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e(e,t){this.mode=void 0,this.gullet=void 0,this.settings=void 0,this.leftrightDepth=void 0,this.nextToken=void 0,this.mode="math",this.gullet=new Un(e,t,this.mode),this.settings=t,this.leftrightDepth=0}var t=e.prototype;return t.expect=function(e,t){if(void 0===t&&(t=!0),this.fetch().text!==e)throw new n("Expected '"+e+"', got '"+this.fetch().text+"'",this.fetch());t&&this.consume()},t.consume=function(){this.nextToken=null},t.fetch=function(){return null==this.nextToken&&(this.nextToken=this.gullet.expandNextToken()),this.nextToken},t.switchMode=function(e){this.mode=e,this.gullet.switchMode(e)},t.parse=function(){this.settings.globalGroup||this.gullet.beginGroup(),this.settings.colorIsTextColor&&this.gullet.macros.set("\\color","\\textcolor");var e=this.parseExpression(!1);return this.expect("EOF"),this.settings.globalGroup||this.gullet.endGroup(),e},t.parseExpression=function(t,r){for(var n=[];;){"math"===this.mode&&this.consumeSpaces();var a=this.fetch();if(-1!==e.endOfExpression.indexOf(a.text))break;if(r&&a.text===r)break;if(t&&Tn[a.text]&&Tn[a.text].infix)break;var i=this.parseAtom(r);if(!i)break;"internal"!==i.type&&n.push(i)}return"text"===this.mode&&this.formLigatures(n),this.handleInfixNodes(n)},t.handleInfixNodes=function(e){for(var t,r=-1,a=0;a=0&&this.settings.reportNonstrict("unicodeTextInMathMode",'Latin-1/Unicode text character "'+t[0]+'" used in math mode',e);var s,l=X[this.mode][t].group,h=Bn.range(e);if(U.hasOwnProperty(l)){var m=l;s={type:"atom",mode:this.mode,family:m,loc:h,text:t}}else s={type:l,mode:this.mode,loc:h,text:t};i=s}else{if(!(t.charCodeAt(0)>=128))return null;this.settings.strict&&(w(t.charCodeAt(0))?"math"===this.mode&&this.settings.reportNonstrict("unicodeTextInMathMode",'Unicode text character "'+t[0]+'" used in math mode',e):this.settings.reportNonstrict("unknownSymbol",'Unrecognized Unicode character "'+t[0]+'" ('+t.charCodeAt(0)+")",e)),i={type:"textord",mode:"text",loc:Bn.range(e),text:t}}if(this.consume(),o)for(var c=0;c 0
+ || $(event.target).filter(".fold-unfold").length > 0;
+ if (trigger) {
+ $(">*:not(h2)", this).toggle(400);
+ $(">h2>span.fold-unfold", this).toggleClass("glyphicon-collapse-down glyphicon-collapse-up");
+ event.stopPropagation();
+ }
+});
+$(".solution").each(function() {
+ $(">*:not(h2)", this).toggle();
+ var h2 = $("h2:first", this);
+ h2.append("");
+});
+
+
+// Handle searches.
+// Relies on document having 'meta' element with name 'search-domain'.
+function google_search() {
+ var query = document.getElementById("google-search").value;
+ var domain = $("meta[name=search-domain]").attr("value");
+ window.open("https://www.google.com/search?q=" + query + "+site:" + domain);
+}
+
+// function to shrink the life cycle bar when scrolling
+$(function(){
+ $('#life-cycle').data('size','big');
+});
+
+$(window).scroll(function(){
+ if($(document).scrollTop() > 0)
+ {
+ if($('#life-cycle').data('size') == 'big')
+ {
+ $('#life-cycle').data('size','small');
+ $('#life-cycle').stop().animate({
+ padding: '5px'
+ },100);
+ }
+ }
+ else
+ {
+ if($('#life-cycle').data('size') == 'small')
+ {
+ $('#life-cycle').data('size','big');
+ $('#life-cycle').stop().animate({
+ padding: '15px'
+ },100);
+ }
+ }
+});
diff --git a/bin/boilerplate/AUTHORS b/bin/boilerplate/AUTHORS
new file mode 100644
index 0000000..04e1f5a
--- /dev/null
+++ b/bin/boilerplate/AUTHORS
@@ -0,0 +1 @@
+FIXME: list authors' names and email addresses.
\ No newline at end of file
diff --git a/bin/boilerplate/CITATION b/bin/boilerplate/CITATION
new file mode 100644
index 0000000..56ece3c
--- /dev/null
+++ b/bin/boilerplate/CITATION
@@ -0,0 +1 @@
+FIXME: describe how to cite this lesson.
\ No newline at end of file
diff --git a/bin/boilerplate/CONTRIBUTING.md b/bin/boilerplate/CONTRIBUTING.md
new file mode 100644
index 0000000..8c095d8
--- /dev/null
+++ b/bin/boilerplate/CONTRIBUTING.md
@@ -0,0 +1,151 @@
+# Contributing
+
+[The Carpentries][c-site] ([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects,
+and we welcome contributions of all kinds:
+new lessons,
+fixes to existing material,
+bug reports,
+and reviews of proposed changes are all welcome.
+
+## Contributor Agreement
+
+By contributing,
+you agree that we may redistribute your work under [our license](LICENSE.md).
+In exchange,
+we will address your issues and/or assess your change proposal as promptly as we can,
+and help you become a member of our community.
+Everyone involved in [The Carpentries][c-site]
+agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md).
+
+## How to Contribute
+
+The easiest way to get started is to file an issue
+to tell us about a spelling mistake,
+some awkward wording,
+or a factual error.
+This is a good way to introduce yourself
+and to meet some of our community members.
+
+1. If you do not have a [GitHub][github] account,
+ you can [send us comments by email][email].
+ However,
+ we will be able to respond more quickly if you use one of the other methods described below.
+
+2. If you have a [GitHub][github] account,
+ or are willing to [create one][github-join],
+ but do not know how to use Git,
+ you can report problems or suggest improvements by [creating an issue][issues].
+ This allows us to assign the item to someone
+ and to respond to it in a threaded discussion.
+
+3. If you are comfortable with Git,
+ and would like to add or change material,
+ you can submit a pull request (PR).
+ Instructions for doing this are [included below](#using-github).
+
+## Where to Contribute
+
+1. If you wish to change this lesson,
+ please work in ,
+ which can be viewed at .
+
+2. If you wish to change the example lesson,
+ please work in ,
+ which documents the format of our lessons
+ and can be viewed at .
+
+3. If you wish to change the template used for workshop websites,
+ please work in .
+ The home page of that repository explains how to set up workshop websites,
+ while the extra pages in
+ provide more background on our design choices.
+
+4. If you wish to change CSS style files, tools,
+ or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
+ please work in .
+
+## What to Contribute
+
+There are many ways to contribute,
+from writing new exercises and improving existing ones
+to updating or filling in the documentation
+and submitting [bug reports][issues]
+about things that do not work, are not clear, or are missing.
+If you are looking for ideas, please see the 'Issues' tab for
+a list of issues associated with this repository,
+or you may also look at the issues for [Data Carpentry][dc-issues],
+[Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects.
+
+Comments on issues and reviews of pull requests are just as welcome:
+we are smarter together than we are on our own.
+Reviews from novices and newcomers are particularly valuable:
+it is easy for people who have been using these lessons for a while
+to forget how impenetrable some of this material can be,
+so fresh eyes are always welcome.
+
+## What *Not* to Contribute
+
+Our lessons already contain more material than we can cover in a typical workshop,
+so we are usually *not* looking for more concepts or tools to add to them.
+As a rule,
+if you want to introduce a new idea,
+you must (a) estimate how long it will take to teach
+and (b) explain what you would take out to make room for it.
+The first encourages contributors to be honest about requirements;
+the second, to think hard about priorities.
+
+We are also not looking for exercises or other material that will only run on one platform.
+Our workshops typically contain a mixture of Windows, macOS, and Linux users;
+in order to be usable,
+our lessons must run equally well on all three.
+
+## Using GitHub
+
+If you choose to contribute via GitHub, you may want to look at
+[How to Contribute to an Open Source Project on GitHub][how-contribute].
+To manage changes, we follow [GitHub flow][github-flow].
+Each lesson has at least two maintainers who review issues and pull requests or encourage others to do so.
+The maintainers are community volunteers and have final say over what gets merged into the lesson.
+To use the web interface for contributing to a lesson:
+
+1. Fork the originating repository to your GitHub profile.
+2. Within your version of the forked repository, move to the `gh-pages` branch and
+create a new branch for each significant change being made.
+3. Navigate to the file(s) you wish to change within the new branches and make revisions as required.
+4. Commit all changed files within the appropriate branches.
+5. Create individual pull requests from each of your changed branches
+to the `gh-pages` branch within the originating repository.
+6. If you receive feedback, make changes using your issue-specific branches of the forked
+repository and the pull requests will update automatically.
+7. Repeat as needed until all feedback has been addressed.
+
+When starting work, please make sure your clone of the originating `gh-pages` branch is up-to-date
+before creating your own revision-specific branch(es) from there.
+Additionally, please only work from your newly-created branch(es) and *not*
+your clone of the originating `gh-pages` branch.
+Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
+repository for reference while revising.
+
+## Other Resources
+
+General discussion of [Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]
+happens on the [discussion mailing list][discuss-list],
+which everyone is welcome to join.
+You can also [reach us by email][email].
+
+[email]: mailto:team@carpentries.org
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
+[dc-lessons]: http://datacarpentry.org/lessons/
+[dc-site]: http://datacarpentry.org/
+[discuss-list]: https://carpentries.topicbox.com/groups/discuss
+[github]: https://github.com
+[github-flow]: https://guides.github.com/introduction/flow/
+[github-join]: https://github.com/join
+[how-contribute]: https://app.egghead.io/playlists/how-to-contribute-to-an-open-source-project-on-github
+[issues]: https://guides.github.com/features/issues/
+[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
+[c-site]: https://carpentries.org/
+[lc-site]: https://librarycarpentry.org/
+[lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry
diff --git a/bin/boilerplate/README.md b/bin/boilerplate/README.md
new file mode 100644
index 0000000..060994a
--- /dev/null
+++ b/bin/boilerplate/README.md
@@ -0,0 +1,40 @@
+# FIXME Lesson title
+
+[](https://swc-slack-invite.herokuapp.com/)
+
+This repository generates the corresponding lesson website from [The Carpentries](https://carpentries.org/) repertoire of lessons.
+
+## 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 . This indicates that the maintainers will welcome a pull request fixing this issue.
+
+
+## Maintainer(s)
+
+Current maintainers of this lesson are
+
+* FIXME
+* FIXME
+* FIXME
+
+
+## Authors
+
+A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
+
+## Citation
+
+To cite this lesson, please consult with [CITATION](CITATION)
+
+[lesson-example]: https://carpentries.github.io/lesson-example
diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml
new file mode 100644
index 0000000..3fab917
--- /dev/null
+++ b/bin/boilerplate/_config.yml
@@ -0,0 +1,104 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this ("swc", "dc", "lc", or "cp")?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor traning for instance)
+# incubator: Carpentries Incubator
+carpentry: "swc"
+
+# Overall title for pages.
+title: "Lesson Title"
+
+# Life cycle stage of the lesson
+# See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html
+# Possible values: "pre-alpha", "alpha", "beta", "stable"
+life_cycle: "pre-alpha"
+
+#------------------------------------------------------------
+# Generic settings (should not need to change).
