2 |
33 |
--------------------------------------------------------------------------------
/assets/js/lesson.js:
--------------------------------------------------------------------------------
1 | // Make all tables striped by default.
2 | $("table").addClass("table table-striped");
3 |
4 |
5 | // Handle foldable challenges and solutions (on click and at start).
6 | $(".solution").click(function(event) {
7 | var trigger = $(event.target).has(".fold-unfold").length > 0
8 | || $(event.target).filter(".fold-unfold").length > 0;
9 | if (trigger) {
10 | $(">*:not(h2)", this).toggle(400);
11 | $(">h2>span.fold-unfold", this).toggleClass("glyphicon-collapse-down glyphicon-collapse-up");
12 | event.stopPropagation();
13 | }
14 | });
15 | $(".solution").each(function() {
16 | $(">*:not(h2)", this).toggle();
17 | var h2 = $("h2:first", this);
18 | h2.append("");
19 | });
20 |
21 |
22 | // Handle searches.
23 | // Relies on document having 'meta' element with name 'search-domain'.
24 | function google_search() {
25 | var query = document.getElementById("google-search").value;
26 | var domain = $("meta[name=search-domain]").attr("value");
27 | window.open("https://www.google.com/search?q=" + query + "+site:" + domain);
28 | }
29 |
30 | // function to shrink the life cycle bar when scrolling
31 | $(function(){
32 | $('#life-cycle').data('size','big');
33 | });
34 |
35 | $(window).scroll(function(){
36 | if($(document).scrollTop() > 0)
37 | {
38 | if($('#life-cycle').data('size') == 'big')
39 | {
40 | $('#life-cycle').data('size','small');
41 | $('#life-cycle').stop().animate({
42 | padding: '5px'
43 | },100);
44 | }
45 | }
46 | else
47 | {
48 | if($('#life-cycle').data('size') == 'small')
49 | {
50 | $('#life-cycle').data('size','big');
51 | $('#life-cycle').stop().animate({
52 | padding: '15px'
53 | },100);
54 | }
55 | }
56 | });
57 |
--------------------------------------------------------------------------------
/setup/index.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | title: Testing Setup
4 | root: ..
5 | ---
6 |
7 | This directory contains scripts for testing your machine to make sure
8 | you have the software you'll need for your workshop installed. To use
9 | these scripts:
10 |
11 | 1. Download [swc-installation-test-1.py](swc-installation-test-1.py).
12 |
13 | 2. Run it from the shell:
14 |
15 | ~~~
16 | $ python swc-installation-test-1.py
17 | Passed
18 | ~~~
19 |
20 | 3. Download [swc-installation-test-2.py](swc-installation-test-2.py).
21 |
22 | 4. Run it from the shell:
23 |
24 | ~~~
25 | $ python swc-installation-test-2.py
26 | check virtual-shell... pass
27 | ...
28 | Successes:
29 |
30 | virtual-shell Bourne Again Shell (bash) 4.2.37
31 | ...
32 | ~~~
33 |
34 | If you see something like:
35 |
36 | ~~~
37 | $ python swc-installation-test-2.py
38 | check virtual-shell... fail
39 | ...
40 | check for command line shell (virtual-shell) failed:
41 | command line shell (virtual-shell) requires at least one of the following dependencies
42 | For instructions on installing an up-to-date version, see
43 | http://software-carpentry.org/setup/
44 | causes:
45 | check for Bourne Again Shell (bash) failed:
46 | could not find 'bash' executable for Bourne Again Shell (bash)
47 | For instructions on installing an up-to-date version, see
48 | http://software-carpentry.org/setup/
49 | ...
50 | ~~~
51 |
52 | follow the suggestions to try and install any missing software. For
53 | additional troubleshooting information, you can use the `--verbose`
54 | option:
55 |
56 | ~~~
57 | $ python swc-installation-test-2.py --verbose
58 | check virtual-shell... fail
59 | ...
60 | ==================
61 | System information
62 | ==================
63 | os.name : posix
64 | ...
65 | ~~~
66 |
--------------------------------------------------------------------------------
/_includes/lc/setup.html:
--------------------------------------------------------------------------------
1 |
3 |
5 |
16 |
17 | Day 1
4 || Before | Pre-workshop survey |
| 09:00 | Automating Tasks with the Unix Shell |
| 10:30 | Morning break |
| 11:00 | Automating Tasks with the Unix Shell (Continued) |
| 12:00 | Lunch break |
| 13:00 | Building Programs with Python |
| 14:30 | Afternoon break |
| 15:00 | Building Programs with Python (Continued) |
| 16:00 | Wrap-up |
| 16:30 | END |
18 |
20 |
31 |
32 | Day 2
19 || 09:00 | Version Control with Git |
| 10:30 | Morning break |
| 11:00 | Version Control with Git (Continued) |
| 12:00 | Lunch break |
| 13:00 | Managing Data with SQL |
| 14:30 | Afternoon break |
| 15:00 | Managing Data with SQL (Continued) |
| 16:00 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
{% comment %} Start of 'shell' section. {% endcomment %}
2 |
9 |
10 | The Bash Shell
3 |4 | Bash is a commonly-used shell that gives you the power to do simple tasks 5 | more quickly. Please find setup instructions in 6 | the lesson. 7 |
8 |
11 |
18 |
19 | OpenRefine
12 |13 | OpenRefine is a tool to clean up and organize messy data. Please find instructions to 14 | install it and the data used in the lesson in the 15 | lesson. 16 |
17 | {% comment %} Start of 'Git' section. GitHub browser compatibility
20 | is given at https://help.github.com/articles/supported-browsers/{% endcomment %}
21 |
46 |
--------------------------------------------------------------------------------
/_layouts/base.html:
--------------------------------------------------------------------------------
1 | ---
2 | ---
3 | {% include base_path.html %}
4 | {% include gh_variables.html %}
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
14 |
15 |
16 |
17 |
18 |
19 | {% if page.math %}
20 |
21 | {% endif %}
22 |
23 |
24 | {% include favicons.html %}
25 |
26 |
27 |
28 |
32 |
33 | Git
22 |23 | Git is a version control system that lets you track who made changes 24 | to what when and has options for easily updating a shared or public 25 | version of your code 26 | on https://github.com. 27 |
28 |29 | Follow the instructions on 30 | the lesson to 31 | install Git on your system. 32 |
