{{ e.title }}
18 | 19 | {% include episode_overview.html teaching_time=e.teaching exercise_time=e.exercises episode_questions=e.questions episode_objectives=e.objectives %} 20 | 21 | {{ e.content }} 22 | 23 | {% include episode_keypoints.html episode_keypoints=e.keypoints %} 24 |25 | {% endfor %} 26 | -------------------------------------------------------------------------------- /_includes/all_keypoints.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Display key points of all episodes for reference. 3 | {% endcomment %} 4 | 5 | {% include base_path.html %} 6 | {% include manual_episode_order.html %} 7 | 8 |
Key Points
9 || 19 | {{ episode.title }} 20 | | 21 |
22 |
|
28 |
8 |
28 |
9 | 
10 |
11 |
10 |
12 |
27 | 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 in November 2018.
19 | 20 |While individual lessons and workshops continue to be run under each 21 | lesson project, The Carpentries provide overall staffing and governance, as 22 | well as support for assessment, instructor training and mentoring. 23 | Memberships are joint, and the Carpentries project maintains a shared Code 24 | of Conduct. The Carpentries is a fiscally sponsored project of Community 25 | Initiatives, a registered 501(c)3 non-profit based in California, USA.
26 |
29 |
42 |
30 | 
31 |
32 |
31 |
33 |
41 | Since 1998, Software Carpentry has 34 | been teaching researchers across all disciplines the foundational coding 35 | skills they need to get more done in less time and with less pain. Its 36 | volunteer instructors have run hundreds of events for thousands of learners 37 | around the world. Now that all research involves some degree of 38 | computational work, whether with big data, cloud computing, or simple task 39 | automation, these skills are needed more than ever.
40 |43 |
44 |
57 |
45 | 
46 |
47 |
46 |
48 |
56 | Data Carpentry develops and teaches 49 | workshops on the fundamental data skills needed to conduct research. Its 50 | target audience is researchers who have little to no prior computational 51 | experience, and its lessons are domain specific, building on learners' 52 | existing knowledge to enable them to quickly apply skills learned to their 53 | own research. Data Carpentry workshops take researchers through the entire 54 | data life cycle.
55 |58 |
59 |
71 |
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/_includes/dc/intro.html:
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1 |
60 | 
61 |
62 |
61 |
63 |
70 | Library Carpentry develops lessons and 64 | teaches workshops for and with people working in library- and 65 | information-related roles. Its goal is to create an on-ramp to empower this 66 | community to use software and data in their own work, as well as be 67 | advocates for and train others in efficient, effective and reproducible data 68 | and software practices.
69 |2 | Data Carpentry 3 | aims to help researchers get their work done 4 | in less time and with less pain 5 | by teaching them basic research computing skills. 6 | This hands-on workshop will cover basic concepts and tools, 7 | including program design, version control, data management, 8 | and task automation. 9 | Participants will be encouraged to help one another 10 | and to apply what they have learned to their own research problems. 11 |
12 |13 | 14 | For more information on what we teach and why, 15 | please see our paper 16 | "Best Practices for Scientific Computing". 17 | 18 |
19 | -------------------------------------------------------------------------------- /_includes/dc/schedule.html: -------------------------------------------------------------------------------- 1 |
2 |
25 |
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/_includes/dc/syllabus.html:
--------------------------------------------------------------------------------
1 |
3 |
5 |
12 |
13 | Day 1
4 || 09:00 | Automating tasks with the Unix shell |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Building programs with Python |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
14 |
16 |
23 |
24 | Day 2
15 || 09:00 | Version control with Git |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Managing data with SQL |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
2 |
54 |
55 |
3 |
14 | The Unix Shell
4 |-
5 |
- Files and directories 6 |
- History and tab completion 7 |
- Pipes and redirection 8 |
- Looping over files 9 |
- Creating and running shell scripts 10 |
- Finding things 11 |
- Reference... 12 |
15 |
27 |
40 |
53 | Programming in Python
16 |-
17 |
- Using libraries 18 |
- Working with arrays 19 |
- Reading and plotting data 20 |
- Creating and using functions 21 |
- Loops and conditionals 22 |
- Defensive programming 23 |
- Using Python from the command line 24 |
- Reference... 25 |
56 |
97 |
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/_includes/dc/who.html:
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1 |
57 |
70 |
86 | Version Control with Git
58 |-
59 |
- Creating a repository 60 |
- Recording changes to files:
add,commit, ...