+#------------------------------------------------------------
+
+# What kind of thing is this ("workshop" or "lesson")?
+kind: "lesson"
+
+# Magic to make URLs resolve both locally and on GitHub.
+# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+# Please don't change it: / is correct.
+repository: /
+
+# Email address, no mailto:
+email: "team@carpentries.org"
+
+# Sites.
+coc: "https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html"
+amy_site: "https://amy.carpentries.org/"
+carpentries_github: "https://github.com/carpentries"
+carpentries_pages: "https://carpentries.github.io"
+carpentries_site: "https://carpentries.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.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://carpentries.typeform.com/to/wi32rS#slug="
+post_survey: "https://carpentries.typeform.com/to/UgVdRQ#slug="
+instructor_pre_survey: "https://carpentries.typeform.com/to/QVOarK#slug="
+instructor_post_survey: "https://carpentries.typeform.com/to/cjJ9UP#slug="
+
+# Set to 'true' for instructor training websites only.
+instructor_training: false
+
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
+start_time: 0
+
+# Specify that things in the episodes collection should be output.
+collections:
+ episodes:
+ output: true
+ permalink: /:path/index.html
+ extras:
+ output: true
+ permalink: /:path/index.html
+
+# Set the default layout for things in the episodes collection.
+defaults:
+ - values:
+ root: .
+ layout: page
+ - scope:
+ path: ""
+ type: episodes
+ values:
+ root: ..
+ layout: episode
+ - scope:
+ path: ""
+ type: extras
+ values:
+ root: ..
+ layout: page
+
+# Files and directories that are not to be copied.
+exclude:
+ - Makefile
+ - bin/
+ - .Rproj.user/
+ - .vendor/
+ - vendor/
+ - .docker-vendor/
+
+# Turn on built-in syntax highlighting.
+highlighter: rouge
diff --git a/bin/boilerplate/_episodes/01-introduction.md b/bin/boilerplate/_episodes/01-introduction.md
new file mode 100644
index 0000000..2e156c2
--- /dev/null
+++ b/bin/boilerplate/_episodes/01-introduction.md
@@ -0,0 +1,15 @@
+---
+title: "Introduction"
+teaching: 0
+exercises: 0
+questions:
+- "Key question (FIXME)"
+objectives:
+- "First learning objective. (FIXME)"
+keypoints:
+- "First key point. Brief Answer to questions. (FIXME)"
+---
+FIXME
+
+{% include links.md %}
+
diff --git a/bin/boilerplate/_extras/about.md b/bin/boilerplate/_extras/about.md
new file mode 100644
index 0000000..5f07f65
--- /dev/null
+++ b/bin/boilerplate/_extras/about.md
@@ -0,0 +1,5 @@
+---
+title: About
+---
+{% include carpentries.html %}
+{% include links.md %}
diff --git a/bin/boilerplate/_extras/discuss.md b/bin/boilerplate/_extras/discuss.md
new file mode 100644
index 0000000..bfc33c5
--- /dev/null
+++ b/bin/boilerplate/_extras/discuss.md
@@ -0,0 +1,6 @@
+---
+title: Discussion
+---
+FIXME
+
+{% include links.md %}
diff --git a/bin/boilerplate/_extras/figures.md b/bin/boilerplate/_extras/figures.md
new file mode 100644
index 0000000..0012c88
--- /dev/null
+++ b/bin/boilerplate/_extras/figures.md
@@ -0,0 +1,79 @@
+---
+title: Figures
+---
+
+{% include base_path.html %}
+{% include manual_episode_order.html %}
+
+
+
+{% 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 %}
+
+{% endfor %}
+
+{% include links.md %}
diff --git a/bin/boilerplate/_extras/guide.md b/bin/boilerplate/_extras/guide.md
new file mode 100644
index 0000000..50f266f
--- /dev/null
+++ b/bin/boilerplate/_extras/guide.md
@@ -0,0 +1,6 @@
+---
+title: "Instructor Notes"
+---
+FIXME
+
+{% include links.md %}
diff --git a/bin/boilerplate/index.md b/bin/boilerplate/index.md
new file mode 100644
index 0000000..95ccdbd
--- /dev/null
+++ b/bin/boilerplate/index.md
@@ -0,0 +1,17 @@
+---
+layout: lesson
+root: . # Is the only page that doesn't follow the pattern /:path/index.html
+permalink: index.html # Is the only page that doesn't follow the pattern /:path/index.html
+---
+FIXME: home page introduction
+
+
+
+{% comment %} This is a comment in Liquid {% endcomment %}
+
+> ## Prerequisites
+>
+> FIXME
+{: .prereq}
+
+{% include links.md %}
diff --git a/bin/boilerplate/reference.md b/bin/boilerplate/reference.md
new file mode 100644
index 0000000..8c82616
--- /dev/null
+++ b/bin/boilerplate/reference.md
@@ -0,0 +1,9 @@
+---
+layout: reference
+---
+
+## Glossary
+
+FIXME
+
+{% include links.md %}
diff --git a/bin/boilerplate/setup.md b/bin/boilerplate/setup.md
new file mode 100644
index 0000000..b8c5032
--- /dev/null
+++ b/bin/boilerplate/setup.md
@@ -0,0 +1,7 @@
+---
+title: Setup
+---
+FIXME
+
+
+{% include links.md %}
diff --git a/bin/chunk-options.R b/bin/chunk-options.R
new file mode 100644
index 0000000..8e0d62a
--- /dev/null
+++ b/bin/chunk-options.R
@@ -0,0 +1,70 @@
+# These settings control the behavior of all chunks in the novice R materials.
+# For example, to generate the lessons with all the output hidden, simply change
+# `results` from "markup" to "hide".
+# For more information on available chunk options, see
+# http://yihui.name/knitr/options#chunk_options
+
+library("knitr")
+
+fix_fig_path <- function(pth) file.path("..", pth)
+
+
+## We set the path for the figures globally below, so if we want to
+## customize it for individual episodes, we can append a prefix to the
+## global path. For instance, if we call knitr_fig_path("01-") in the
+## first episode of the lesson, it will generate the figures in
+## `fig/rmd-01-`
+knitr_fig_path <- function(prefix) {
+ new_path <- paste0(opts_chunk$get("fig.path"),
+ prefix)
+ opts_chunk$set(fig.path = new_path)
+}
+
+## We use the rmd- prefix for the figures generated by the lessons so
+## they can be easily identified and deleted by `make clean-rmd`. The
+## working directory when the lessons are generated is the root so the
+## figures need to be saved in fig/, but when the site is generated,
+## the episodes will be one level down. We fix the path using the
+## `fig.process` option.
+
+opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
+ fig.align = "center", fig.path = "fig/rmd-",
+ fig.process = fix_fig_path,
+ fig.width = 8.5, fig.height = 8.5,
+ fig.retina = 2)
+
+# The hooks below add html tags to the code chunks and their output so that they
+# are properly formatted when the site is built.
+
+hook_in <- function(x, options) {
+ lg <- tolower(options$engine)
+ style <- paste0(".language-", lg)
+
+ stringr::str_c("\n\n~~~\n",
+ paste0(x, collapse="\n"),
+ "\n~~~\n{: ", style, "}\n\n")
+}
+
+hook_out <- function(x, options) {
+ x <- gsub("\n$", "", x)
+ stringr::str_c("\n\n~~~\n",
+ paste0(x, collapse="\n"),
+ "\n~~~\n{: .output}\n\n")
+}
+
+hook_error <- function(x, options) {
+ x <- gsub("\n$", "", x)
+ stringr::str_c("\n\n~~~\n",
+ paste0(x, collapse="\n"),
+ "\n~~~\n{: .error}\n\n")
+}
+
+hook_warning <- function(x, options) {
+ x <- gsub("\n$", "", x)
+ stringr::str_c("\n\n~~~\n",
+ paste0(x, collapse = "\n"),
+ "\n~~~\n{: .warning}\n\n")
+}
+
+knit_hooks$set(source = hook_in, output = hook_out, warning = hook_warning,
+ error = hook_error, message = hook_out)
diff --git a/bin/dependencies.R b/bin/dependencies.R
new file mode 100644
index 0000000..4eeeb21
--- /dev/null
+++ b/bin/dependencies.R
@@ -0,0 +1,107 @@
+install_required_packages <- function(lib = NULL, repos = getOption("repos", default = c(CRAN = "https://cran.rstudio.com/"))) {
+
+ if (is.null(lib)) {
+ lib <- .libPaths()[[1]]
+ }
+
+ message("lib paths: ", paste(lib, collapse = ", "))
+ # Note: RMarkdown is needed for renv to detect packages in Rmd documents.
+ required_pkgs <- c("rprojroot", "desc", "remotes", "renv", "BiocManager", "rmarkdown")
+ installed_pkgs <- rownames(installed.packages(lib.loc = lib))
+ missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
+
+ # The default installation of R will have "@CRAN@" as the default repository,
+ # which directs contrib.url() to either force the user to choose a mirror if
+ # interactive or fail if not. Since we are not interactve, we need to force
+ # the mirror here.
+ if ("@CRAN@" %in% repos) {
+ repos <- c(CRAN = "https://cran.rstudio.com/")
+ }
+
+ if (length(missing_pkgs) != 0) {
+ install.packages(missing_pkgs, lib = lib, repos = repos)
+ }
+}
+
+find_root <- function() {
+
+ cfg <- rprojroot::has_file_pattern("^_config.y*ml$")
+ root <- rprojroot::find_root(cfg)
+
+ root
+}
+
+# set the BiocManager repositories and return a function that resets the default
+# repositories.
+#
+# @example
+# bioc_repos_example <- function() {
+# message("User repos")
+# as.data.frame(getOption("repos"))
+# reset_repos <- use_bioc_repos()
+# on.exit(reset_repos())
+# message("Bioc repos")
+# as.data.frame(getOption("repos"))
+# }
+# bioc_repos_example()
+# as.data.frame(getOption("repos")
+use_bioc_repos <- function() {
+ repos <- getOption("repos")
+ suppressMessages(options(repos = BiocManager::repositories()))
+ function() {
+ options(repos = repos)
+ }
+}
+
+identify_dependencies <- function() {
+
+ root <- find_root()
+
+ reset_repos <- use_bioc_repos()
+ on.exit(reset_repos(), add = TRUE)
+ eps <- file.path(root, "_episodes_rmd")
+ bin <- file.path(root, "bin")
+
+ required_pkgs <- unique(c(
+ ## Packages for episodes
+ renv::dependencies(eps, progress = FALSE, error = "ignored")$Package,
+ ## Packages for tools
+ renv::dependencies(bin, progress = FALSE, error = "ignored")$Package
+ ))
+
+ required_pkgs
+}
+
+create_description <- function(required_pkgs) {
+ d <- desc::description$new("!new")
+ d$set_deps(data.frame(type = "Imports", package = required_pkgs, version = "*"))
+ d$write("DESCRIPTION")
+ # We have to write the description twice to get the hidden dependencies
+ # because renv only considers explicit dependencies.
+ #
+ # This is needed because some of the hidden dependencis will require system
+ # libraries to be configured.