33 |34 | You will need an account at github.com 35 | for parts of the Git lesson. Basic GitHub accounts are free. We encourage 36 | you to create a GitHub account if you don't have one already. 37 | Please consider what personal information you'd like to reveal. For 38 | example, you may want to review these 39 | instructions 40 | for keeping your email address private provided at GitHub. You will 41 | need a 42 | supported 43 | web browser. 44 |
45 |
43 | {% include navbar.html %}
44 | {{ content }}
45 | {% if site.kind == "workshop" %}
46 | {% include workshop_footer.html %}
47 | {% else %}
48 | {% include lesson_footer.html %}
49 | {% endif %}
50 |
51 | {% include javascript.html %}
52 |
53 |
54 |
--------------------------------------------------------------------------------
/_includes/install_instructions/videoconferencing.html:
--------------------------------------------------------------------------------
1 |
2 | Install the videoconferencing client
3 | 4 | {% comment %} 5 | Replace the paragraph below with the relevant installation instructions 6 | if you do not use Zoom 7 | {% endcomment %} 8 |9 | We will use Blackboard Collaborate. An up-to-date web browser is needed. 10 | Further help can be found on the 11 | 12 | Collaborate Ultra Help for Participants page. 13 |
14 | 15 | 16 |Set up your workspace
17 | 18 |19 | Like other Carpentries workshops, 20 | you will be learning by "coding along" with the Instructors. 21 | To do this, you will need to have both the window for the tool 22 | you will be learning about (a terminal, RStudio, your web browser, etc..) 23 | and the window for the Zoom video conference client open. 24 | In order to see both at once, 25 | we recommend using one of the following set up options: 26 |
-
27 |
- Two monitors: If you have two monitors, 28 | plan to have the tool you are learning up on one monitor and 29 | the video conferencing software on the other. 30 |
- Two devices: If you don't have two monitors, 31 | do you have another device (tablet, smartphone) with a medium to large 32 | sized screen? If so, try using the smaller device as your video 33 | conference connection and your larger device (laptop or desktop) 34 | to follow along with the tool you will be learning about. 35 |
- Divide your screen: If you only have one device 36 | and one screen, practice having two windows 37 | (the video conference program and one of the tools you will be using 38 | at the workshop) open together. 39 | How can you best fit both on your screen? 40 | Will it work better for you to toggle between them 41 | using a keyboard shortcut? 42 | Try it out in advance to decide what will work best for you. 43 |
45 |77 | -------------------------------------------------------------------------------- /_includes/dc/who.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Astronomy workshops 3 | {% endcomment %} 4 | 5 | 6 | {% if site.curriculum == "dc-astronomy" %} 7 | 8 |Overview
46 | 47 |48 |62 | 63 |49 | Teaching: {{ teaching_time }} min 50 |53 |
51 | Exercises: {{ exercise_time }} min 52 |54 | Questions 55 |61 |56 | {% for question in episode_questions %} 57 |
60 |- {{ question|markdownify }}
58 | {% endfor %} 59 |64 |75 | 76 |65 |66 |67 | Objectives 68 |74 |69 | {% for objective in episode_objectives %} 70 |
73 |- {{ objective|markdownify }}
71 | {% endfor %} 72 |
9 | Who: 10 | This lesson assumes you have a working knowledge of Python and some previous exposure to the Bash shell. 11 | These requirements can be fulfilled by: 12 | a) completing a Software Carpentry Python workshop or 13 | b) completing a Data Carpentry Ecology workshop (with Python) and a Data Carpentry Genomics workshop or 14 | c) independent exposure to both Python and the Bash shell. 15 | 16 | If you’re unsure whether you have enough experience to participate in this workshop, please read over 17 | this detailed list, 18 | which gives all of the functions, operators, and other concepts you will need to be familiar with. 19 | 20 | In addition, this lesson assumes that learners have some familiarity with astronomical concepts, 21 | including reference frames, proper motion, color-magnitude diagrams, globular clusters, and isochrones. 22 | Participants should bring their own laptops and plan to participate actively. 23 |
24 | 25 | {% comment %} 26 | Image workshops 27 | {% endcomment %} 28 | 29 | {% elsif site.curriculum == "dc-image" %} 30 | 31 |32 | Who: 33 | This lesson assumes you have a working knowledge of Python and some previous exposure to the Bash shell. 34 | These requirements can be fulfilled by: 35 | a) completing a Software Carpentry Python workshop or 36 | b) completing a Data Carpentry Ecology workshop (with Python) and a Data Carpentry Genomics workshop or 37 | c) independent exposure to both Python and the Bash shell. 38 | 39 | If you’re unsure whether you have enough experience to participate in this workshop, please read over 40 | this detailed list, 41 | which gives all of the functions, operators, and other concepts you will need to be familiar with. 42 |
43 | 44 | {% comment %} 45 | All other workshops 46 | {% endcomment %} 47 | 48 | {% else %} 49 | 50 |51 | Who: 52 | The course is aimed at graduate students and other researchers. 53 | 54 | You don't need to have any previous knowledge of the tools 55 | that will be presented at the workshop. 56 | 57 |
58 | 59 | {% endif %} 60 | -------------------------------------------------------------------------------- /_includes/dc/schedule.html: -------------------------------------------------------------------------------- 1 |
2 |
22 |
3 |
5 |
11 |
12 | Mon, 12 Feb 2024
4 || 09:30 | Pre-workshop Survey and Setup |
| 10:00 | Data Organization in Spreadsheets |
| 11:00 | Morning break |
| 11:30 | OpenRefine for Data Cleaning |
| 13:00 | END |
13 |
15 |
20 |
21 | Tue, 13 Feb 2024
14 || 09:30 | Introduction to R |
| 11:00 | Morning break |
| 11:30 | Introduction to R (Continued) |
| 13:00 | END |
23 |
--------------------------------------------------------------------------------
/_includes/lesson_footer.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | Footer for lesson pages.