61 | - Viewing changes:
status,diff, ...
62 | - Ignoring files 63 |
- Working on the web:
clone,pull,push, ...
64 | - Resolving conflicts 65 |
- Open licenses 66 |
- Where to host work, and why 67 |
- Reference... 68 |
87 |
96 | Open Refine
88 |-
89 |
- Introduction to OpenRefine 90 |
- Importing data 91 |
- Basic functions 92 |
- Advanced Functions 93 |
- Reference... 94 |
2 | Who: 3 | The course is aimed at graduate students and other researchers. 4 | 5 | You don't need to have any previous knowledge of the tools 6 | that will be presented at the workshop. 7 | 8 |
9 | -------------------------------------------------------------------------------- /_includes/episode_break.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Display a break's timings in a box similar to a learning episode's. 3 | {% endcomment %} 4 |5 |16 | -------------------------------------------------------------------------------- /_includes/episode_keypoints.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Display key points for an episode. 3 | {% endcomment %} 4 | 5 | {% if page.keypoints == nil %} 6 | {% assign episode_keypoints = include.episode_keypoints %} 7 | {% else %} 8 | {% assign episode_keypoints = page.keypoints %} 9 | {% endif %} 10 | 11 |Overview
6 | 7 |8 |14 | 15 |9 | Break: {{ page.break }} min 10 |11 |12 |13 |
12 |19 | -------------------------------------------------------------------------------- /_includes/episode_navbar.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | For some reason, the relative_root_path seems out of scope in this file, so we 3 | need to re-assign it here 4 | {% endcomment %} 5 | 6 | {% include base_path.html %} 7 | 8 | {% comment %} 9 | Navigation bar for an episode. 10 | {% endcomment %} 11 | 12 | {% include manual_episode_order.html %} 13 | {% comment %} 14 | 'previous_episode' and 'next_episodes' are defined in 'manual_episode_order.html'. 15 | These replace 'page.previous' and 'page.next' objects, correspondingly. 16 | {% endcomment %} 17 | 18 |Key Points
13 |14 | {% for keypoint in episode_keypoints %} 15 |
18 |- {{ keypoint|markdownify }}
16 | {% endfor %} 17 |
19 |
43 |
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/_includes/episode_overview.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | Display episode's timings and learning objectives.
3 |
4 | Regarding the `if page.*** == nil` below:
5 | all-in-one page combines all episodes into one.
6 | It, therefore, does not define its own objectives, exercises,
7 | and questions, which 'normal' episodes define in the front matter.
8 |
9 | To display episodes' teaching and exercise times, as well as episode
10 | questions and objectives, we pass them as parameters to the Liquid's
11 | `include` statement when we generate the page:
12 |
13 | include episode_overview.html teaching_time=e.teaching ...
14 |
15 | Here we obtain the information we need either from the episode itself or
16 | from the parameters passed in.
