https://carpentries.wedid.it"]

‎.github/ISSUE_TEMPLATE.md

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Please delete this line and the text below before submitting your contribution.
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<details>
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<summary><strong>Instructions</strong></summary>
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---
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Thanks for contributing! :heart:
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Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] 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.
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If this contribution is for instructor training, please email the link to this contribution to
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[email protected] so we can record your progress. You've completed your contribution
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step for instructor checkout by submitting this contribution!
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If this issue is about a specific episode within a lesson, please provide its link or filename.
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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 The Carpentries Team at [email protected].
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Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
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respond to your contribution. Although not all contributions can be incorporated into the lesson
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materials, we appreciate your time and effort to improve the curriculum. If you have any questions
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about the lesson maintenance process or would like to volunteer your time as a contribution
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reviewer, please contact The Carpentries Team at [email protected].
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---
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You may delete these instructions from your comment.
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\- The Carpentries
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</details>

‎.github/PULL_REQUEST_TEMPLATE.md

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Please delete this line and the text below before submitting your contribution.
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<details>
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<summary><strong>Instructions</strong></summary>
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---
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Thanks for contributing! :heart:
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Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] 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.
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If this contribution is for instructor training, please email the link to this contribution to
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[email protected] so we can record your progress. You've completed your contribution
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step for instructor checkout by submitting this contribution!
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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 The Carpentries Team at [email protected].
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Keep in mind that **lesson maintainers are volunteers** and it may take them some time to
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respond to your contribution. Although not all contributions can be incorporated into the lesson
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materials, we appreciate your time and effort to improve the curriculum. If you have any questions
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about the lesson maintenance process or would like to volunteer your time as a contribution
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reviewer, please contact The Carpentries Team at [email protected].
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---
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You may delete these instructions from your comment.
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\- The Carpentries
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</details>

‎.gitignore

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.DS_Store
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.ipynb_checkpoints
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.sass-cache
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.jekyll-cache/
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__pycache__
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_site
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.Rproj.user
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.Rhistory
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.RData
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/Gemfile.lock
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.bundle/
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.vendor/
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.docker-vendor/
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Gemfile.lock
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.*history

‎Gemfile

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# frozen_string_literal: true
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source 'https://rubygems.org'
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git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
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# Synchronize with https://pages.github.com/versions
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ruby '>=2.5.8'
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gem 'github-pages', group: :jekyll_plugins

‎Makefile

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

‎_includes/aio-script.md

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

‎_includes/all_keypoints.html

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{% endcomment %}
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{% include base_path.html %}
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{% include manual_episode_order.html %}
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<h2>Key Points</h2>
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<table class="table table-striped">
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{% for episode in site.episodes %}
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{% for lesson_episode in lesson_episodes %}
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{% if site.episode_order %}
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{% assign episode = site.episodes | where: "slug", lesson_episode | first %}
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{% else %}
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{% assign episode = lesson_episode %}
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{% endif %}
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{% unless episode.break %}
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<tr>
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<td class="col-md-3">

‎_includes/episode_keypoints.html

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{% comment %}
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Display key points for an episode.
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{% endcomment %}
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{% if page.keypoints == nil %}
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{% assign episode_keypoints = include.episode_keypoints %}
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{% else %}
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{% assign episode_keypoints = page.keypoints %}
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{% endif %}
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<blockquote class="keypoints">
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<h2>Key Points</h2>
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<ul>
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{% for keypoint in page.keypoints %}
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{% for keypoint in episode_keypoints %}
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<li>{{ keypoint|markdownify }}</li>
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{% endfor %}
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</ul>

‎_includes/episode_navbar.html

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Navigation bar for an episode.
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{% endcomment %}
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{% include manual_episode_order.html %}
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{% comment %}
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'previous_episode' and 'next_episodes' are defined in 'manual_episode_order.html'.
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These replace 'page.previous' and 'page.next' objects, correspondingly.
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{% endcomment %}
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<div class="row">
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<div class="col-xs-1">
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<h3 class="text-left">
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{% if page.previous.url %}
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<a href="{{ relative_root_path }}{{ page.previous.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
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{% if previous_episode %}
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<a href="{{ relative_root_path }}{{ previous_episode.url }}"><span class="glyphicon glyphicon-menu-left" aria-hidden="true"></span><span class="sr-only">previous episode</span></a>
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{% else %}
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<a href="{{ relative_root_path }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
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{% endif %}
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</div>
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<div class="col-xs-1">
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<h3 class="text-right">
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{% if page.next.url %}
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<a href="{{ relative_root_path }}{{ page.next.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
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{% if next_episode %}
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<a href="{{ relative_root_path }}{{ next_episode.url }}"><span class="glyphicon glyphicon-menu-right" aria-hidden="true"></span><span class="sr-only">next episode</span></a>
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{% else %}
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<a href="{{ relative_root_path }}/"><span class="glyphicon glyphicon-menu-up" aria-hidden="true"></span><span class="sr-only">lesson home</span></a>
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{% endif %}

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