3 | {% endcomment %}
4 |
5 | {% include gh_variables.html %}
6 |
7 |
55 |
--------------------------------------------------------------------------------
/_includes/links.md:
--------------------------------------------------------------------------------
1 | {% include base_path.html %}
2 | [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
3 | [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
4 | [ci]: http://communityin.org/
5 | [coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
6 | [coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
7 | [concept-maps]: https://carpentries.github.io/instructor-training/05-memory/
8 | [contrib-covenant]: https://contributor-covenant.org/
9 | [contributing]: {{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md
10 | [cran-checkpoint]: https://cran.r-project.org/package=checkpoint
11 | [cran-knitr]: https://cran.r-project.org/package=knitr
12 | [cran-stringr]: https://cran.r-project.org/package=stringr
13 | [dc-lessons]: http://www.datacarpentry.org/lessons/
14 | [email]: mailto:team@carpentries.org
15 | [github-importer]: https://import2.github.com/
16 | [importer]: https://github.com/new/import
17 | [jekyll-collection]: https://jekyllrb.com/docs/collections/
18 | [jekyll-install]: https://jekyllrb.com/docs/installation/
19 | [jekyll-windows]: http://jekyll-windows.juthilo.com/
20 | [jekyll]: https://jekyllrb.com/
21 | [jupyter]: https://jupyter.org/
22 | [kramdown]: https://kramdown.gettalong.org/
23 | [lc-lessons]: https://librarycarpentry.org/lessons/
24 | [lesson-coc]: {{ relative_root_path }}{% link CODE_OF_CONDUCT.md %}
25 | [lesson-example]: https://carpentries.github.io/lesson-example/
26 | [lesson-license]: {{ relative_root_path }}{% link LICENSE.md %}
27 | [lesson-mainpage]: {{ relative_root_path }}{% link index.md %}
28 | [mit-license]: https://opensource.org/licenses/mit-license.html
29 | [morea]: https://morea-framework.github.io/
30 | [numfocus]: https://numfocus.org/
31 | [osi]: https://opensource.org
32 | [pandoc]: https://pandoc.org/
33 | [paper-now]: https://github.com/PeerJ/paper-now
34 | [python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
35 | [pyyaml]: https://pypi.org/project/PyYAML/
36 | [r-markdown]: https://rmarkdown.rstudio.com/
37 | [rstudio]: https://www.rstudio.com/
38 | [ruby-install-guide]: https://www.ruby-lang.org/en/downloads/
39 | [ruby-installer]: https://rubyinstaller.org/
40 | [rubygems]: https://rubygems.org/pages/download/
41 | [styles]: https://github.com/carpentries/styles/
42 | [swc-lessons]: https://software-carpentry.org/lessons/
43 | [swc-releases]: https://github.com/swcarpentry/swc-releases
44 | [training]: https://carpentries.github.io/instructor-training/
45 | [workshop-repo]: {{ site.workshop_repo }}
46 | [yaml]: http://yaml.org/
47 |
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/_includes/favicons.html:
--------------------------------------------------------------------------------
1 | {% assign favicon_url = relative_root_path | append: '/assets/favicons/' | append: site.carpentry %}
2 |
3 | {% if site.carpentry == 'swc' %}
4 | {% assign carpentry = 'Software Carpentry' %}
5 | {% elsif site.carpentry == 'dc' %}
6 | {% assign carpentry = 'Data Carpentry' %}
7 | {% elsif site.carpentry == 'lc' %}
8 | {% assign carpentry = 'Library Carpentry' %}
9 | {% elsif site.carpentry == 'cp' %}
10 | {% assign carpentry = 'The Carpentries' %}
11 | {% endif %}
12 |
13 |
14 |
15 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
--------------------------------------------------------------------------------
/_includes/install_instructions/editor.html:
--------------------------------------------------------------------------------
1 |
24 |
26 |
31 |
32 | Wed, 14 Feb 2024
25 || 09:30 | Continuation of R: Data analysis and Visualization |
| 11:00 | Morning break |
| 11:30 | Continuation of R: Data analysis and Visualization (Continued) |
| 13:00 | END |
33 |
35 |
41 |
42 | Thu, 15 Feb 2024
34 || 09:30 | Data Management with SQL |
| 11:00 | Morning break |
| 11:30 | ARCHER2 course feedback and Post-workshop Survey |
| 11:45 | Data Management with SQL (Continued) |
| 13:00 | END |
2 |
52 |
--------------------------------------------------------------------------------
/bin/chunk-options.R:
--------------------------------------------------------------------------------
1 | # These settings control the behavior of all chunks in the novice R materials.
2 | # For example, to generate the lessons with all the output hidden, simply change
3 | # `results` from "markup" to "hide".
4 | # For more information on available chunk options, see
5 | # http://yihui.name/knitr/options#chunk_options
6 |
7 | library("knitr")
8 |
9 | fix_fig_path <- function(pth) file.path("..", pth)
10 |
11 |
12 | ## We set the path for the figures globally below, so if we want to
13 | ## customize it for individual episodes, we can append a prefix to the
14 | ## global path. For instance, if we call knitr_fig_path("01-") in the
15 | ## first episode of the lesson, it will generate the figures in
16 | ## `fig/rmd-01-`
17 | knitr_fig_path <- function(prefix) {
18 | new_path <- paste0(opts_chunk$get("fig.path"),
19 | prefix)
20 | opts_chunk$set(fig.path = new_path)
21 | }
22 |
23 | ## We use the rmd- prefix for the figures generated by the lessons so
24 | ## they can be easily identified and deleted by `make clean-rmd`. The
25 | ## working directory when the lessons are generated is the root so the
26 | ## figures need to be saved in fig/, but when the site is generated,
27 | ## the episodes will be one level down. We fix the path using the
28 | ## `fig.process` option.
29 |
30 | opts_chunk$set(tidy = FALSE, results = "markup", comment = NA,
31 | fig.align = "center", fig.path = "fig/rmd-",
32 | fig.process = fix_fig_path,
33 | fig.width = 8.5, fig.height = 8.5,
34 | fig.retina = 2)
35 |
36 | # The hooks below add html tags to the code chunks and their output so that they
37 | # are properly formatted when the site is built.
38 |
39 | hook_in <- function(x, options) {
40 | lg <- tolower(options$engine)
41 | style <- paste0(".language-", lg)
42 |
43 | stringr::str_c("\n\n~~~\n",
44 | paste0(x, collapse="\n"),
45 | "\n~~~\n{: ", style, "}\n\n")
46 | }
47 |
48 | hook_out <- function(x, options) {
49 | x <- gsub("\n$", "", x)
50 | stringr::str_c("\n\n~~~\n",
51 | paste0(x, collapse="\n"),
52 | "\n~~~\n{: .output}\n\n")
53 | }
54 |
55 | hook_error <- function(x, options) {
56 | x <- gsub("\n$", "", x)
57 | stringr::str_c("\n\n~~~\n",
58 | paste0(x, collapse="\n"),
59 | "\n~~~\n{: .error}\n\n")
60 | }
61 |
62 | hook_warning <- function(x, options) {
63 | x <- gsub("\n$", "", x)
64 | stringr::str_c("\n\n~~~\n",
65 | paste0(x, collapse = "\n"),
66 | "\n~~~\n{: .warning}\n\n")
67 | }
68 |
69 | knit_hooks$set(source = hook_in, output = hook_out, warning = hook_warning,
70 | error = hook_error, message = hook_out)
71 |
--------------------------------------------------------------------------------
/_includes/custom-schedule.html:
--------------------------------------------------------------------------------
1 | Text Editor
3 | 4 |5 | When you're writing code, it's nice to have a text editor that is 6 | optimized for writing code, with features like automatic 7 | color-coding of key words. The default text editor on macOS and 8 | Linux is usually set to Vim, which is not famous for being 9 | intuitive. If you accidentally find yourself stuck in it, hit 10 | the Esc key, followed by :+Q+! 11 | (colon, lower-case 'q', exclamation mark), then hitting Return to 12 | return to the shell. 13 |
14 | 15 |
16 |
21 |
22 |
51 |
23 |
24 |
29 |
30 |
43 |
44 |
49 |
50 | 25 | nano is a basic editor and the default that instructors use in the workshop. 26 | It is installed along with Git. 27 |
28 |31 | nano is a basic editor and the default that instructors use in the workshop. 32 | See the Git installation video tutorial 33 | for an example on how to open nano. 34 | It should be pre-installed. 35 |
36 |Video Tutorial
37 |
38 |
42 |
39 |
40 |
41 | 45 | nano is a basic editor and the default that instructors use in the workshop. 46 | It should be pre-installed. 47 |
48 |
2 |
37 |
3 |
5 |
18 |
19 | Day 1
4 || Before starting | 7 |Pre-workshop survey | 8 |
| 11 | | 12 | |
| 15 | | 16 | |
20 |
22 |
35 |
36 | Day 2
21 || 24 | | 25 | |
| 28 | | 29 | |
| 32 | | 33 | |
38 |
73 |
--------------------------------------------------------------------------------
/bin/reporter.py:
--------------------------------------------------------------------------------
1 | import sys
2 |
3 | class Reporter:
4 | """Collect and report errors."""