17 | {% endcomment %}
18 |
19 | {% if page.teaching == nil %}
20 | {% assign teaching_time = include.teaching_time %}
21 | {% else %}
22 | {% assign teaching_time = page.teaching %}
23 | {% endif %}
24 |
25 | {% if page.exercises == nil %}
26 | {% assign exercise_time = include.exercise_time %}
27 | {% else %}
28 | {% assign exercise_time = page.exercises %}
29 | {% endif %}
30 |
31 | {% if page.questions == nil %}
32 | {% assign episode_questions = include.episode_questions %}
33 | {% else %}
34 | {% assign episode_questions = page.questions %}
35 | {% endif %}
36 |
37 | {% if page.objectives == nil %}
38 | {% assign episode_objectives = include.episode_objectives %}
39 | {% else %}
40 | {% assign episode_objectives = page.objectives %}
41 | {% endif %}
42 |
43 |
44 |
20 |
28 | 21 | {% if previous_episode %} 22 | previous episode 23 | {% else %} 24 | lesson home 25 | {% endif %} 26 |
27 |
29 | {% if include.episode_navbar_title %}
30 |
33 | {{ site.title }}
31 | {% endif %} 32 |
34 |
42 | 35 | {% if next_episode %} 36 | next episode 37 | {% else %} 38 | lesson home 39 | {% endif %} 40 |
41 |45 |77 | -------------------------------------------------------------------------------- /_includes/episode_title.html: -------------------------------------------------------------------------------- 1 |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 |
2 |
10 |
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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/gh_variables.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | When rendering websites locally, `site.github.url` doesn't get resolved properly
3 | unless a GitHub Personal Access Token is set up and available in the
4 | environment. This leads to warnings and errors when trying to serve the site
5 | locally. To work around this, we use the `jekyll.environment` variable which is
6 | set to `development` when rendering the site locally, and set to `production` on
7 | GitHub where `site.github.url` is defined.
8 | {% endcomment %}
9 |
10 | {% if jekyll.environment == "production" %}
11 |
12 | {% comment %}
13 | First, get the name of the repository
14 | {% endcomment %}
15 | {% assign repo_name = site.github.repository_name %}
16 |
17 | {% comment %}
18 | `site.github.public_repositories` contains comprehensive information for all public repositories for the organization. We use `where` to extract the part
19 | of the metadata that is relevant to the present repository.
20 | {% endcomment %}
21 | {% assign repo_info = site.github.public_repositories | where: "name", repo_name %}
22 |
23 | {% comment %}
24 | Now, we can extract the default branch for the repo
25 | {% endcomment %}
26 | {% assign default_branch = repo_info[0].default_branch %}
27 |
28 | {% comment %}
29 | Other variables requested by the template
30 | {% endcomment %}
31 | {% assign repo_url = site.github.repository_url %}
32 | {% assign search_domain_url = site.github.url %}
33 | {% assign project_title = site.github.project_title %}
34 | {% assign source_branch = site.github.source.branch %}
35 |
36 | {% elsif jekyll.environment == "development" %}
37 |
38 | {% assign repo_name = "" %}
39 | {% assign repo_url = "" %}
40 | {% assign default_branch = "" %}
41 | {% assign search_domain_url = "" %}
42 | {% assign project_title = "" %}
43 | {% assign source_branch = "" %}
44 |
45 | {% endif %}
46 |
--------------------------------------------------------------------------------
/_includes/javascript.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | JavaScript used in lesson and workshop pages.
3 | {% endcomment %}
4 |
5 |
6 |
7 |
15 |
--------------------------------------------------------------------------------
/_includes/lc/intro.html:
--------------------------------------------------------------------------------
1 |
3 |
4 |
5 |
7 | {{ page.title }}
6 |
8 |
9 | 2 | Library Carpentry 3 | is made by people working in library- and information-related roles to help you: 4 |
5 |-
6 |
- automate repetitive, boring, error-prone tasks 7 |
- create, maintain and analyze sustainable and reusable data 8 |
- work effectively with IT and systems colleagues 9 |
- better understand the use of software in research 10 |
- and much more... 11 |
13 | 14 | Library Carpentry introduces you to the fundamentals of computing 15 | and provides you with a platform for further self-directed learning. 16 | For more information on what we teach and why, please see our paper 17 | "Library Carpentry: software skills training for library professionals". 18 | 19 |
20 | -------------------------------------------------------------------------------- /_includes/lc/schedule.html: -------------------------------------------------------------------------------- 1 |
2 |
25 |
--------------------------------------------------------------------------------
/_includes/lc/syllabus.html:
--------------------------------------------------------------------------------
1 |
3 |
5 |
12 |
13 | Day 1
4 || 09:00 | Data Intro for Librarians |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Shell Lessons for Libraries |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
14 |
16 |
23 |
24 | Day 2
15 || 09:00 | Git Intro for Librarians |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | OpenRefine for Librarians |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
2 |
27 |
28 |
3 |
14 | Data Intro
4 |-
5 |
- Intro to data 6 |
- Jargon busting 7 |
- Keyboard shortcuts 8 |
- Plain text formats 9 |
- Naming files 10 |
- Regular expressions 11 |
- Reference... 12 |
15 |
25 |
26 | The Unix Shell
16 |-
17 |
- Files and directories 18 |
- History and tab completion 19 |
- Counting and sorting contents in files 20 |
- Pipes and redirection 21 |
- Mining or searching in files 22 |
- Reference... 23 |
29 |
54 |
70 |
--------------------------------------------------------------------------------
/_includes/lc/who.html:
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1 |
30 |
41 | Version Control with Git
31 |-
32 |
- Creating a repository 33 |
- Configuring git 34 |
- Recording changes to files:
add,commit, ...