+ suppressMessages(repo <- BiocManager::repositories())
+ deps <- remotes::dev_package_deps(dependencies = TRUE, repos = repo)
+ deps <- deps$package[deps$diff < 0]
+ if (length(deps)) {
+ # only create new DESCRIPTION file if there are dependencies to install
+ d$set_deps(data.frame(type = "Imports", package = deps, version = "*"))
+ d$write("DESCRIPTION")
+ }
+}
+
+install_dependencies <- function(required_pkgs, ...) {
+
+ reset_repos <- use_bioc_repos()
+ on.exit(reset_repos(), add = TRUE)
+
+ create_description(required_pkgs)
+ on.exit(file.remove("DESCRIPTION"), add = TRUE)
+ remotes::install_deps(dependencies = TRUE, ...)
+
+ if (require("knitr") && packageVersion("knitr") < '1.9.19') {
+ stop("knitr must be version 1.9.20 or higher")
+ }
+
+}
diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
new file mode 100644
index 0000000..7fb4c5a
--- /dev/null
+++ b/bin/generate_md_episodes.R
@@ -0,0 +1,44 @@
+generate_md_episodes <- function() {
+
+ # avoid ansi color characters from being printed in the output
+ op <- options()
+ on.exit(options(op), add = TRUE)
+ options(crayon.enabled = FALSE)
+ ## get the Rmd file to process from the command line, and generate the path
+ ## for their respective outputs
+ args <- commandArgs(trailingOnly = TRUE)
+ if (!identical(length(args), 2L)) {
+ stop("input and output file must be passed to the script")
+ }
+
+ src_rmd <- args[1]
+ dest_md <- args[2]
+
+ ## knit the Rmd into markdown
+ knitr::knit(src_rmd, output = dest_md)
+
+ # Read the generated md files and add comments advising not to edit them
+ add_no_edit_comment <- function(y) {
+ con <- file(y)
+ mdfile <- readLines(con)
+ if (mdfile[1] != "---")
+ stop("Input file does not have a valid header")
+ mdfile <- append(
+ mdfile,
+ "# Please do not edit this file directly; it is auto generated.",
+ after = 1
+ )
+ mdfile <- append(
+ mdfile,
+ paste("# Instead, please edit", basename(y), "in _episodes_rmd/"),
+ after = 2
+ )
+ writeLines(mdfile, con)
+ close(con)
+ return(paste("Warning added to YAML header of", y))
+ }
+
+ vapply(dest_md, add_no_edit_comment, character(1))
+}
+
+generate_md_episodes()
diff --git a/bin/install_r_deps.sh b/bin/install_r_deps.sh
new file mode 100755
index 0000000..0280f24
--- /dev/null
+++ b/bin/install_r_deps.sh
@@ -0,0 +1 @@
+Rscript -e "source(file.path('bin', 'dependencies.R')); install_required_packages(); install_dependencies(identify_dependencies())"
diff --git a/bin/knit_lessons.sh b/bin/knit_lessons.sh
new file mode 100755
index 0000000..141c136
--- /dev/null
+++ b/bin/knit_lessons.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+# Only try running R to translate files if there are some files present.
+# The Makefile passes in the names of files.
+
+if [ $# -eq 2 ] ; then
+ Rscript -e "source('bin/generate_md_episodes.R')" "$@"
+fi
diff --git a/bin/lesson_check.py b/bin/lesson_check.py
new file mode 100644
index 0000000..86e4249
--- /dev/null
+++ b/bin/lesson_check.py
@@ -0,0 +1,628 @@
+"""
+Check lesson files and their contents.
+"""
+
+
+import os
+import glob
+import re
+import sys
+from argparse import ArgumentParser
+
+# This uses the `__all__` list in `util.py` to determine what objects to import
+# see https://docs.python.org/3/tutorial/modules.html#importing-from-a-package
+from util import *
+from reporter import Reporter
+
+__version__ = '0.3'
+
+# Where to look for source Markdown files.
+SOURCE_DIRS = ['', '_episodes', '_extras']
+
+# Where to look for source Rmd files.
+SOURCE_RMD_DIRS = ['_episodes_rmd']
+
+# Required files: each entry is ('path': YAML_required).
+# FIXME: We do not yet validate whether any files have the required
+# YAML headers, but should in the future.
+# The '%' is replaced with the source directory path for checking.
+# Episodes are handled specially, and extra files in '_extras' are also handled
+# specially. This list must include all the Markdown files listed in the
+# 'bin/initialize' script.
+REQUIRED_FILES = {
+ 'CODE_OF_CONDUCT.md': True,
+ 'CONTRIBUTING.md': False,
+ 'LICENSE.md': True,
+ 'README.md': False,
+ os.path.join('_extras', 'discuss.md'): True,
+ os.path.join('_extras', 'guide.md'): True,
+ 'index.md': True,
+ 'reference.md': True,
+ 'setup.md': True,
+}
+
+# Episode filename pattern.
+P_EPISODE_FILENAME = re.compile(r'(\d\d)-[-\w]+.md$')
+
+# Pattern to match lines ending with whitespace.
+P_TRAILING_WHITESPACE = re.compile(r'\s+$')
+
+# Pattern to match figure references in HTML.
+P_FIGURE_REFS = re.compile(r'
]+src="([^"]+)"[^>]*>')
+
+# Pattern to match internally-defined Markdown links.
+P_INTERNAL_LINK_REF = re.compile(r'\[([^\]]+)\]\[([^\]]+)\]')
+
+# Pattern to match reference links (to resolve internally-defined references).
+P_INTERNAL_LINK_DEF = re.compile(r'^\[([^\]]+)\]:\s*(.+)')
+
+# Pattern to match {% include ... %} statements
+P_INTERNAL_INCLUDE_LINK = re.compile(r'^{% include ([^ ]*) %}$')
+
+# Pattern to match image-only and link-only lines
+P_LINK_IMAGE_LINE = re.compile(r'''
+ [> #]* # any number of '>', '#', and spaces
+ \W{,3} # up to 3 non-word characters
+ !? # ! or nothing
+ \[[^]]+\] # [any text]
+ [([] # ( or [
+ [^])]+ # 1+ characters that are neither ] nor )
+ [])] # ] or )
+ (?:{:[^}]+})? # {:any text} or nothing
+ \W{,3} # up to 3 non-word characters
+ [ ]* # any number of spaces
+ \\?$ # \ or nothing + end of line''', re.VERBOSE)
+
+# What kinds of blockquotes are allowed?
+KNOWN_BLOCKQUOTES = {
+ 'callout',
+ 'caution',
+ 'challenge',
+ 'checklist',
+ 'discussion',
+ 'keypoints',
+ 'objectives',
+ 'prereq',
+ 'quotation',
+ 'solution',
+ 'testimonial',
+ 'warning'
+}
+
+# What kinds of code fragments are allowed?
+# Below we allow all 'language-*' code blocks
+KNOWN_CODEBLOCKS = {
+ 'error',
+ 'output',
+ 'source',
+ 'warning'
+}
+
+# What fields are required in teaching episode metadata?
+TEACHING_METADATA_FIELDS = {
+ ('title', str),
+ ('teaching', int),
+ ('exercises', int),
+ ('questions', list),
+ ('objectives', list),
+ ('keypoints', list)
+}
+
+# What fields are required in break episode metadata?
+BREAK_METADATA_FIELDS = {
+ ('layout', str),
+ ('title', str),
+ ('break', int)
+}
+
+# How long are lines allowed to be?
+# Please keep this in sync with .editorconfig!
+MAX_LINE_LEN = 100
+
+# Contents of _config.yml
+CONFIG = {}
+
+def main():
+ """Main driver."""
+
+ args = parse_args()
+ args.reporter = Reporter()
+
+ global CONFIG
+ config_file = os.path.join(args.source_dir, '_config.yml')
+ CONFIG = load_yaml(config_file)
+ CONFIG["config_file"] = config_file
+
+ life_cycle = CONFIG.get('life_cycle', None)
+ # pre-alpha lessons should report without error
+ if life_cycle == "pre-alpha":
+ args.permissive = True
+
+ check_config(args.reporter)
+ check_source_rmd(args.reporter, args.source_dir, args.parser)
+
+ args.references = read_references(args.reporter, args.reference_path)
+
+ docs = read_all_markdown(args.source_dir, args.parser)
+ check_fileset(args.source_dir, args.reporter, list(docs.keys()))
+ check_unwanted_files(args.source_dir, args.reporter)
+ for filename in list(docs.keys()):
+ checker = create_checker(args, filename, docs[filename])
+ checker.check()
+
+ args.reporter.report()
+ if args.reporter.messages:
+ if args.permissive:
+ print("Problems detected but ignored (permissive mode).")
+ else:
+ print("Problems detected.")
+ sys.exit(1)
+ else:
+ print("No problems found.")
+
+ return
+
+
+def parse_args():
+ """Parse command-line arguments."""
+
+ parser = ArgumentParser(description="""Check episode files in a lesson.""")
+ parser.add_argument('-l', '--linelen',
+ default=False,
+ action="store_true",
+ dest='line_lengths',
+ help='Check line lengths')
+ parser.add_argument('-p', '--parser',
+ default=None,
+ dest='parser',
+ help='path to Markdown parser')
+ parser.add_argument('-r', '--references',
+ default=None,
+ dest='reference_path',
+ help='path to Markdown file of external references')
+ parser.add_argument('-s', '--source',
+ default=os.curdir,
+ dest='source_dir',
+ help='source directory')
+ parser.add_argument('-w', '--whitespace',
+ default=False,
+ action="store_true",
+ dest='trailing_whitespace',
+ help='Check for trailing whitespace')
+ parser.add_argument('--permissive',
+ default=False,
+ action="store_true",
+ dest='permissive',
+ help='Do not raise an error even if issues are detected')
+
+ args, extras = parser.parse_known_args()
+ require(args.parser is not None,
+ 'Path to Markdown parser not provided',
+ True)
+ require(not extras,
+ 'Unexpected trailing command-line arguments "{0}"'.format(extras))
+
+ return args
+
+def check_config(reporter):
+ """Check configuration file."""
+
+ reporter.check_field(CONFIG["config_file"], 'configuration',
+ CONFIG, 'kind', 'lesson')
+ reporter.check_field(CONFIG["config_file"], 'configuration',
+ CONFIG, 'carpentry', ('swc', 'dc', 'lc', 'cp', 'incubator'))
+ reporter.check_field(CONFIG["config_file"], 'configuration', CONFIG, 'title')
+ reporter.check_field(CONFIG["config_file"], 'configuration', CONFIG, 'email')
+
+ for defaults in [
+ {'values': {'root': '.', 'layout': 'page'}},
+ {'values': {'root': '..', 'layout': 'episode'}, 'scope': {'type': 'episodes', 'path': ''}},
+ {'values': {'root': '..', 'layout': 'page'}, 'scope': {'type': 'extras', 'path': ''}}
+ ]:
+ error_text = 'incorrect settings for: root "{0}" layout "{1}"'
+ root = defaults["values"]["root"]
+ layout = defaults["values"]["layout"]
+ error_message = error_text.format(root, layout)
+
+ defaults_test = defaults in CONFIG.get('defaults', [])
+ reporter.check(defaults_test, 'configuration', error_message)
+
+def check_source_rmd(reporter, source_dir, parser):
+ """Check that Rmd episode files include `source: Rmd`"""
+
+ episode_rmd_dir = [os.path.join(source_dir, d) for d in SOURCE_RMD_DIRS]
+ episode_rmd_files = [os.path.join(d, '*.Rmd') for d in episode_rmd_dir]
+ results = {}
+ for pat in episode_rmd_files:
+ for f in glob.glob(pat):
+ data = read_markdown(parser, f)
+ dy = data['metadata']
+ if dy:
+ reporter.check_field(f, 'episode_rmd',
+ dy, 'source', 'Rmd')
+
+def read_references(reporter, ref_path):
+ """Read shared file of reference links, returning dictionary of valid references
+ {symbolic_name : URL}
+ """
+
+ if 'remote_theme' in CONFIG:
+ return {}
+
+ if not ref_path:
+ raise Warning("No filename has been provided.")