5 |
6 | # Marker to show that an expected value hasn't been provided.
7 | # (Can't use 'None' because that might be a legitimate value.)
8 | _DEFAULT_REPORTER = []
9 |
10 | def __init__(self):
11 | """Constructor."""
12 | self.messages = []
13 |
14 | def check_field(self, filename, name, values, key, expected=_DEFAULT_REPORTER):
15 | """Check that a dictionary has an expected value."""
16 |
17 | if key not in values:
18 | self.add(filename, '{0} does not contain {1}', name, key)
19 | elif expected is self._DEFAULT_REPORTER:
20 | pass
21 | elif type(expected) in (tuple, set, list):
22 | if values[key] not in expected:
23 | self.add(
24 | filename, '{0} {1} value {2} is not in {3}', name, key, values[key], expected)
25 | elif values[key] != expected:
26 | self.add(filename, '{0} {1} is {2} not {3}',
27 | name, key, values[key], expected)
28 |
29 | def check(self, condition, location, fmt, *args):
30 | """Append error if condition not met."""
31 |
32 | if not condition:
33 | self.add(location, fmt, *args)
34 |
35 | def add(self, location, fmt, *args):
36 | """Append error unilaterally."""
37 |
38 | self.messages.append((location, fmt.format(*args)))
39 |
40 | @staticmethod
41 | def pretty(item):
42 | location, message = item
43 | if isinstance(location, type(None)):
44 | return message
45 | elif isinstance(location, str):
46 | return location + ': ' + message
47 | elif isinstance(location, tuple):
48 | return '{0}:{1}: '.format(*location) + message
49 |
50 | print('Unknown item "{0}"'.format(item), file=sys.stderr)
51 | return NotImplemented
52 |
53 | @staticmethod
54 | def key(item):
55 | location, message = item
56 | if isinstance(location, type(None)):
57 | return ('', -1, message)
58 | elif isinstance(location, str):
59 | return (location, -1, message)
60 | elif isinstance(location, tuple):
61 | return (location[0], location[1], message)
62 |
63 | print('Unknown item "{0}"'.format(item), file=sys.stderr)
64 | return NotImplemented
65 |
66 | def report(self, stream=sys.stdout):
67 | """Report all messages in order."""
68 |
69 | if not self.messages:
70 | return
71 |
72 | for m in sorted(self.messages, key=self.key):
73 | print(self.pretty(m), file=stream)
74 |
75 |
76 |
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/_includes/dc/setup.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | Astronomy workshops
3 | {% endcomment %}
4 |
5 |
6 | {% if site.curriculum == "dc-astronomy" %}
7 |
8 |
39 |
41 |
54 |
55 | Day 3
40 || 43 | | 44 | |
| 47 | | 48 | |
| 51 | | 52 | |
56 |
58 |
71 |
72 | Day 4
57 || 60 | | 61 | |
| 64 | | 65 | |
| End | 68 |Post-workshop survey | 69 |
9 | The setup instructions for the Data Carpentry Astronomy workshops 10 | can be found at 11 | the curriculum site. 12 |
13 | 14 | {% comment %} 15 | Ecology workshops 16 | {% endcomment %} 17 | 18 | 19 | {% elsif site.curriculum == "dc-ecology" %} 20 | 21 | {% if site.flavor == "r" %} 22 |23 | The setup instructions for the Data Carpentry Ecology workshops (with R) 24 | can be found at 25 | the workshop overview site. 26 |
27 | 28 | {% elsif site.flavor == "python" %} 29 |30 | The setup instructions for the Data Carpentry Ecology workshops (with Python) 31 | can be found at 32 | the workshop overview site. 33 |
34 | {% else %} 35 | {% include warning-flavor.html %} 36 | {% endif %} 37 | 38 | {% comment %} 39 | Genomics workshops 40 | {% endcomment %} 41 | 42 | {% elsif site.curriculum == "dc-genomics" %} 43 |The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site
. 44 | 45 | {% comment %} 46 | Geospatial workshops 47 | {% endcomment %} 48 | 49 | {% elsif site.curriculum == "dc-geospatial" %} 50 |The setup instructions for the Data Carpentry Geospatial workshop can be found at the workshop overview site.
51 | 52 | {% comment %} 53 | Image workshops 54 | {% endcomment %} 55 | 56 | {% elsif site.curriculum == "dc-image" %} 57 | 58 |The setup instructions for Data Carpentry Image Processing workshops can be found at the curriculum site.
59 | 60 | {% comment %} 61 | Social sciences workshops 62 | {% endcomment %} 63 | 64 | {% elsif site.curriculum == "dc-socsci" %} 65 | 66 | {% if site.flavor == "r" %} 67 |68 | The setup instructions for the Data Carpentry Social Sciences 69 | workshops (with R) can be found at 70 | the workshop overview site. 71 |
72 | 73 | {% elsif site.flavor == "python" %} 74 |75 | The setup instructions for the Data Carpentry Social Sciences workshops (with Python) 76 | can be found at 77 | the workshop overview site. 78 |
79 | {% else %} 80 | {% include warning-flavor.html %} 81 | {% endif %} 82 | 83 | {% else %} 84 | {% include warning-curriculum.html %} 85 | {% endif %} 86 | -------------------------------------------------------------------------------- /bin/boilerplate/_extras/figures.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Figures 3 | --- 4 | 5 | {% include base_path.html %} 6 | {% include manual_episode_order.html %} 7 | 8 | 67 | 68 | {% comment %} Create anchor for each one of the episodes. {% endcomment %} 69 | 70 | {% for lesson_episode in lesson_episodes %} 71 | {% if site.episode_order %} 72 | {% assign episode = site.episodes | where: "slug", lesson_episode | first %} 73 | {% else %} 74 | {% assign episode = lesson_episode %} 75 | {% endif %} 76 | 77 | {% endfor %} 78 | 79 | {% include links.md %} 80 | -------------------------------------------------------------------------------- /_includes/install_instructions/sql.html: -------------------------------------------------------------------------------- 1 |
2 |
54 |
--------------------------------------------------------------------------------
/_layouts/workshop.html:
--------------------------------------------------------------------------------
1 | ---
2 | ---
3 | {% include base_path.html %}
4 | {% include gh_variables.html %}
5 |
6 | {% comment %}
7 |
8 | If the workshop is online, we add ' (online)' after the name of the venue
9 | in the metadata so it's easier for Regional Coordinators to identify
10 | online workshops.
11 |
12 | {% endcomment %}
13 |
14 | {% assign begin_address = page.address | slice: 0, 4 | downcase %}
15 | {% if page.address == "online" or begin_address contains "http" %}
16 | {% assign online = " (online)" %}
17 | {% else %}
18 | {% assign online = "" %}
19 | {% endif %}
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 | {% if page.redirect %}
44 |
45 | {% endif %}
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 | {% include favicons.html %}
57 |
58 |
59 |
60 |
64 | SQLite
3 | 4 |5 | SQL is a specialized programming language used with databases. We 6 | use a database manager called 7 | SQLite in our lessons. 8 |
9 | 10 |
11 |
17 |
49 |
50 |
18 |
19 |
29 |
30 |
34 |
35 |
39 |
40 |
47 |
48 | -
20 |
- Run "Git Bash" from the Start menu 21 |
- Copy the following
curl -fsSL {{site.url}}{{site.baseurl}}/getsql.sh | bash
22 | - Paste it into the window that Git Bash opened. If you're unsure, ask an instructor for help 23 |
- You should see something like
3.27.2 2019-02-25 16:06:06 ...