35 | - Viewing state changes with
status
36 | - Working on the web:
clone,pull,push, ...
37 | - Where to host work, and why 38 |
- Reference... 39 |
42 |
53 |
43 |
52 | Open Refine
44 |-
45 |
- Introduction to OpenRefine 46 |
- Importing data 47 |
- Basic functions 48 |
- Advanced Functions 49 |
- Reference... 50 |
2 | Who: 3 | The course is for people working in library- and information-related roles. 4 | 5 | You don't need to have any previous knowledge of the tools that 6 | will be presented at the workshop. 7 | 8 |
9 | -------------------------------------------------------------------------------- /_includes/lesson_footer.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Footer for lesson pages. 3 | {% endcomment %} 4 | 5 | {% include gh_variables.html %} 6 | 7 | 55 | -------------------------------------------------------------------------------- /_includes/life_cycle.html: -------------------------------------------------------------------------------- 1 | 2 | {% if site.life_cycle == "pre-alpha" %} 3 | 4 |
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 don't do anything special for now
32 | {% endcomment %}
33 |
34 | {% endif %}
35 |
--------------------------------------------------------------------------------
/_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://import.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-aio]: {{ relative_root_path }}{% link aio.md %}
25 | [lesson-coc]: {{ relative_root_path }}{% link CODE_OF_CONDUCT.md %}
26 | [lesson-example]: https://carpentries.github.io/lesson-example/
27 | [lesson-license]: {{ relative_root_path }}{% link LICENSE.md %}
28 | [lesson-mainpage]: {{ relative_root_path }}{% link index.md %}
29 | [lesson-reference]: {{ relative_root_path }}{% link reference.md %}
30 | [lesson-setup]: {{ relative_root_path }}{% link setup.md %}
31 | [mit-license]: https://opensource.org/licenses/mit-license.html
32 | [morea]: https://morea-framework.github.io/
33 | [numfocus]: https://numfocus.org/
34 | [osi]: https://opensource.org
35 | [pandoc]: https://pandoc.org/
36 | [paper-now]: https://github.com/PeerJ/paper-now
37 | [python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
38 | [pyyaml]: https://pypi.org/project/PyYAML/
39 | [r-markdown]: https://rmarkdown.rstudio.com/
40 | [rstudio]: https://www.rstudio.com/
41 | [ruby-install-guide]: https://www.ruby-lang.org/en/downloads/
42 | [ruby-installer]: https://rubyinstaller.org/
43 | [rubygems]: https://rubygems.org/pages/download/
44 | [styles]: https://github.com/carpentries/styles/
45 | [swc-lessons]: https://software-carpentry.org/lessons/
46 | [swc-releases]: https://github.com/swcarpentry/swc-releases
47 | [training]: https://carpentries.github.io/instructor-training/
48 | [workshop-repo]: {{ site.workshop_repo }}
49 | [yaml]: http://yaml.org/
50 |
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/_includes/main_title.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 | Main title for lesson pages.