+
+ result = {}
+ urls_seen = set()
+
+ with open(ref_path, 'r', encoding='utf-8') as reader:
+ for (num, line) in enumerate(reader, 1):
+
+ # Skip empty lines
+ if len(line.strip()) == 0:
+ continue
+
+ # Skip HTML comments
+ if line.strip().startswith(""):
+ continue
+
+ # Skip Liquid's {% include ... %} lines
+ if P_INTERNAL_INCLUDE_LINK.search(line):
+ continue
+
+ m = P_INTERNAL_LINK_DEF.search(line)
+
+ message = '{}: {} not a valid reference: {}'
+ require(m, message.format(ref_path, num, line.rstrip()))
+
+ name = m.group(1)
+ url = m.group(2)
+
+ message = 'Empty reference at {0}:{1}'
+ require(name, message.format(ref_path, num))
+
+ unique_name = name not in result
+ unique_url = url not in urls_seen
+
+ reporter.check(unique_name,
+ ref_path,
+ 'Duplicate reference name {0} at line {1}',
+ name, num)
+
+ reporter.check(unique_url,
+ ref_path,
+ 'Duplicate definition of URL {0} at line {1}',
+ url, num)
+
+ result[name] = url
+ urls_seen.add(url)
+
+ return result
+
+
+def read_all_markdown(source_dir, parser):
+ """Read source files, returning
+ {path : {'metadata':yaml, 'metadata_len':N, 'text':text, 'lines':[(i, line, len)], 'doc':doc}}
+ """
+
+ all_dirs = [os.path.join(source_dir, d) for d in SOURCE_DIRS]
+ all_patterns = [os.path.join(d, '*.md') for d in all_dirs]
+ result = {}
+ for pat in all_patterns:
+ for filename in glob.glob(pat):
+ data = read_markdown(parser, filename)
+ if data:
+ result[filename] = data
+ return result
+
+
+def check_fileset(source_dir, reporter, filenames_present):
+ """Are all required files present? Are extraneous files present?"""
+
+ # Check files with predictable names.
+ required = [os.path.join(source_dir, p) for p in REQUIRED_FILES]
+ missing = set(required) - set(filenames_present)
+ for m in missing:
+ reporter.add(None, 'Missing required file {0}', m)
+
+ # Check episode files' names.
+ seen = []
+ for filename in filenames_present:
+ if '_episodes' not in filename:
+ continue
+
+ # split path to check episode name
+ base_name = os.path.basename(filename)
+ m = P_EPISODE_FILENAME.search(base_name)
+ if m and m.group(1):
+ seen.append(m.group(1))
+ else:
+ reporter.add(
+ None, 'Episode {0} has badly-formatted filename', filename)
+
+ # Check for duplicate episode numbers.
+ reporter.check(len(seen) == len(set(seen)),
+ None,
+ 'Duplicate episode numbers {0} vs {1}',
+ sorted(seen), sorted(set(seen)))
+
+ # Check that numbers are consecutive.
+ seen = sorted([int(s) for s in seen])
+ clean = True
+ for i in range(len(seen) - 1):
+ clean = clean and ((seen[i+1] - seen[i]) == 1)
+ reporter.check(clean,
+ None,
+ 'Missing or non-consecutive episode numbers {0}',
+ seen)
+
+
+def create_checker(args, filename, info):
+ """Create appropriate checker for file."""
+
+ for (pat, cls) in CHECKERS:
+ if pat.search(filename):
+ return cls(args, filename, **info)
+ return NotImplemented
+
+class CheckBase:
+ """Base class for checking Markdown files."""
+
+ def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
+ """Cache arguments for checking."""
+
+ self.args = args
+ self.reporter = self.args.reporter # for convenience
+ self.filename = filename
+ self.metadata = metadata
+ self.metadata_len = metadata_len
+ self.text = text
+ self.lines = lines
+ self.doc = doc
+
+ self.layout = None
+
+ def check(self):
+ """Run tests."""
+
+ self.check_metadata()
+ self.check_line_lengths()
+ self.check_trailing_whitespace()
+ self.check_blockquote_classes()
+ self.check_codeblock_classes()
+ self.check_defined_link_references()
+
+ def check_metadata(self):
+ """Check the YAML metadata."""
+
+ self.reporter.check(self.metadata is not None,
+ self.filename,
+ 'Missing metadata entirely')
+
+ if self.metadata and (self.layout is not None):
+ self.reporter.check_field(
+ self.filename, 'metadata', self.metadata, 'layout', self.layout)
+
+ def check_line_lengths(self):
+ """Check the raw text of the lesson body."""
+
+ if self.args.line_lengths:
+ over_limit = []
+
+ for (i, l, n) in self.lines:
+ # Report lines that are longer than the suggested
+ # line length limit only if they're not
+ # link-only or image-only lines.
+ if n > MAX_LINE_LEN and not P_LINK_IMAGE_LINE.match(l):
+ over_limit.append(i)
+
+ self.reporter.check(not over_limit,
+ self.filename,
+ 'Line(s) too long: {0}',
+ ', '.join([str(i) for i in over_limit]))
+
+ def check_trailing_whitespace(self):
+ """Check for whitespace at the ends of lines."""
+
+ if self.args.trailing_whitespace:
+ trailing = [
+ i for (i, l, n) in self.lines if P_TRAILING_WHITESPACE.match(l)]
+ self.reporter.check(not trailing,
+ self.filename,
+ 'Line(s) end with whitespace: {0}',
+ ', '.join([str(i) for i in trailing]))
+
+ def check_blockquote_classes(self):
+ """Check that all blockquotes have known classes."""
+
+ for node in self.find_all(self.doc, {'type': 'blockquote'}):
+ cls = self.get_val(node, 'attr', 'class')
+ self.reporter.check(cls in KNOWN_BLOCKQUOTES,
+ (self.filename, self.get_loc(node)),
+ 'Unknown or missing blockquote type {0}',
+ cls)
+
+ def check_codeblock_classes(self):
+ """Check that all code blocks have known classes."""
+
+ for node in self.find_all(self.doc, {'type': 'codeblock'}):
+ cls = self.get_val(node, 'attr', 'class')
+ self.reporter.check(cls is not None and (cls in KNOWN_CODEBLOCKS or
+ cls.startswith('language-')),
+ (self.filename, self.get_loc(node)),
+ 'Unknown or missing code block type {0}',
+ cls)
+
+ def check_defined_link_references(self):
+ """Check that defined links resolve in the file.
+
+ Internally-defined links match the pattern [text][label].
+ """
+
+ result = set()
+ for node in self.find_all(self.doc, {'type': 'text'}):
+ for match in P_INTERNAL_LINK_REF.findall(node['value']):
+ text = match[0]
+ link = match[1]
+ if link not in self.args.references:
+ result.add('"{0}"=>"{1}"'.format(text, link))
+ self.reporter.check(not result,
+ self.filename,
+ 'Internally-defined links may be missing definitions: {0}',
+ ', '.join(sorted(result)))
+
+ def find_all(self, node, pattern, accum=None):
+ """Find all matches for a pattern."""
+
+ assert isinstance(pattern, dict), 'Patterns must be dictionaries'
+ if accum is None:
+ accum = []
+ if self.match(node, pattern):
+ accum.append(node)
+ for child in node.get('children', []):
+ self.find_all(child, pattern, accum)
+ return accum
+
+ def match(self, node, pattern):
+ """Does this node match the given pattern?"""
+
+ for key in pattern:
+ if key not in node:
+ return False
+ val = pattern[key]
+ if isinstance(val, str):
+ if node[key] != val:
+ return False
+ elif isinstance(val, dict):
+ if not self.match(node[key], val):
+ return False
+ return True
+
+ @staticmethod
+ def get_val(node, *chain):
+ """Get value one or more levels down."""
+
+ curr = node
+ for selector in chain:
+ curr = curr.get(selector, None)
+ if curr is None:
+ break
+ return curr
+
+ def get_loc(self, node):
+ """Convenience method to get node's line number."""
+
+ result = self.get_val(node, 'options', 'location')
+ if self.metadata_len is not None:
+ result += self.metadata_len
+ return result
+
+
+class CheckNonJekyll(CheckBase):
+ """Check a file that isn't translated by Jekyll."""
+
+ def check_metadata(self):
+ self.reporter.check(self.metadata is None,
+ self.filename,
+ 'Unexpected metadata')
+
+
+class CheckIndex(CheckBase):
+ """Check the main index page."""
+
+ def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
+ self.layout = 'lesson'
+
+ def check_metadata(self):
+ super().check_metadata()
+ self.reporter.check(self.metadata.get('root', '') == '.',
+ self.filename,
+ 'Root not set to "."')
+
+
+class CheckEpisode(CheckBase):
+ """Check an episode page."""
+
+ def check(self):
+ """Run extra tests."""
+
+ super().check()
+ self.check_reference_inclusion()
+
+ def check_metadata(self):
+ super().check_metadata()
+ if self.metadata:
+ if 'layout' in self.metadata:
+ if self.metadata['layout'] == 'break':
+ self.check_metadata_fields(BREAK_METADATA_FIELDS)
+ else:
+ self.reporter.add(self.filename,
+ 'Unknown episode layout "{0}"',
+ self.metadata['layout'])
+ else:
+ self.check_metadata_fields(TEACHING_METADATA_FIELDS)
+
+ def check_metadata_fields(self, expected):
+ """Check metadata fields."""
+ for (name, type_) in expected:
+ if name not in self.metadata:
+ self.reporter.add(self.filename,
+ 'Missing metadata field {0}',
+ name)
+ elif not isinstance(self.metadata[name], type_):
+ self.reporter.add(self.filename,
+ '"{0}" has wrong type in metadata ({1} instead of {2})',
+ name, type(self.metadata[name]), type_)
+
+ def check_reference_inclusion(self):
+ """Check that links file has been included."""
+
+ if 'remote_theme' in CONFIG:
+ return
+
+ if not self.args.reference_path:
+ return
+
+ for (i, last_line, line_len) in reversed(self.lines):
+ if last_line:
+ break
+
+ require(last_line,
+ 'No non-empty lines in {0}'.format(self.filename))
+
+ include_filename = os.path.split(self.args.reference_path)[-1]
+ if include_filename not in last_line:
+ self.reporter.add(self.filename,
+ 'episode does not include "{0}"',
+ include_filename)
+
+
+class CheckReference(CheckBase):
+ """Check the reference page."""
+
+ def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
+ self.layout = 'reference'
+
+
+class CheckGeneric(CheckBase):
+ """Check a generic page."""