24 |
If you want to do this manually, download sqlite3, make a bin directory in the user's home directory, unzip sqlite3, move it into the bin directory, and then add the bin directory to the path.
27 | 28 |31 | SQLite comes pre-installed on macOS. 32 |
33 |36 | SQLite comes pre-installed on Linux. 37 |
38 |-
41 |
- In case of problems: register for an account at https://www.pythonanywhere.com 42 |
- Download survey.db 43 |
- Click on files and upload survey.db 44 |
- Click on dashboard and Choose new console
bash
45 |
If you installed Anaconda, it also has a copy of SQLite
51 | without support to readline.
52 | Instructors will provide a workaround for it if needed.
68 | {% include navbar.html %}
69 | {% include workshop_ad.html %}
70 | {{ content }}
71 | {% include workshop_footer.html %}
72 |
73 | {% include javascript.html %}
74 |
75 |
76 |
--------------------------------------------------------------------------------
/assets/js/katex-auto-render.min.js:
--------------------------------------------------------------------------------
1 | !function(e,t){"object"==typeof exports&&"object"==typeof module?module.exports=t(require("katex")):"function"==typeof define&&define.amd?define(["katex"],t):"object"==typeof exports?exports.renderMathInElement=t(require("katex")):e.renderMathInElement=t(e.katex)}("undefined"!=typeof self?self:this,(function(e){return function(){"use strict";var t={974:function(t){t.exports=e}},r={};function n(e){var a=r[e];if(void 0!==a)return a.exports;var i=r[e]={exports:{}};return t[e](i,i.exports,n),i.exports}n.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return n.d(t,{a:t}),t},n.d=function(e,t){for(var r in t)n.o(t,r)&&!n.o(e,r)&&Object.defineProperty(e,r,{enumerable:!0,get:t[r]})},n.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)};var a={};return function(){n.d(a,{default:function(){return s}});var e=n(974),t=n.n(e),r=function(e,t,r){for(var n=r,a=0,i=e.length;nR
3 | 4 |5 | R is a programming language 6 | that is especially powerful for data exploration, visualization, and 7 | statistical analysis. To interact with R, we use 8 | RStudio. 9 |
10 | 11 |
12 |
17 |
18 |
67 |
68 |
--------------------------------------------------------------------------------
/_includes/carpentries.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | General description of Software, Data, and Library Carpentry.
3 | {% endcomment %}
4 |
5 | {% include base_path.html %}
6 |
7 |
19 |
20 |
38 |
39 |
53 |
54 |
65 |
66 | 21 | Install R by downloading and running 22 | this .exe file 23 | from CRAN. 24 | Also, please install the 25 | RStudio IDE. 26 | Note that if you have separate user and admin accounts, you should run the 27 | installers as administrator (right-click on .exe file and select "Run as 28 | administrator" instead of double-clicking). Otherwise problems may occur later, 29 | for example when installing R packages. 30 |
31 |Video Tutorial
32 |
33 |
37 |
34 |
35 |
36 | 40 | Install R by downloading and running 41 | this .pkg file 42 | from CRAN. 43 | Also, please install the 44 | RStudio IDE. 45 |
46 |Video Tutorial
47 |
48 |
52 |
49 |
50 |
51 |
55 | Instructions for R installation on various Linux platforms (debian,
56 | fedora, redhat, and ubuntu) can be found at
57 | sudo dnf install R and for Debian/Ubuntu, add a ppa
60 | repository and then run sudo apt-get install r-base).
61 | Also, please install the
62 | RStudio IDE.
63 |
8 |
30 |
9 | 
10 |
11 |
10 |
12 |
29 | The Carpentries comprises 13 | Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, 14 | Maintainers, helpers, and supporters who share a mission to teach 15 | foundational coding and data science skills to researchers and people 16 | working in library- and information-related roles. In January, 17 | 2018, The Carpentries was formed by the merger of Software Carpentry and 18 | Data Carpentry. Library Carpentry became an official Carpentries Lesson Program 19 | in November 2018.
20 | 21 | 22 |While individual lessons and workshops continue to be run under each 23 | lesson project, The Carpentries provide overall staffing and governance, as 24 | well as support for assessment, instructor training and mentoring. 25 | Memberships are joint, and the Carpentries project maintains a shared Code 26 | of Conduct. The Carpentries is a fiscally sponsored project of Community 27 | Initiatives, a registered 501(c)3 non-profit based in California, USA.
28 |
31 |
44 |
32 | 
33 |
34 |
33 |
35 |
43 | Since 1998, Software Carpentry has 36 | been teaching researchers across all disciplines the foundational coding 37 | skills they need to get more done in less time and with less pain. Its 38 | volunteer instructors have run hundreds of events for thousands of learners 39 | around the world. Now that all research involves some degree of 40 | computational work, whether with big data, cloud computing, or simple task 41 | automation, these skills are needed more than ever.
42 |45 |
46 |
59 |
47 | 
48 |
49 |
48 |
50 |
58 | Data Carpentry develops and teaches 51 | workshops on the fundamental data skills needed to conduct research. Its 52 | target audience is researchers who have little to no prior computational 53 | experience, and its lessons are domain specific, building on learners' 54 | existing knowledge to enable them to quickly apply skills learned to their 55 | own research. Data Carpentry workshops take researchers through the entire 56 | data life cycle.
57 |60 |
61 |
73 |
--------------------------------------------------------------------------------
/LICENSE.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: page
3 | title: "Licenses"
4 | ---
5 | ## Instructional Material
6 |
7 | All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
8 | made available under the [Creative Commons Attribution
9 | license][cc-by-human]. The following is a human-readable summary of
10 | (and not a substitute for) the [full legal text of the CC BY 4.0
11 | license][cc-by-legal].
12 |
13 | You are free:
14 |
15 | * to **Share**---copy and redistribute the material in any medium or format
16 | * to **Adapt**---remix, transform, and build upon the material
17 |
18 | for any purpose, even commercially.
19 |
20 | The licensor cannot revoke these freedoms as long as you follow the
21 | license terms.
22 |
23 | Under the following terms:
24 |
25 | * **Attribution**---You must give appropriate credit by:
26 | - mentioning that your work is derived from work that is
27 | Copyright © Software Carpentry, Data Carpentry, Library Carpentry,
28 | or The Carpentries.
29 | - where practical, linking to the respective lesson program website
30 | (https://software-carpentry.org/, https://datacarpentry.org, https://librarycarpentry.org, or
31 | https://carpentries.org), provide a [link to the license][cc-by-human]
32 | - and indicate if changes were made. You may do so in any reasonable manner, but not in any way
33 | that suggests the licensor endorses you or your use.