3 | {% endcomment %}
4 |
5 | {% include base_path.html %}
6 |
7 | {% if site.kind == "lesson" %}
8 |
24 | This lesson is being piloted (Beta version)
25 |
26 | {{ site.title }}{% if page.title %}: {{ page.title }}{% endif %}
9 | 10 | {% else %} 11 | 12 |{{ page.title }}
13 | 14 | {% endif %} 15 | -------------------------------------------------------------------------------- /_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 won't 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 syllabus.html and 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 | -------------------------------------------------------------------------------- /_includes/navbar.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | Lesson navigation bar. 3 | {% endcomment %} 4 | 5 | {% include gh_variables.html %} 6 | {% include manual_episode_order.html %} 7 | 8 | 107 | -------------------------------------------------------------------------------- /_includes/sc/intro.html: -------------------------------------------------------------------------------- 1 |2 | Software Carpentry 3 | aims to help researchers get their work done 4 | in less time and with less pain 5 | by teaching them basic research computing skills. 6 | This hands-on workshop will cover basic concepts and tools, 7 | including program design, version control, data management, 8 | and task automation. 9 | Participants will be encouraged to help one another 10 | and to apply what they have learned to their own research problems. 11 |
12 |13 | 14 | For more information on what we teach and why, 15 | please see our paper 16 | "Best Practices for Scientific Computing". 17 | 18 |
19 | -------------------------------------------------------------------------------- /_includes/sc/schedule.html: -------------------------------------------------------------------------------- 1 |
2 |
25 |
--------------------------------------------------------------------------------
/_includes/sc/syllabus.html:
--------------------------------------------------------------------------------
1 |
3 |
5 |
12 |
13 | Day 1
4 || 09:00 | Automating tasks with the Unix shell |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Building programs with Python |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
14 |
16 |
23 |
24 | Day 2
15 || 09:00 | Version control with Git |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Managing data with SQL |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
2 |
54 |
55 |
3 |
14 | The Unix Shell
4 |-
5 |
- Files and directories 6 |
- History and tab completion 7 |
- Pipes and redirection 8 |
- Looping over files 9 |
- Creating and running shell scripts 10 |
- Finding things 11 |
- Reference... 12 |
15 |
27 |
40 |
53 | Programming in Python
16 |-
17 |
- Using libraries 18 |
- Working with arrays 19 |
- Reading and plotting data 20 |
- Creating and using functions 21 |
- Loops and conditionals 22 |
- Defensive programming 23 |
- Using Python from the command line 24 |
- Reference... 25 |
56 |
97 |
--------------------------------------------------------------------------------
/_includes/sc/who.html:
--------------------------------------------------------------------------------
1 |
57 |
70 |
86 | Version Control with Git
58 |-
59 |
- Creating a repository 60 |
- Recording changes to files:
add,commit, ...
61 | - Viewing changes:
status,diff, ...
62 | - Ignoring files 63 |
- Working on the web:
clone,pull,push, ...
64 | - Resolving conflicts 65 |
- Open licenses 66 |
- Where to host work, and why 67 |
- Reference... 68 |
87 |
96 | Open Refine
88 |-
89 |
- Introduction to OpenRefine 90 |
- Importing data 91 |
- Basic functions 92 |
- Advanced Functions 93 |
- Reference... 94 |
2 | Who: 3 | The course is aimed at graduate students and other researchers. 4 | 5 | You don't need to have any previous knowledge of the tools 6 | that will be presented at the workshop. 7 | 8 |
9 | -------------------------------------------------------------------------------- /_includes/syllabus.html: -------------------------------------------------------------------------------- 1 | {% include base_path.html %} 2 | 3 | {% comment %} 4 | Display syllabus in tabular form. 5 | Days are displayed if at least one episode has 'start = true'. 6 | {% endcomment %} 7 | 8 | {% include manual_episode_order.html %} 9 | 10 |
11 |
27 |
88 |
89 |
94 |
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/_includes/workshop_ad.html:
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1 | {% comment %}
2 | Advertising box at the top of a workshop website home page.