+
+ def __init__(self, args, filename, metadata, metadata_len, text, lines, doc):
+ super().__init__(args, filename, metadata, metadata_len, text, lines, doc)
+
+
+CHECKERS = [
+ (re.compile(r'CONTRIBUTING\.md'), CheckNonJekyll),
+ (re.compile(r'README\.md'), CheckNonJekyll),
+ (re.compile(r'index\.md'), CheckIndex),
+ (re.compile(r'reference\.md'), CheckReference),
+ # '.' below is what's passed on the command line via '-s' flag
+ (re.compile(os.path.join('.','_episodes', '[^/]*\.md')), CheckEpisode),
+ (re.compile(r'.*\.md'), CheckGeneric)
+]
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
new file mode 100644
index 0000000..79ec05c
--- /dev/null
+++ b/bin/lesson_initialize.py
@@ -0,0 +1,47 @@
+"""Initialize a newly-created repository."""
+
+
+import sys
+import os
+import shutil
+
+BOILERPLATE = (
+ 'AUTHORS',
+ 'CITATION',
+ 'CONTRIBUTING.md',
+ 'README.md',
+ '_config.yml',
+ os.path.join('_episodes', '01-introduction.md'),
+ os.path.join('_extras', 'about.md'),
+ os.path.join('_extras', 'discuss.md'),
+ os.path.join('_extras', 'figures.md'),
+ os.path.join('_extras', 'guide.md'),
+ 'index.md',
+ 'reference.md',
+ 'setup.md',
+)
+
+
+def main():
+ """Check for collisions, then create."""
+
+ # Check.
+ errors = False
+ for path in BOILERPLATE:
+ if os.path.exists(path):
+ print('Warning: {0} already exists.'.format(path), file=sys.stderr)
+ errors = True
+ if errors:
+ print('**Exiting without creating files.**', file=sys.stderr)
+ sys.exit(1)
+
+ # Create.
+ for path in BOILERPLATE:
+ shutil.copyfile(
+ os.path.join('bin', 'boilerplate', path),
+ path
+ )
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bin/markdown_ast.rb b/bin/markdown_ast.rb
new file mode 100755
index 0000000..2ef3f77
--- /dev/null
+++ b/bin/markdown_ast.rb
@@ -0,0 +1,13 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+# Use Kramdown parser to produce AST for Markdown document.
+
+require 'kramdown'
+require 'kramdown-parser-gfm'
+require 'json'
+
+markdown = $stdin.read
+doc = Kramdown::Document.new(markdown, input: 'GFM', hard_wrap: false)
+tree = doc.to_hash_a_s_t
+puts JSON.pretty_generate(tree)
diff --git a/bin/repo_check.py b/bin/repo_check.py
new file mode 100644
index 0000000..6988ca5
--- /dev/null
+++ b/bin/repo_check.py
@@ -0,0 +1,181 @@
+"""
+Check repository settings.
+"""
+
+
+import sys
+import os
+from subprocess import Popen, PIPE
+import re
+from argparse import ArgumentParser
+
+from util import require
+from reporter import Reporter
+
+# Import this way to produce a more useful error message.
+try:
+ import requests
+except ImportError:
+ print('Unable to import requests module: please install requests', file=sys.stderr)
+ sys.exit(1)
+
+
+# Pattern to match Git command-line output for remotes => (user name, project name).
+P_GIT_REMOTE = re.compile(r'upstream\s+(?:https://|git@)github.com[:/]([^/]+)/([^.]+)(\.git)?\s+\(fetch\)')
+
+# Repository URL format string.
+F_REPO_URL = 'https://github.com/{0}/{1}/'
+
+# Pattern to match repository URLs => (user name, project name)
+P_REPO_URL = re.compile(r'https?://github\.com/([^.]+)/([^/]+)/?')
+
+# API URL format string.
+F_API_URL = 'https://api.github.com/repos/{0}/{1}/labels'
+
+# Expected labels and colors.
+EXPECTED = {
+ 'help wanted': 'dcecc7',
+ 'status:in progress': '9bcc65',
+ 'status:changes requested': '679f38',
+ 'status:wait': 'fff2df',
+ 'status:refer to cac': 'ffdfb2',
+ 'status:need more info': 'ee6c00',
+ 'status:blocked': 'e55100',
+ 'status:out of scope': 'eeeeee',
+ 'status:duplicate': 'bdbdbd',
+ 'type:typo text': 'f8bad0',
+ 'type:bug': 'eb3f79',
+ 'type:formatting': 'ac1357',
+ 'type:template and tools': '7985cb',
+ 'type:instructor guide': '00887a',
+ 'type:discussion': 'b2e5fc',
+ 'type:enhancement': '7fdeea',
+ 'type:clarification': '00acc0',
+ 'type:teaching example': 'ced8dc',
+ 'good first issue': 'ffeb3a',
+ 'high priority': 'd22e2e'
+}
+
+
+def main():
+ """
+ Main driver.
+ """
+
+ args = parse_args()
+ reporter = Reporter()
+ repo_url = get_repo_url(args.repo_url)
+ check_labels(reporter, repo_url)
+ reporter.report()
+
+
+def parse_args():
+ """
+ Parse command-line arguments.
+ """
+
+ parser = ArgumentParser(description="""Check repository settings.""")
+ parser.add_argument('-r', '--repo',
+ default=None,
+ dest='repo_url',
+ help='repository URL')
+ parser.add_argument('-s', '--source',
+ default=os.curdir,
+ dest='source_dir',
+ help='source directory')
+
+ args, extras = parser.parse_known_args()
+ require(not extras,
+ 'Unexpected trailing command-line arguments "{0}"'.format(extras))
+
+ return args
+
+
+def get_repo_url(repo_url):
+ """
+ Figure out which repository to query.
+ """
+
+ # Explicitly specified.
+ if repo_url is not None:
+ return repo_url
+
+ # Guess.
+ cmd = 'git remote -v'
+ p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
+ close_fds=True, universal_newlines=True, encoding='utf-8')
+ stdout_data, stderr_data = p.communicate()
+ stdout_data = stdout_data.split('\n')
+ matches = [P_GIT_REMOTE.match(line) for line in stdout_data]
+ matches = [m for m in matches if m is not None]
+ require(len(matches) == 1,
+ 'Unexpected output from git remote command: "{0}"'.format(matches))
+
+ username = matches[0].group(1)
+ require(
+ username, 'empty username in git remote output {0}'.format(matches[0]))
+
+ project_name = matches[0].group(2)
+ require(
+ username, 'empty project name in git remote output {0}'.format(matches[0]))
+
+ url = F_REPO_URL.format(username, project_name)
+ return url
+
+
+def check_labels(reporter, repo_url):
+ """
+ Check labels in repository.
+ """
+
+ actual = get_labels(repo_url)
+ extra = set(actual.keys()) - set(EXPECTED.keys())
+
+ reporter.check(not extra,
+ None,
+ 'Extra label(s) in repository {0}: {1}',
+ repo_url, ', '.join(sorted(extra)))
+
+ missing = set(EXPECTED.keys()) - set(actual.keys())
+ reporter.check(not missing,
+ None,
+ 'Missing label(s) in repository {0}: {1}',
+ repo_url, ', '.join(sorted(missing)))
+
+ overlap = set(EXPECTED.keys()).intersection(set(actual.keys()))
+ 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}',
+ name, repo_url, EXPECTED[name], actual[name])
+
+
+def get_labels(repo_url):
+ """
+ Get actual labels from repository.
+ """
+
+ m = P_REPO_URL.match(repo_url)
+ require(
+ m, 'repository URL {0} does not match expected pattern'.format(repo_url))
+
+ username = m.group(1)
+ require(username, 'empty username in repository URL {0}'.format(repo_url))
+
+ project_name = m.group(2)
+ require(
+ username, 'empty project name in repository URL {0}'.format(repo_url))
+
+ url = F_API_URL.format(username, project_name)
+ r = requests.get(url)
+ require(r.status_code == 200,
+ 'Request for {0} failed with {1}'.format(url, r.status_code))
+
+ result = {}
+ for entry in r.json():
+ result[entry['name']] = entry['color']
+ return result
+
+
+if __name__ == '__main__':
+ main()
diff --git a/bin/reporter.py b/bin/reporter.py
new file mode 100644
index 0000000..550dbf0
--- /dev/null
+++ b/bin/reporter.py
@@ -0,0 +1,75 @@
+import sys
+
+class Reporter:
+ """Collect and report errors."""
+
+ # Marker to show that an expected value hasn't been provided.
+ # (Can't use 'None' because that might be a legitimate value.)
+ _DEFAULT_REPORTER = []
+
+ def __init__(self):
+ """Constructor."""
+ self.messages = []
+
+ def check_field(self, filename, name, values, key, expected=_DEFAULT_REPORTER):
+ """Check that a dictionary has an expected value."""
+
+ if key not in values:
+ self.add(filename, '{0} does not contain {1}', name, key)
+ elif expected is self._DEFAULT_REPORTER:
+ pass
+ elif type(expected) in (tuple, set, list):
+ if values[key] not in expected:
+ self.add(
+ filename, '{0} {1} value {2} is not in {3}', name, key, values[key], expected)
+ elif values[key] != expected:
+ self.add(filename, '{0} {1} is {2} not {3}',
+ name, key, values[key], expected)
+
+ def check(self, condition, location, fmt, *args):
+ """Append error if condition not met."""
+
+ if not condition:
+ self.add(location, fmt, *args)
+
+ def add(self, location, fmt, *args):
+ """Append error unilaterally."""
+
+ self.messages.append((location, fmt.format(*args)))
+
+ @staticmethod
+ def pretty(item):
+ location, message = item
+ if isinstance(location, type(None)):
+ return message
+ elif isinstance(location, str):
+ return location + ': ' + message
+ elif isinstance(location, tuple):
+ return '{0}:{1}: '.format(*location) + message
+
+ print('Unknown item "{0}"'.format(item), file=sys.stderr)
+ return NotImplemented
+
+ @staticmethod
+ def key(item):
+ location, message = item
+ if isinstance(location, type(None)):
+ return ('', -1, message)
+ elif isinstance(location, str):
+ return (location, -1, message)
+ elif isinstance(location, tuple):
+ return (location[0], location[1], message)
+
+ print('Unknown item "{0}"'.format(item), file=sys.stderr)
+ return NotImplemented
+
+ def report(self, stream=sys.stdout):
+ """Report all messages in order."""
+
+ if not self.messages:
+ return
+
+ for m in sorted(self.messages, key=self.key):
+ print(self.pretty(m), file=stream)
+
+
diff --git a/bin/run-make-docker-serve.sh b/bin/run-make-docker-serve.sh
new file mode 100755
index 0000000..1e09178
--- /dev/null
+++ b/bin/run-make-docker-serve.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -o errexit
+set -o pipefail
+set -o nounset
+
+
+bundle install
+bundle update
+exec bundle exec jekyll serve --host 0.0.0.0
diff --git a/bin/test_lesson_check.py b/bin/test_lesson_check.py
new file mode 100644
index 0000000..7a6d603
--- /dev/null
+++ b/bin/test_lesson_check.py
@@ -0,0 +1,19 @@
+import unittest
+
+import lesson_check
+import reporter
+
+
+class TestFileList(unittest.TestCase):
+ def setUp(self):
+ self.reporter = reporter.Reporter() # TODO: refactor reporter class.
+
+ def test_file_list_has_expected_entries(self):
+ # For first pass, simply assume that all required files are present
+
+ lesson_check.check_fileset('', self.reporter, lesson_check.REQUIRED_FILES)
+ self.assertEqual(len(self.reporter.messages), 0)
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/bin/util.py b/bin/util.py
new file mode 100644
index 0000000..1398c37
--- /dev/null
+++ b/bin/util.py
@@ -0,0 +1,111 @@
+import sys
+import os
+import json
+from subprocess import Popen, PIPE
+
+# Import this way to produce a more useful error message.