34 |
35 | **No additional restrictions**---You may not apply legal terms or
36 | technological measures that legally restrict others from doing
37 | anything the license permits. With the understanding that:
38 |
39 | Notices:
40 |
41 | * You do not have to comply with the license for elements of the
42 | material in the public domain or where your use is permitted by an
43 | applicable exception or limitation.
44 | * No warranties are given. The license may not give you all of the
45 | permissions necessary for your intended use. For example, other
46 | rights such as publicity, privacy, or moral rights may limit how you
47 | use the material.
48 |
49 | ## Software
50 |
51 | Except where otherwise noted, the example programs and other software
52 | provided by Software Carpentry and Data Carpentry are made available under the
53 | [OSI][osi]-approved
54 | [MIT license][mit-license].
55 |
56 | Permission is hereby granted, free of charge, to any person obtaining
57 | a copy of this software and associated documentation files (the
58 | "Software"), to deal in the Software without restriction, including
59 | without limitation the rights to use, copy, modify, merge, publish,
60 | distribute, sublicense, and/or sell copies of the Software, and to
61 | permit persons to whom the Software is furnished to do so, subject to
62 | the following conditions:
63 |
64 | The above copyright notice and this permission notice shall be
65 | included in all copies or substantial portions of the Software.
66 |
67 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
68 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
69 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
70 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
71 | LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
72 | OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
73 | WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
74 |
75 | ## Trademark
76 |
77 | "The Carpentries", "Software Carpentry" and "Data Carpentry" and their respective logos are
78 | registered trademarks of [Community Initiatives][CI].
79 |
80 | [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
81 | [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
82 | [mit-license]: https://opensource.org/licenses/mit-license.html
83 | [ci]: http://communityin.org/
84 | [osi]: https://opensource.org
85 |
--------------------------------------------------------------------------------
/bin/dependencies.R:
--------------------------------------------------------------------------------
1 | install_required_packages <- function(lib = NULL, repos = getOption("repos", default = c(CRAN = "https://cran.rstudio.com/"))) {
2 |
3 | if (is.null(lib)) {
4 | lib <- .libPaths()[[1]]
5 | }
6 |
7 | message("lib paths: ", paste(lib, collapse = ", "))
8 | # Note: RMarkdown is needed for renv to detect packages in Rmd documents.
9 | required_pkgs <- c("rprojroot", "desc", "remotes", "renv", "BiocManager", "rmarkdown")
10 | installed_pkgs <- rownames(installed.packages(lib.loc = lib))
11 | missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
12 |
13 | # The default installation of R will have "@CRAN@" as the default repository,
14 | # which directs contrib.url() to either force the user to choose a mirror if
15 | # interactive or fail if not. Since we are not interactve, we need to force
16 | # the mirror here.
17 | if ("@CRAN@" %in% repos) {
18 | repos <- c(CRAN = "https://cran.rstudio.com/")
19 | }
20 |
21 | if (length(missing_pkgs) != 0) {
22 | install.packages(missing_pkgs, lib = lib, repos = repos)
23 | }
24 | }
25 |
26 | find_root <- function() {
27 |
28 | cfg <- rprojroot::has_file_pattern("^_config.y*ml$")
29 | root <- rprojroot::find_root(cfg)
30 |
31 | root
32 | }
33 |
34 | # set the BiocManager repositories and return a function that resets the default
35 | # repositories.
36 | #
37 | # @example
38 | # bioc_repos_example <- function() {
39 | # message("User repos")
40 | # as.data.frame(getOption("repos"))
41 | # reset_repos <- use_bioc_repos()
42 | # on.exit(reset_repos())
43 | # message("Bioc repos")
44 | # as.data.frame(getOption("repos"))
45 | # }
46 | # bioc_repos_example()
47 | # as.data.frame(getOption("repos")
48 | use_bioc_repos <- function() {
49 | repos <- getOption("repos")
50 | suppressMessages(options(repos = BiocManager::repositories()))
51 | function() {
52 | options(repos = repos)
53 | }
54 | }
55 |
56 | identify_dependencies <- function() {
57 |
58 | root <- find_root()
59 |
60 | reset_repos <- use_bioc_repos()
61 | on.exit(reset_repos(), add = TRUE)
62 | eps <- file.path(root, "_episodes_rmd")
63 | bin <- file.path(root, "bin")
64 |
65 | required_pkgs <- unique(c(
66 | ## Packages for episodes
67 | renv::dependencies(eps, progress = FALSE, error = "ignored")$Package,
68 | ## Packages for tools
69 | renv::dependencies(bin, progress = FALSE, error = "ignored")$Package
70 | ))
71 |
72 | required_pkgs
73 | }
74 |
75 | create_description <- function(required_pkgs) {
76 | d <- desc::description$new("!new")
77 | d$set_deps(data.frame(type = "Imports", package = required_pkgs, version = "*"))
78 | d$write("DESCRIPTION")
79 | # We have to write the description twice to get the hidden dependencies
80 | # because renv only considers explicit dependencies.
81 | #
82 | # This is needed because some of the hidden dependencis will require system
83 | # libraries to be configured.
84 | suppressMessages(repo <- BiocManager::repositories())
85 | deps <- remotes::dev_package_deps(dependencies = TRUE, repos = repo)
86 | deps <- deps$package[deps$diff < 0]
87 | if (length(deps)) {
88 | # only create new DESCRIPTION file if there are dependencies to install
89 | d$set_deps(data.frame(type = "Imports", package = deps, version = "*"))
90 | d$write("DESCRIPTION")
91 | }
92 | }
93 |
94 | install_dependencies <- function(required_pkgs, ...) {
95 |
96 | reset_repos <- use_bioc_repos()
97 | on.exit(reset_repos(), add = TRUE)
98 |
99 | create_description(required_pkgs)
100 | on.exit(file.remove("DESCRIPTION"), add = TRUE)
101 | remotes::install_deps(dependencies = TRUE, ...)
102 |
103 | if (require("knitr") && packageVersion("knitr") < '1.9.19') {
104 | stop("knitr must be version 1.9.20 or higher")
105 | }
106 |
107 | }
108 |
--------------------------------------------------------------------------------
/_includes/install_instructions/git.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | Git Setup instructions rely on Shell instructions. If you don't include
3 | Shell instructions as part of your workshop website, make sure to adjust
4 | the text below accordingly.
5 | {% endcomment %}
6 |
62 | 
63 |
64 |
63 |
65 |
72 | Library Carpentry develops lessons and 66 | teaches workshops for and with people working in library- and 67 | information-related roles. Its goal is to create an on-ramp to empower this 68 | community to use software and data in their own work, as well as be 69 | advocates for and train others in efficient, effective and reproducible data 70 | and software practices.