3 | {% endcomment %}
4 | Schedule
12 | 13 | {% assign lesson_number = 0 %} 14 | {% assign day = 0 %} 15 | {% assign multiday = false %} 16 | {% for lesson_episode in lesson_episodes %} 17 | {% if site.episode_order %} 18 | {% assign episode = site.episodes | where: "slug", lesson_episode | first %} 19 | {% else %} 20 | {% assign episode = lesson_episode %} 21 | {% endif %} 22 | {% if episode.start %}{% assign multiday = true %}{% break %}{% endif %} 23 | {% endfor %} 24 | {% assign current = site.start_time %} 25 | 26 || {% endif %} 29 | | 30 | | Setup | 31 |Download files required for the lesson | 32 |
| {% endif %} 46 | | {% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} | 47 |Finish | 48 |49 | |
| {% if episode.start %}Day {{ day }}{% endif %} | {% endif %} 57 |{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} | 58 |59 | {% assign lesson_number = lesson_number | plus: 1 %} 60 | {{ lesson_number }}. {{ episode.title }} 61 | | 62 |
63 | {% if episode.break %}
64 | Break
65 | {% else %}
66 | {% if episode.questions %}
67 | {% for question in episode.questions %}
68 | {{question|markdownify|strip_html}}
69 | {% unless forloop.last %}
70 | 71 | {% endunless %} 72 | {% endfor %} 73 | {% endif %} 74 | {% endif %} 75 | |
76 |
| {% endif %} 83 | | {% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} | 84 |Finish | 85 |86 | |
90 | The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor. 91 |
92 | 93 |
5 |
33 |
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/_includes/workshop_calendar.html:
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1 | Add to your Google Calendar.
2 |
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/_includes/workshop_footer.html:
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1 | {% comment %}
2 | Footer for a standard workshop.
3 | {% endcomment %}
4 |
27 |
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/_layouts/base.html:
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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 |
20 |
21 | {% include favicons.html %}
22 |
23 |
24 |
25 |
29 |
30 |
6 |
32 |
7 |
31 | {{page.venue}}
8 |
9 |
30 |
10 |
13 | {{page.humandate}}
11 |{% if page.humantime %}{{page.humantime}}{% endif %}
12 |
14 |
29 | 15 | Instructors: 16 | {% if page.instructor %} 17 | {{page.instructor | join: ', ' %}} 18 | {% else %} 19 | to be announced. 20 | {% endif %} 21 |
22 | {% if page.helper %} 23 |24 | Helpers: 25 | {{page.helper | join: ', ' %}} 26 |
27 | {% endif %} 28 |
40 | {% include navbar.html %}
41 | {{ content }}
42 | {% if site.kind == "workshop" %}
43 | {% include workshop_footer.html %}
44 | {% else %}
45 | {% include lesson_footer.html %}
46 | {% endif %}
47 |
48 | {% include javascript.html %}
49 |
50 |
51 |
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/_layouts/break.html:
--------------------------------------------------------------------------------
1 | ---
2 | layout: base
3 | ---
4 | {% include episode_navbar.html episode_navbar_title=true %}
5 |
49 | {% include navbar.html %}
50 | {% include workshop_ad.html %}
51 | {{ content }}
52 | {% include workshop_footer.html %}
53 |
54 | {% include javascript.html %}
55 |
56 |
57 |
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/aio.md:
--------------------------------------------------------------------------------
1 | ---
2 | permalink: /aio/index.html
3 | ---
4 |
5 | {% comment %}
6 | As a maintainer, you don't need to edit this file.