+try:
+ import yaml
+except ImportError:
+ print('Unable to import YAML module: please install PyYAML', file=sys.stderr)
+ sys.exit(1)
+
+__all__ = ['check_unwanted_files', 'load_yaml', 'read_markdown', 'require']
+
+# Files that shouldn't be present.
+UNWANTED_FILES = [
+ '.nojekyll'
+]
+
+def read_markdown(parser, path):
+ """
+ Get YAML and AST for Markdown file, returning
+ {'metadata':yaml, 'metadata_len':N, 'text':text, 'lines':[(i, line, len)], 'doc':doc}.
+ """
+
+ # Split and extract YAML (if present).
+ with open(path, 'r', encoding='utf-8') as reader:
+ body = reader.read()
+ metadata_raw, metadata_yaml, body = split_metadata(path, body)
+
+ # Split into lines.
+ metadata_len = 0 if metadata_raw is None else metadata_raw.count('\n')
+ lines = [(metadata_len+i+1, line, len(line))
+ for (i, line) in enumerate(body.split('\n'))]
+
+ # Parse Markdown.
+ cmd = 'bundle exec ruby {0}'.format(parser)
+ p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE,
+ close_fds=True, universal_newlines=True, encoding='utf-8')
+ stdout_data, stderr_data = p.communicate(body)
+ doc = json.loads(stdout_data)
+
+ return {
+ 'metadata': metadata_yaml,
+ 'metadata_len': metadata_len,
+ 'text': body,
+ 'lines': lines,
+ 'doc': doc
+ }
+
+
+def split_metadata(path, text):
+ """
+ Get raw (text) metadata, metadata as YAML, and rest of body.
+ If no metadata, return (None, None, body).
+ """
+
+ metadata_raw = None
+ metadata_yaml = None
+
+ pieces = text.split('---', 2)
+ if len(pieces) == 3:
+ metadata_raw = pieces[1]
+ text = pieces[2]
+ try:
+ metadata_yaml = yaml.load(metadata_raw, Loader=yaml.SafeLoader)
+ except yaml.YAMLError as e:
+ message = 'Unable to parse YAML header in {0}:\n{1}'
+ print(message.format(path, e), file=sys.stderr)
+
+ return metadata_raw, metadata_yaml, text
+
+
+def load_yaml(filename):
+ """
+ Wrapper around YAML loading so that 'import yaml' is only needed
+ in one file.
+ """
+
+ try:
+ with open(filename, 'r', encoding='utf-8') as reader:
+ return yaml.load(reader, Loader=yaml.SafeLoader)
+ except yaml.YAMLError as e:
+ message = 'ERROR: Unable to load YAML file {0}:\n{1}'
+ print(message.format(filename, e), file=sys.stderr)
+ except (FileNotFoundError, IOError):
+ message = 'ERROR: File {} not found'
+ print(message.format(filename), file=sys.stderr)
+
+ return {}
+
+def check_unwanted_files(dir_path, reporter):
+ """
+ Check that unwanted files are not present.
+ """
+
+ for filename in UNWANTED_FILES:
+ path = os.path.join(dir_path, filename)
+ reporter.check(not os.path.exists(path),
+ path,
+ "Unwanted file found")
+
+
+def require(condition, message, fatal=False):
+ """Fail if condition not met."""
+
+ if not condition:
+ print(message, file=sys.stderr)
+
+ if fatal:
+ sys.exit(1)
diff --git a/bin/workshop_check.py b/bin/workshop_check.py
new file mode 100644
index 0000000..312b1a1
--- /dev/null
+++ b/bin/workshop_check.py
@@ -0,0 +1,419 @@
+'''Check that a workshop's index.html metadata is valid. See the
+docstrings on the checking functions for a summary of the checks.
+'''
+
+
+import sys
+import os
+import re
+from datetime import date
+from util import split_metadata, load_yaml, check_unwanted_files
+from reporter import Reporter
+
+# Metadata field patterns.
+EMAIL_PATTERN = r'[^@]+@[^@]+\.[^@]+'
+HUMANTIME_PATTERN = r'((0?[1-9]|1[0-2]):[0-5]\d(am|pm)(-|to)(0?[1-9]|1[0-2]):[0-5]\d(am|pm))|((0?\d|1\d|2[0-3]):[0-5]\d(-|to)(0?\d|1\d|2[0-3]):[0-5]\d)'
+EVENTBRITE_PATTERN = r'\d{9,10}'
+URL_PATTERN = r'https?://.+'
+
+# Defaults.
+CARPENTRIES = ("dc", "swc", "lc", "cp")
+DEFAULT_CONTACT_EMAIL = 'team@carpentries.org'
+
+USAGE = 'Usage: "workshop_check.py path/to/root/directory"'
+
+# Country and language codes. Note that codes mean different things: 'ar'
+# is 'Arabic' as a language but 'Argentina' as a country.
+
+ISO_COUNTRY = [
+ 'ad', 'ae', 'af', 'ag', 'ai', 'al', 'am', 'an', 'ao', 'aq', 'ar', 'as',
+ 'at', 'au', 'aw', 'ax', 'az', 'ba', 'bb', 'bd', 'be', 'bf', 'bg', 'bh',
+ 'bi', 'bj', 'bm', 'bn', 'bo', 'br', 'bs', 'bt', 'bv', 'bw', 'by', 'bz',
+ 'ca', 'cc', 'cd', 'cf', 'cg', 'ch', 'ci', 'ck', 'cl', 'cm', 'cn', 'co',
+ 'cr', 'cu', 'cv', 'cx', 'cy', 'cz', 'de', 'dj', 'dk', 'dm', 'do', 'dz',
+ 'ec', 'ee', 'eg', 'eh', 'er', 'es', 'et', 'eu', 'fi', 'fj', 'fk', 'fm',
+ 'fo', 'fr', 'ga', 'gb', 'gd', 'ge', 'gf', 'gg', 'gh', 'gi', 'gl', 'gm',
+ 'gn', 'gp', 'gq', 'gr', 'gs', 'gt', 'gu', 'gw', 'gy', 'hk', 'hm', 'hn',
+ 'hr', 'ht', 'hu', 'id', 'ie', 'il', 'im', 'in', 'io', 'iq', 'ir', 'is',
+ 'it', 'je', 'jm', 'jo', 'jp', 'ke', 'kg', 'kh', 'ki', 'km', 'kn', 'kp',
+ 'kr', 'kw', 'ky', 'kz', 'la', 'lb', 'lc', 'li', 'lk', 'lr', 'ls', 'lt',
+ 'lu', 'lv', 'ly', 'ma', 'mc', 'md', 'me', 'mg', 'mh', 'mk', 'ml', 'mm',
+ 'mn', 'mo', 'mp', 'mq', 'mr', 'ms', 'mt', 'mu', 'mv', 'mw', 'mx', 'my',
+ 'mz', 'na', 'nc', 'ne', 'nf', 'ng', 'ni', 'nl', 'no', 'np', 'nr', 'nu',
+ 'nz', 'om', 'pa', 'pe', 'pf', 'pg', 'ph', 'pk', 'pl', 'pm', 'pn', 'pr',
+ 'ps', 'pt', 'pw', 'py', 'qa', 're', 'ro', 'rs', 'ru', 'rw', 'sa', 'sb',
+ 'sc', 'sd', 'se', 'sg', 'sh', 'si', 'sj', 'sk', 'sl', 'sm', 'sn', 'so',
+ 'sr', 'st', 'sv', 'sy', 'sz', 'tc', 'td', 'tf', 'tg', 'th', 'tj', 'tk',
+ 'tl', 'tm', 'tn', 'to', 'tr', 'tt', 'tv', 'tw', 'tz', 'ua', 'ug', 'um',
+ 'us', 'uy', 'uz', 'va', 'vc', 've', 'vg', 'vi', 'vn', 'vu', 'wf', 'ws',
+ 'ye', 'yt', 'za', 'zm', 'zw'
+]
+
+ISO_LANGUAGE = [
+ 'aa', 'ab', 'ae', 'af', 'ak', 'am', 'an', 'ar', 'as', 'av', 'ay', 'az',
+ 'ba', 'be', 'bg', 'bh', 'bi', 'bm', 'bn', 'bo', 'br', 'bs', 'ca', 'ce',
+ 'ch', 'co', 'cr', 'cs', 'cu', 'cv', 'cy', 'da', 'de', 'dv', 'dz', 'ee',
+ 'el', 'en', 'eo', 'es', 'et', 'eu', 'fa', 'ff', 'fi', 'fj', 'fo', 'fr',
+ 'fy', 'ga', 'gd', 'gl', 'gn', 'gu', 'gv', 'ha', 'he', 'hi', 'ho', 'hr',
+ 'ht', 'hu', 'hy', 'hz', 'ia', 'id', 'ie', 'ig', 'ii', 'ik', 'io', 'is',
+ 'it', 'iu', 'ja', 'jv', 'ka', 'kg', 'ki', 'kj', 'kk', 'kl', 'km', 'kn',
+ 'ko', 'kr', 'ks', 'ku', 'kv', 'kw', 'ky', 'la', 'lb', 'lg', 'li', 'ln',
+ 'lo', 'lt', 'lu', 'lv', 'mg', 'mh', 'mi', 'mk', 'ml', 'mn', 'mr', 'ms',
+ 'mt', 'my', 'na', 'nb', 'nd', 'ne', 'ng', 'nl', 'nn', 'no', 'nr', 'nv',
+ 'ny', 'oc', 'oj', 'om', 'or', 'os', 'pa', 'pi', 'pl', 'ps', 'pt', 'qu',
+ 'rm', 'rn', 'ro', 'ru', 'rw', 'sa', 'sc', 'sd', 'se', 'sg', 'si', 'sk',
+ 'sl', 'sm', 'sn', 'so', 'sq', 'sr', 'ss', 'st', 'su', 'sv', 'sw', 'ta',
+ 'te', 'tg', 'th', 'ti', 'tk', 'tl', 'tn', 'to', 'tr', 'ts', 'tt', 'tw',
+ 'ty', 'ug', 'uk', 'ur', 'uz', 've', 'vi', 'vo', 'wa', 'wo', 'xh', 'yi',
+ 'yo', 'za', 'zh', 'zu'
+]
+
+
+def look_for_fixme(func):
+ """Decorator to fail test if text argument starts with "FIXME"."""
+
+ def inner(arg):
+ if (arg is not None) and \
+ isinstance(arg, str) and \
+ arg.lstrip().startswith('FIXME'):
+ return False
+ return func(arg)
+ return inner
+
+
+@look_for_fixme
+def check_layout(layout):
+ '''"layout" in YAML header must be "workshop".'''
+
+ return layout == 'workshop'
+
+
+@look_for_fixme
+def check_carpentry(layout):
+ '''"carpentry" in YAML header must be "dc", "swc", "lc", or "cp".'''
+
+ return layout in CARPENTRIES
+
+
+@look_for_fixme
+def check_country(country):
+ '''"country" must be a lowercase ISO-3166 two-letter code.'''
+
+ return country in ISO_COUNTRY
+
+
+@look_for_fixme
+def check_language(language):
+ '''"language" must be a lowercase ISO-639 two-letter code.'''