71 |
7 |
73 |
--------------------------------------------------------------------------------
/_includes/life_cycle.html:
--------------------------------------------------------------------------------
1 |
2 | {% if site.life_cycle == "pre-alpha" %}
3 |
4 | Git
8 |9 | Git is a version control system that lets you track who made changes 10 | to what when and has options for easily updating a shared or public 11 | version of your code 12 | on github.com. You will need a 13 | supported 14 | web browser. 15 |
16 |17 | You will need an account at github.com 18 | for parts of the Git lesson. Basic GitHub accounts are free. We encourage 19 | you to create a GitHub account if you don't have one already. 20 | Please consider what personal information you'd like to reveal. For 21 | example, you may want to review these 22 | instructions 23 | for keeping your email address private provided at GitHub. 24 |
25 | 26 |
27 |
32 |
33 |
72 |
34 |
35 |
41 |
42 |
62 |
63 |
70 |
71 | 36 | Git should be installed on your computer as part of your Bash 37 | install (see the 38 | Shell installation instructions). 39 |
40 |
43 | For macOS, install Git for Mac
44 | by downloading and running the most recent "mavericks" installer from
45 | this list.
46 | Because this installer is not signed by the developer, you may have to
47 | right click (control click) on the .pkg file, click Open, and click
48 | Open on the pop up window.
49 | After installing Git, there will not be anything in your /Applications folder,
50 | as Git is a command line program.
51 | For older versions of OS X (10.5-10.8) use the
52 | most recent available installer labelled "snow-leopard"
53 | available here.
54 |
Video Tutorial
56 |
57 |
61 |
58 |
59 |
60 |
64 | If Git is not already available on your machine you can try to
65 | install it via your distro's package manager. For Debian/Ubuntu run
66 | sudo apt-get install git and for Fedora run
67 | sudo dnf install git.
68 |
5 |
9 |
10 |
11 | {% elsif site.life_cycle == "alpha" %}
12 |
13 |
6 | This lesson is still being designed and assembled (Pre-Alpha version)
7 |
8 |
14 |
18 |
19 |
20 | {% elsif site.life_cycle == "beta" %}
21 |
22 |
15 | This lesson is in the early stages of development (Alpha version)
16 |
17 |
23 |
27 |
28 | {% elsif site.life_cycle == "stable" %}
29 |
30 | {% comment %}
31 | We do not do anything special for lessons in stable
32 | {% endcomment %}
33 |
34 |
35 | {% comment %}
36 | Below we cover the 2 phases of lesson transition towards the Carpentries Workbench:
37 | Variables needed:
38 | - transition_date_prebeta: the date of the prebeta stage
39 | - transition_date_beta: the date of the beta stage
40 | - transition_date_prerelease: the date of the prerelease stage
41 |
42 | - transition-step-1: We notify that there is a snapshot of the lesson available for testing, and that it will supersede this version.
43 | - transition-step-2 We indicate that this version of the lesson is a snapshot and a new version of the lesson is avaiable and will supersede this version at a given date.
44 | {% endcomment %}
45 |
46 | {% elsif site.life_cycle == "transition-step-1" %}
47 | {% include check_transition_variables.html need_transition_date = 'true' %}
48 |
49 |
24 | This lesson is being piloted (Beta version)
25 |
26 |
50 | A snapshot of this lesson from {{ site.transition_date_prebeta }} is being tested on
51 | The Carpentries Workbench:
52 | https://preview.carpentries.org/{{ repo_name }}.
53 |
54 | The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}. 55 | 58 |
59 |
60 | {% elsif site.life_cycle == "transition-step-2" %}
61 | {% include check_transition_variables.html need_transition_date = 'true' %}
62 |
63 | 54 | The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}. 55 | 58 |
64 | This lesson is a snapshot from {{ site.transition_date_beta }}.
65 | A newer version is being tested on The Carpentries Workbench:
66 | https://preview.carpentries.org/{{ repo_name }}.
67 |
68 | The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}. 69 | 72 |
73 |
74 | {% endif %}
75 |
76 |
77 |
78 | {% comment %}
79 | For Carpentries Lab lessons we add a banner about the review status
80 | {% endcomment %}
81 |
82 | {% if site.carpentry == "lab" %}
83 | {% if site.doi contains "zenodo" %}{% assign listing=" on Zenodo" %}
84 | {% elsif site.doi contains "jose" %}{% assign listing=" in JOSE" %}
85 | {% else %}{% assign listing="none" %}
86 | {% endif %}
87 |
88 | 68 | The Workbench version of this lesson will become default on {{ site.transition_date_prerelease }}. 69 | 72 |
89 |
93 | {% endif %}
94 |
--------------------------------------------------------------------------------
/_includes/javascript.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | JavaScript used in lesson and workshop pages.
3 | {% endcomment %}
4 |
5 |
6 |
7 |
8 |
54 | {% if site.kind == "lesson" %}
55 |
56 |
73 |
74 | {% endif %}
75 |
76 | {% if page.math %}
77 |
78 |
89 |
90 | {% endif %}
91 |
92 | {%- comment -%}
93 | AnchorJS: A JavaScript utility for adding deep anchor links
94 | https://github.com/bryanbraun/anchorjs
95 | https://cdn.jsdelivr.net/npm/anchor-js/anchor.min.js
96 | {%- endcomment -%}
97 |
98 |
99 |
102 |
--------------------------------------------------------------------------------
/_includes/manual_episode_order.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | This file enables manual episode ordering until
3 | GitHub Pages switches to Jekyll that supports it
4 | without any major hackery. Note, some logic will
5 | be required even when this transition happens
6 | but it will not be as involved as what we have to do
7 | in this file.
8 |
9 | To order lesson episodes or extras manually
10 | (instead of the default alpha-numerical order),
11 | create array variables 'episode_order' and
12 | 'extras_order' in `_config.yml` like so:
13 |
14 | episode_order:
15 | - episodeA
16 | - episodeB
17 |
18 | extras_order:
19 | - extraA
20 | - extraB
21 |
22 | Note that "Reference" page is currently always
23 | added to "Extras" as the first item.
24 |
25 | The main outcomes of the code in this file are:
26 | - 'lesson_episodes' variable that replaces
27 | 'site.episodes' variable when manual episode
28 | order is defined.
29 | - 'lesson_extras' variable that replaces
30 | 'site.extras' variable when manual ordering of
31 | files in '_extras' is used
32 | - 'previous_episode' and 'next_episode' objects
33 | that replace 'page.previous' and 'page.next' variables,
34 | correspondingly, and that have such properties
35 | as 'url' and 'title' and that are used in
36 | 'episode_navbar.html'.
37 |
38 | When episode order is specified manually, the 'lesson_episodes'
39 | variable contains a list of episode names ("slugs", to be precise;
40 | "slug" is the episode name without '.md'). Therefore, when we
41 | iterate over 'lesson_episodes' (in navbar.html) ,
42 | we have to check whether we use manual episode ordering and, if so,
43 | find the corresponding episode object. This is what we do with the
44 | following code in every loop over 'lesson_episodes':
45 |
46 | {% if site.episode_order %}
47 | {% assign episode = site.episodes | where: "slug", lesson_episode | first %}
48 | {% else %}
49 | {% assign episode = lesson_episode %}
50 | {% endif %}
51 | {% endcomment %}
52 |
53 | {% comment %}
54 | Manual ordering of Episodes begins here
55 | {% endcomment %}
56 |
57 | {% if site.episode_order %}
58 | {% assign lesson_episodes = site.episode_order %}
59 | {% else %}
60 | {% assign lesson_episodes = site.episodes %}
61 | {% endif %}
62 |
63 |
64 | {% comment %}
65 | If 'episode_order' is defined, we need to determine
66 | - previous episode object ('previous_episode')
67 | - and next episode object ('next_episode')
68 | {% endcomment %}
69 |
70 |
71 | {% if site.episode_order %}
72 | {% for lesson_episode in lesson_episodes %}
73 |
74 | {% comment %}
75 | We iterate over the specified lesson episodes using
76 | a 'for' loop because we can use
77 | 'forloop.first', 'forloop.last', and 'forloop.index0'.