+
+ return language in ISO_LANGUAGE
+
+
+@look_for_fixme
+def check_humandate(date):
+ """
+ 'humandate' must be a human-readable date with a 3-letter month
+ and 4-digit year. Examples include 'Feb 18-20, 2025' and 'Feb 18
+ and 20, 2025'. It may be in languages other than English, but the
+ month name should be kept short to aid formatting of the main
+ Carpentries web site.
+ """
+
+ if ',' not in date:
+ return False
+
+ month_dates, year = date.split(',')
+
+ # The first three characters of month_dates are not empty
+ month = month_dates[:3]
+ if any(char == ' ' for char in month):
+ return False
+
+ # But the fourth character is empty ("February" is illegal)
+ if month_dates[3] != ' ':
+ return False
+
+ # year contains *only* numbers
+ try:
+ int(year)
+ except:
+ return False
+
+ return True
+
+
+@look_for_fixme
+def check_humantime(time):
+ """
+ 'humantime' is a human-readable start and end time for the
+ workshop, such as '09:00 - 16:00'.
+ """
+
+ return bool(re.match(HUMANTIME_PATTERN, time.replace(' ', '')))
+
+
+def check_date(this_date):
+ """
+ 'startdate' and 'enddate' are machine-readable start and end dates
+ for the workshop, and must be in YYYY-MM-DD format, e.g.,
+ '2015-07-01'.
+ """
+
+ # YAML automatically loads valid dates as datetime.date.
+ return isinstance(this_date, date)
+
+
+@look_for_fixme
+def check_latitude_longitude(latlng):
+ """
+ 'latlng' must be a valid latitude and longitude represented as two
+ floating-point numbers separated by a comma.
+ """
+
+ try:
+ lat, lng = latlng.split(',')
+ lat = float(lat)
+ lng = float(lng)
+ return (-90.0 <= lat <= 90.0) and (-180.0 <= lng <= 180.0)
+ except ValueError:
+ return False
+
+
+def check_instructors(instructors):
+ """
+ 'instructor' must be a non-empty comma-separated list of quoted
+ names, e.g. ['First name', 'Second name', ...']. Do not use 'TBD'
+ or other placeholders.
+ """
+
+ # YAML automatically loads list-like strings as lists.
+ return isinstance(instructors, list) and len(instructors) > 0
+
+
+def check_helpers(helpers):
+ """
+ 'helper' must be a comma-separated list of quoted names,
+ e.g. ['First name', 'Second name', ...']. The list may be empty.
+ Do not use 'TBD' or other placeholders.
+ """
+
+ # YAML automatically loads list-like strings as lists.
+ return isinstance(helpers, list) and len(helpers) >= 0
+
+
+@look_for_fixme
+def check_emails(emails):
+ """
+ 'emails' must be a comma-separated list of valid email addresses.
+ The list may be empty. A valid email address consists of characters,
+ an '@', and more characters. It should not contain the default contact
+ """
+
+ # YAML automatically loads list-like strings as lists.
+ if (isinstance(emails, list) and len(emails) >= 0):
+ for email in emails:
+ if ((not bool(re.match(EMAIL_PATTERN, email))) or (email == DEFAULT_CONTACT_EMAIL)):
+ return False
+ else:
+ return False
+
+ return True
+
+
+def check_eventbrite(eventbrite):
+ """
+ 'eventbrite' (the Eventbrite registration key) must be 9 or more
+ digits. It may appear as an integer or as a string.
+ """
+
+ if isinstance(eventbrite, int):
+ return True
+ else:
+ return bool(re.match(EVENTBRITE_PATTERN, eventbrite))
+
+
+@look_for_fixme
+def check_collaborative_notes(collaborative_notes):
+ """
+ 'collaborative_notes' must be a valid URL.
+ """
+
+ return bool(re.match(URL_PATTERN, collaborative_notes))
+
+
+@look_for_fixme
+def check_pass(value):
+ """
+ This test always passes (it is used for 'checking' things like the
+ workshop address, for which no sensible validation is feasible).
+ """
+
+ return True
+
+
+HANDLERS = {
+ 'layout': (True, check_layout, 'layout isn\'t "workshop"'),
+
+ 'carpentry': (True, check_carpentry, 'carpentry isn\'t in ' +
+ ', '.join(CARPENTRIES)),
+
+ 'country': (True, check_country,
+ 'country invalid: must use lowercase two-letter ISO code ' +
+ 'from ' + ', '.join(ISO_COUNTRY)),
+
+ 'language': (False, check_language,
+ 'language invalid: must use lowercase two-letter ISO code' +
+ ' from ' + ', '.join(ISO_LANGUAGE)),
+
+ 'humandate': (True, check_humandate,
+ 'humandate invalid. Please use three-letter months like ' +
+ '"Jan" and four-letter years like "2025"'),
+
+ 'humantime': (True, check_humantime,
+ 'humantime doesn\'t include numbers'),
+
+ 'startdate': (True, check_date,
+ 'startdate invalid. Must be of format year-month-day, ' +
+ 'i.e., 2014-01-31'),
+
+ 'enddate': (False, check_date,
+ 'enddate invalid. Must be of format year-month-day, i.e.,' +
+ ' 2014-01-31'),
+
+ 'latlng': (True, check_latitude_longitude,
+ 'latlng invalid. Check that it is two floating point ' +
+ 'numbers, separated by a comma'),
+
+ 'instructor': (True, check_instructors,
+ 'instructor list isn\'t a valid list of format ' +
+ '["First instructor", "Second instructor",..]'),
+
+ 'helper': (True, check_helpers,
+ 'helper list isn\'t a valid list of format ' +
+ '["First helper", "Second helper",..]'),
+
+ 'email': (True, check_emails,
+ 'contact email list isn\'t a valid list of format ' +
+ '["me@example.org", "you@example.org",..] or contains incorrectly formatted email addresses or ' +
+ '"{0}".'.format(DEFAULT_CONTACT_EMAIL)),
+
+ 'eventbrite': (False, check_eventbrite, 'Eventbrite key appears invalid'),
+
+ 'collaborative_notes': (False, check_collaborative_notes, 'Collaborative Notes URL appears invalid'),
+
+ 'venue': (False, check_pass, 'venue name not specified'),
+
+ 'address': (False, check_pass, 'address not specified')
+}
+
+# REQUIRED is all required categories.
+REQUIRED = {k for k in HANDLERS if HANDLERS[k][0]}
+
+# OPTIONAL is all optional categories.
+OPTIONAL = {k for k in HANDLERS if not HANDLERS[k][0]}
+
+
+def check_blank_lines(reporter, raw):
+ """
+ Blank lines are not allowed in category headers.
+ """
+
+ lines = [(i, x) for (i, x) in enumerate(
+ raw.strip().split('\n')) if not x.strip()]
+ reporter.check(not lines,
+ None,
+ 'Blank line(s) in header: {0}',
+ ', '.join(["{0}: {1}".format(i, x.rstrip()) for (i, x) in lines]))
+
+
+def check_categories(reporter, left, right, msg):
+ """
+ Report differences (if any) between two sets of categories.
+ """
+
+ diff = left - right
+ reporter.check(len(diff) == 0,
+ None,
+ '{0}: offending entries {1}',
+ msg, sorted(list(diff)))
+
+
+def check_file(reporter, path, data):
+ """
+ Get header from file, call all other functions, and check file for
+ validity.
+ """
+
+ # Get metadata as text and as YAML.
+ raw, header, body = split_metadata(path, data)
+
+ # Do we have any blank lines in the header?
+ check_blank_lines(reporter, raw)
+
+ # Look through all header entries. If the category is in the input
+ # file and is either required or we have actual data (as opposed to
+ # a commented-out entry), we check it. If it *isn't* in the header
+ # but is required, report an error.
+ for category in HANDLERS:
+ required, handler, message = HANDLERS[category]
+ if category in header:
+ if required or header[category]:
+ reporter.check(handler(header[category]),
+ None,
+ '{0}\n actual value "{1}"',
+ message, header[category])
+ elif required:
+ reporter.add(None,
+ 'Missing mandatory key "{0}"',
+ category)
+
+ # Check whether we have missing or too many categories
+ seen_categories = set(header.keys())
+ check_categories(reporter, REQUIRED, seen_categories,
+ 'Missing categories')
+ check_categories(reporter, seen_categories, REQUIRED.union(OPTIONAL),
+ 'Superfluous categories')
+
+
+def check_config(reporter, filename):
+ """
+ Check YAML configuration file.
+ """
+
+ config = load_yaml(filename)
+
+ kind = config.get('kind', None)
+ reporter.check(kind == 'workshop',
+ filename,
+ 'Missing or unknown kind of event: {0}',
+ kind)
+
+ carpentry = config.get('carpentry', None)
+ reporter.check(carpentry in ('swc', 'dc', 'lc', 'cp'),
+ filename,
+ 'Missing or unknown carpentry: {0}',
+ carpentry)
+
+
+def main():
+ '''Run as the main program.'''
+
+ if len(sys.argv) != 2:
+ print(USAGE, file=sys.stderr)
+ sys.exit(1)
+
+ root_dir = sys.argv[1]
+ index_file = os.path.join(root_dir, 'index.html')
+ config_file = os.path.join(root_dir, '_config.yml')
+
+ reporter = Reporter()
+ check_config(reporter, config_file)
+ check_unwanted_files(root_dir, reporter)
+ with open(index_file, encoding='utf-8') as reader:
+ data = reader.read()
+ check_file(reporter, index_file, data)
+ reporter.report()
+
+
+if __name__ == '__main__':
+ main()
diff --git a/code/.gitkeep b/code/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/config.yaml b/config.yaml
deleted file mode 100644
index 53000c2..0000000
--- a/config.yaml
+++ /dev/null
@@ -1,80 +0,0 @@
-#------------------------------------------------------------
-# Values for this lesson.
-#------------------------------------------------------------
-
-# Which carpentry is this (swc, dc, lc, or cp)?
-# swc: Software Carpentry
-# dc: Data Carpentry
-# lc: Library Carpentry
-# cp: Carpentries (to use for instructor training for instance)
-# incubator: The Carpentries Incubator
-#
-# This option supports custom types so lessons can be branded
-# and themed with your own logo and alt-text (see `carpentry_description`)
-# See https://carpentries.github.io/sandpaper-docs/editing.html#adding-a-custom-logo
-carpentry: 'incubator'
-
-# Alt-text description of the lesson.
-carpentry_description: 'EIC Tutorials'
-
-# Overall title for pages.
-title: 'Analyzing EIC Simulation Output'
-
-# Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: 2021-01-01
-
-# Comma-separated list of keywords for the lesson
-keywords: 'EIC, ePIC, EICrecon, analysis, ROOT, uproot, RDataFrame, PODIO, reconstruction, simulation'
-
-# Life cycle stage of the lesson
-# possible values: pre-alpha, alpha, beta, stable
-life_cycle: 'stable'
-
-# License of the lesson
-license: 'CC-BY 4.0'
-
-# Link to the source repository for this lesson
-source: 'https://github.com/eic/tutorial-analysis'
-
-# Default branch of your lesson
-branch: 'main'
-
-# Who to contact if there are any issues
-contact: 'stephen.kay@york.ac.uk'
-
-# Navigation ------------------------------------------------
-#
-# Use the following menu items to specify the order of
-# individual pages in each dropdown section. Leave blank to
-# include all pages in the folder.