78 | {% endcomment %}
79 |
80 | {% unless lesson_episode == page.slug %} {% continue %} {% endunless %}
81 |
82 | {% if forloop.first %}
83 | {% assign previous_episode = nil %}
84 | {% else %}
85 | {% assign p_idx = forloop.index0 | minus: 1 %}
86 | {% assign p_name = lesson_episodes[p_idx] %}
87 | {% assign previous_episode = site.episodes | where: "slug", p_name | first %}
88 | {% endif %}
89 |
90 | {% if forloop.last == true %}
91 | {% assign next_episode = nil %}
92 | {% else %}
93 | {% assign n_idx = forloop.index0 | plus: 1 %}
94 | {% assign n_name = lesson_episodes[n_idx] %}
95 | {% assign next_episode = site.episodes | where: "slug", n_name | first %}
96 | {% endif %}
97 | {% endfor %}
98 | {% else %}
99 | {% assign previous_episode = page.previous %}
100 | {% assign next_episode = page.next %}
101 | {% endif %}
102 |
103 |
104 | {% comment %}
105 | Manual ordering of Extras begins here
106 | {% endcomment %}
107 |
108 | {% if site.extras_order %}
109 | {% assign lesson_extras = site.extras_order %}
110 | {% else %}
111 | {% assign lesson_extras = site.extras %}
112 | {% endif %}
113 |
114 | {% comment %}
115 | We do not need to determine "previous" or "next" extra.
116 | {% endcomment %}
117 |
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/_includes/install_instructions/openrefine.html:
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1 |
90 | This lesson has passed peer-review! {% if site.doi != "" %}See the publication{{ listing }}.{% endif %}
91 |
92 |
2 |
58 |
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/assets/css/syntax.css:
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2 | .highlight { background: #f8f8f8; }
3 | .highlight .c { color: #387d7d; font-style: italic } /* Comment */
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7 | .highlight .ch { color: #387d7d; font-style: italic } /* Comment.Hashbang */
8 | .highlight .cm { color: #387d7d; font-style: italic } /* Comment.Multiline */
9 | .highlight .cp { color: #BC7A00 } /* Comment.Preproc */
10 | .highlight .cpf { color: #387d7d; font-style: italic } /* Comment.PreprocFile */
11 | .highlight .c1 { color: #387d7d; font-style: italic } /* Comment.Single */
12 | .highlight .cs { color: #387d7d; font-style: italic } /* Comment.Special */
13 | .highlight .gd { color: #A00000 } /* Generic.Deleted */
14 | .highlight .ge { font-style: italic } /* Generic.Emph */
15 | .highlight .gr { color: #FF0000 } /* Generic.Error */
16 | .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
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21 | .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
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33 | .highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
34 | .highlight .no { color: #880000 } /* Name.Constant */
35 | .highlight .nd { color: #AA22FF } /* Name.Decorator */
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41 | .highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
42 | .highlight .nv { color: #19177C } /* Name.Variable */
43 | .highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
44 | .highlight .w { color: #bbbbbb } /* Text.Whitespace */
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46 | .highlight .mf { color: #666666 } /* Literal.Number.Float */
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70 |
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/bin/boilerplate/_config.yml:
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1 | #------------------------------------------------------------
2 | # Values for this lesson.
3 | #------------------------------------------------------------
4 |
5 | # Which carpentry is this ("swc", "dc", "lc", or "cp")?
6 | # swc: Software Carpentry
7 | # dc: Data Carpentry
8 | # lc: Library Carpentry
9 | # cp: Carpentries (to use for instructor traning for instance)
10 | # incubator: Carpentries Incubator
11 | carpentry: "swc"
12 |
13 | # Overall title for pages.
14 | title: "Lesson Title"
15 |
16 | # Life cycle stage of the lesson
17 | # See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html
18 | # Possible values: "pre-alpha", "alpha", "beta", "stable"
19 | #
20 | # Lessons that are going through the transition to the
21 | # Carpentries Workbench will go through 3 steps:
22 | # 'transition-step-1': notice indicating a new version
23 | # 'transition-step-2': notice encouraging to use new version
24 | # 'transition-step-3': notice indicating the lesson is deprecated,
25 | # with automated redirect
26 | life_cycle: "pre-alpha"
27 |
28 | # For lessons in the life stages in 'transition-step-1' or later:
29 | # - 'transition_url' holds the URL for the version of the lesson that
30 | # uses the Workbench (needed for all 3 steps)
31 | # - 'transition_date' (in yyyy-mm-dd format) is the date when the lesson
32 | # will transition to being deprecated. The date only needs to be decided
33 | # when the lesson is in 'transition-step-2'.
34 | transition_url:
35 | transition_date:
36 |
37 | #------------------------------------------------------------
38 | # Generic settings (should not need to change).
39 | #------------------------------------------------------------
40 |
41 | # What kind of thing is this ("workshop" or "lesson")?
42 | kind: "lesson"
43 |
44 | # Magic to make URLs resolve both locally and on GitHub.
45 | # See https://help.github.com/articles/repository-metadata-on-github-pages/.
46 | # Please don't change it: OpenRefine
3 |4 | For this lesson you will need OpenRefine and a 5 | web browser. Note: this is a Java program that runs on your machine (not in the cloud). 6 | It runs inside a web browser, but no web connection is needed. 7 |
8 | 9 |
10 |
15 |
16 |
57 |
17 |
18 |
32 |
33 |
44 |
45 |
55 |
56 | -
19 |
- 20 | Check that you have either the Firefox or the Chrome browser installed and set as your default browser. 21 | OpenRefine runs in your default browser. 22 | It will not run correctly in Internet Explorer. 23 | 24 |
- Download software from http://openrefine.org/ 25 |
- Create a new directory called OpenRefine. 26 |
- Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...". 27 |
- Go to your newly created OpenRefine directory. 28 |
- Launch OpenRefine by clicking
openrefine.exe(this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
29 | - If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program. 30 |
-
34 |
- Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari. 35 |
- Download software from http://openrefine.org/. 36 |
- Create a new directory called OpenRefine. 37 |
- Unzip the downloaded file into the OpenRefine directory by double-clicking it. 38 |
- Go to your newly created OpenRefine directory. 39 |
- Launch OpenRefine by dragging the icon into the Applications folder. 40 |
- Use Ctrl-click/Open ... to launch it. 41 |
- If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program. 42 |
-
46 |
- Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. 47 |
- Download software from http://openrefine.org/. 48 |
- Make a directory called OpenRefine. 49 |
- Unzip the downloaded file into the OpenRefine directory. 50 |
- Go to your newly created OpenRefine directory. 51 |
- Launch OpenRefine by entering
./refineinto the terminal within the OpenRefine directory.
52 | - If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program. 53 |