-
-# Order of episodes in your lesson
-episodes:
-- 01-introduction.md
-- 02-reconstruction-output.md
-- 03-analysis.md
-- 04-full_chain_analysis.md
-- 05-additional-resources.md
-
-# Information for Learners
-learners:
-- setup.md
-- reference.md
-- branch-dictionary.md
-- exercise-scripts.md
-- tree-pruning-script.md
-- examples-repo.md
-- discuss.md
-
-# Information for Instructors
-instructors:
-- instructor-notes.md
-
-# Learner Profiles
-profiles:
-- learner-profiles.md
-
-# Customisation ---------------------------------------------
-#
-# This space below is where custom yaml items (e.g. pinning
-# sandpaper and varnish versions) should live
diff --git a/data/.gitkeep b/data/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/episodes/05-additional-resources.md b/episodes/05-additional-resources.md
deleted file mode 100644
index f4992ef..0000000
--- a/episodes/05-additional-resources.md
+++ /dev/null
@@ -1,29 +0,0 @@
----
-title: "Additional Resources"
-teaching: 0
-exercises: 0
----
-
-::::::::::::::::::::::::::::::::::::::::::::: questions
-
-- Where can I access additional resources?
-
-:::::::::::::::::::::::::::::::::::::::::::::
-
-::::::::::::::::::::::::::::::::::::::::::::: objectives
-
-- Check out the additional resources under the Extras tab!
-
-:::::::::::::::::::::::::::::::::::::::::::::
-
-Check the "Extras" tab at the top of the page for some additional resources. In particular, check out the [Exercise Scripts](../learners/exercise-scripts.md) page for some skeletons/templates for the scripts above to get you started. I'll also add "completed" exercise scripts a bit later on.
-
-The [Examples Repository](../learners/examples-repo.md) page goes to a repository of analysis scripts/codes currently in use. You might want to refer to this as you get started on your own project if you are struggling to get off the ground. Or, it may just serve as an additional reference point.
-
-::::::::::::::::::::::::::::::::::::::::::::: keypoints
-
-- Starting scripts for the exercises are available.
-- Completed (tm) exercise scripts will be available after the lesson.
-- Talk to your colleagues in your WG if you don't know where to get started. Check the Examples Repository too!
-
-:::::::::::::::::::::::::::::::::::::::::::::
diff --git a/fig/.gitkeep b/fig/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/files/.gitkeep b/files/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/learners/files/TreePrune.C b/files/TreePrune.C
similarity index 100%
rename from learners/files/TreePrune.C
rename to files/TreePrune.C
diff --git a/index.md b/index.md
index a11f6b6..e625948 100644
--- a/index.md
+++ b/index.md
@@ -1,29 +1,19 @@
---
-site: sandpaper::sandpaper_site
+layout: lesson
+root: . # Is the only page that doesn't follow the pattern /:path/index.html
+permalink: index.html # Is the only page that doesn't follow the pattern /:path/index.html
---
-
-Welcome to the EIC Tutorial on analyzing simulation output!
-
-This tutorial covers how to access, explore, and analyze the reconstructed simulation output produced
-by the ePIC software stack (EICrecon), using ROOT, Python/uproot, RDataFrame, and PODIO based
-approaches.
-
-::::::::::::::::::::::::::::::::::::::::::::: prereq
-
-## Prerequisites
-
-Knowledge of CERN ROOT and/or Python/RDataFrames is assumed. Please take a look at the
-[Setup](learners/setup.md) page for necessary prerequisites for this lesson.
-
-This tutorial follows other tutorials in the EIC series:
-
-- [Setting Up Your Environment](https://eic.github.io/tutorial-setting-up-environment/)
-
-Further information is included in other tutorials:
-
-- [Geometry Development with DD4hep](https://eic.github.io/tutorial-geometry-development-using-dd4hep/)
-- [Simulations Using DDsim and Geant4](https://eic.github.io/tutorial-simulations-using-npsim-and-geant4/)
-- [Reconstruction Algorithms in JANA2](https://eic.github.io/tutorial-jana2)
-- [Developing Benchmarks](https://eic.github.io/tutorial-developing-benchmarks/)
-
-:::::::::::::::::::::::::::::::::::::::::::::
+> ## Prerequisites
+> Knowledge of CERN ROOT and/or Python/RDataFrames
+> This tutorial follows other tutorial in the EIC series:
+> - [Setting Up Your Environment](https://eic.github.io/tutorial-setting-up-environment/)
+>
+> Further information is included in other tutorials:
+>
+> - [Geometry Development with DD4hep](https://eic.github.io/tutorial-geometry-development-using-dd4hep/)
+> - [Simulations Using DDsim and Geant4](https://eic.github.io/tutorial-simulations-using-npsim-and-geant4/)
+> - [Reconstruction Algorithms in JANA2](https://eic.github.io/tutorial-jana2)
+> - [Developing Benchmarks](https://eic.github.io/tutorial-developing-benchmarks/)
+{: .prereq}
+
+{% include links.md %}
diff --git a/instructors/instructor-notes.md b/instructors/instructor-notes.md
deleted file mode 100644
index 240cd85..0000000
--- a/instructors/instructor-notes.md
+++ /dev/null
@@ -1,21 +0,0 @@
----
-title: "Instructor Notes"
----
-
-This tutorial teaches learners how to analyze the reconstructed simulation output produced by
-EICrecon. It follows the [Setting Up Your Environment](https://eic.github.io/tutorial-setting-up-environment/)
-tutorial, which establishes the `eic-shell` environment learners rely on here.
-
-## Before the session
-
-- Ask learners to complete the [Setup](../learners/setup.md) page in advance, in particular
- downloading a reconstruction output file (50-80 MB) from the current simulation campaign, since
- this depends on network access to the JLab xrootd server.
-- Confirm learners have a working, interactive ROOT install (either inside `eic-shell` or ROOT
- 6.30+ locally) as described on the Setup page.
-
-## Timing
-
-Most of the lesson is hands-on analysis. Learners should work the exercises in whichever language
-(ROOT C++, Python/uproot, RDataFrame, or PODIO) they are most comfortable with; you do not need to
-cover every approach live.
diff --git a/learners/discuss.md b/learners/discuss.md
deleted file mode 100644
index 273226f..0000000
--- a/learners/discuss.md
+++ /dev/null
@@ -1,8 +0,0 @@
----
-title: Discussion
----
-
-For questions and discussion about analyzing EIC simulation output, see the
-[EIC getting-started guide](https://eic.github.io/documentation/getstarted) and the list of
-[EIC tutorials](https://eic.github.io/documentation/tutorials.html), and ask in the
-[ePIC software-tutorials channel on Mattermost](https://chat.epic-eic.org/main/channels/software-tutorials).
diff --git a/learners/reference.md b/learners/reference.md
deleted file mode 100644
index b224e8c..0000000
--- a/learners/reference.md
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: 'Reference'
----
-
-## Glossary
-
-EIC
-: Electron-Ion Collider
-
-EICrecon
-: The EIC reconstruction software framework, whose output ROOT trees are analyzed in this lesson.
-
-EDM4eic / EDM4hep
-: The event data models describing the branches stored in the reconstruction output trees.
-
-PODIO
-: The Plain Old Data I/O library underlying the EIC event data model.
diff --git a/links.md b/links.md
deleted file mode 100644
index 4c5cd2f..0000000
--- a/links.md
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-[pandoc]: https://pandoc.org/MANUAL.html
-[r-markdown]: https://rmarkdown.rstudio.com/
-[rstudio]: https://www.rstudio.com/
-[carpentries-workbench]: https://carpentries.github.io/sandpaper-docs/
-
diff --git a/profiles/learner-profiles.md b/profiles/learner-profiles.md
deleted file mode 100644
index 3c3877a..0000000
--- a/profiles/learner-profiles.md
+++ /dev/null
@@ -1,9 +0,0 @@
----
-title: 'Learner Profiles'
----
-
-This lesson targets members of the ePIC collaboration — students, postdocs, and researchers — who
-have a working `eic-shell` (or a recent ROOT/Python install) and want to start analyzing the
-reconstructed simulation output produced by EICrecon. Learners are expected to have some familiarity
-with CERN ROOT and/or Python (uproot, RDataFrame). No prior experience with the EIC data model
-(EDM4eic/EDM4hep) is assumed.
diff --git a/reference.md b/reference.md
new file mode 100644
index 0000000..d6fe4ff
--- /dev/null
+++ b/reference.md
@@ -0,0 +1,9 @@
+---
+layout: reference
+---
+
+## Glossary
+
+EIC: Electron-Ion Collider
+
+{% include links.md %}
diff --git a/learners/setup.md b/setup.md
similarity index 77%
rename from learners/setup.md
rename to setup.md
index 458c2fa..39e155f 100644
--- a/learners/setup.md
+++ b/setup.md
@@ -1,14 +1,11 @@
---
title: Setup
---
-
-If you have not done so already, please follow the
-[Setting Up Your Environment tutorial setup instructions](https://eic.github.io/tutorial-setting-up-environment/setup.html)
-well before the start of the tutorial to ensure your system is ready.
+If you have not done so already, please follow the instructions [here](https://eic.github.io/tutorial-setting-up-environment/setup.html) well before the start of the tutorial to ensure your system is ready.
This tutorial will go over how to analyze the reconstructed simulation, so you will need to download a file to work with locally. The files are on the order of 50-80MB each. For consistency, we will use neutral current DIS events from the February 2026 campaign (26.02.0) with minimum Q2 = 10 GeV2 and at the highest electron-proton beam energy combination (if you wish to make an energy comparison, you can download additional files). To browse the available files, you can run the following commands from within the eic-shell environment:
-```bash
+```console
xrdfs root://dtn-eic.jlab.org
ls /volatile/eic/EPIC/RECO/26.02.0/epic_craterlake/DIS/NC/18x275/minQ2=10
exit
@@ -16,18 +13,15 @@ exit
You can download any of the files you want in here. You can do this by (still within eic-shell environment) navigating to the directory you will store your file(s) and run the command:
-```bash
+```console
xrdcp root://dtn-eic.jlab.org//volatile/eic/EPIC/RECO/26.02.0/epic_craterlake/DIS/NC/18x275/minQ2=10/pythia8NCDIS_18x275_minQ2=10_beamEffects_xAngle=-0.025_hiDiv_5.0001.eicrecon.tree.edm4eic.root ./
```
Do not forget the trailing ./ (or just . works too) as this tells the progam to put the file in your current dir.
-::::::::::::::::::::::::::::::::::::::::::::: callout
-
-Note that we can also specify a different filename to copy to as we could with a normal cp command. You might want to do this as the filename is a little cumbersome.
-I called mine NC_DIS_18x275_Feb26Campaign.root, just replace ./ with your file name of choice.
-
-:::::::::::::::::::::::::::::::::::::::::::::
+> Note that we can also specify a different filename to copy to as we could with a normal cp command. You might want to do this as the filename is a little cumbersome.
+> I called mine NC_DIS_18x275_Feb26Campaign.root, just replace ./ with your file name of choice.
+{: .callout}
This command will download the file (0001) specified. You can of course, download a different file in the same directory if you want.
@@ -39,3 +33,5 @@ Note that this tutorial is a little odd in that, for the most part, we don't rel
2. A working version (and relatively recent, 6.30 or above, ideally 6.34.02) of ROOT on your local machine.
If you use option 2, note that you will not be able to "stream" files to your ROOT script unless you have xrootd installed too, you will need them available locally. I will be using option 2 for this tutorial.
+
+{% include links.md %}