7 | If you notice that something doesn't work, please
8 | open an issue: https://github.com/carpentries/styles/issues/new
9 | {% endcomment %}
10 |
11 | {% include base_path.html %}
12 |
13 | {% include aio-script.md %}
14 |
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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 |
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/bin/boilerplate/.travis.yml:
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1 | # Travis CI is only used to check the lesson and is not involved in its deployment
2 | dist: bionic
3 | language: ruby
4 | rvm:
5 | - 2.7.1
6 |
7 | branches:
8 | only:
9 | - gh-pages
10 | - /.*/
11 |
12 | cache:
13 | apt: true
14 | bundler: true
15 | directories:
16 | - /home/travis/.rvm/
17 | - $R_LIBS_USER
18 | - $HOME/.cache/pip
19 |
20 | env:
21 | global:
22 | - NOKOGIRI_USE_SYSTEM_LIBRARIES=true # speeds up installation of html-proofer
23 | - R_LIBS_USER=~/R/Library
24 | - R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/lib/R/site-library
25 | - R_VERSION=4.0.2
26 |
27 | before_install:
28 | ## Install R + pandoc + dependencies
29 | - sudo add-apt-repository -y "ppa:marutter/rrutter4.0"
30 | - sudo add-apt-repository -y "ppa:c2d4u.team/c2d4u4.0+"
31 | - sudo add-apt-repository -y "ppa:ubuntugis/ppa"
32 | - sudo add-apt-repository -y "ppa:cran/travis"
33 | - travis_apt_get_update
34 | - sudo apt-get install -y --no-install-recommends build-essential gcc g++ libblas-dev liblapack-dev libncurses5-dev libreadline-dev libjpeg-dev libpcre3-dev libpng-dev zlib1g-dev libbz2-dev liblzma-dev libicu-dev cdbs qpdf texinfo libssh2-1-dev gfortran jq python3.5 python3-pip r-base
35 | - export PATH=${TRAVIS_HOME}/R-bin/bin:$PATH
36 | - export LD_LIBRARY_PATH=${TRAVIS_HOME}/R-bin/lib:$LD_LIBRARY_PATH
37 | - sudo mkdir -p /usr/local/lib/R/site-library $R_LIBS_USER
38 | - sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library $R_LIBS_USER
39 | - echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))' > ~/.Rprofile.site
40 | - export R_PROFILE=~/.Rprofile.site
41 | - curl -fLo /tmp/texlive.tar.gz https://github.com/jimhester/ubuntu-bin/releases/download/latest/texlive.tar.gz
42 | - tar xzf /tmp/texlive.tar.gz -C ~
43 | - export PATH=${TRAVIS_HOME}/texlive/bin/x86_64-linux:$PATH
44 | - tlmgr update --self
45 | - curl -fLo /tmp/pandoc-2.2-1-amd64.deb https://github.com/jgm/pandoc/releases/download/2.2/pandoc-2.2-1-amd64.deb
46 | - sudo dpkg -i /tmp/pandoc-2.2-1-amd64.deb
47 | - sudo apt-get install -f
48 | - rm /tmp/pandoc-2.2-1-amd64.deb
49 | - Rscript -e "install.packages(setdiff(c('renv', 'rprojroot'), installed.packages()), loc = Sys.getenv('R_LIBS_USER')); update.packages(lib.loc = Sys.getenv('R_LIBS_USER'), ask = FALSE, checkBuilt = TRUE)"
50 | - Rscript -e 'sessionInfo()'
51 | ## Install python and dependencies
52 | - python3 -m pip install --upgrade pip setuptools wheel
53 | - python3 -m pip install pyyaml
54 |
55 | script:
56 | - make lesson-check-all
57 | - make --always-make site
58 |
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/bin/boilerplate/AUTHORS:
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1 | FIXME: list authors' names and email addresses.
--------------------------------------------------------------------------------
/bin/boilerplate/CITATION:
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1 | FIXME: describe how to cite this lesson.
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/bin/boilerplate/README.md:
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1 | # FIXME Lesson title
2 |
3 | [](https://swc-slack-invite.herokuapp.com/)
4 |
5 | This repository generates the corresponding lesson website from [The Carpentries](https://carpentries.org/) repertoire of lessons.
6 |
7 | ## Contributing
8 |
9 | We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any
10 | questions, concerns, or experience any difficulties along the way.
11 |
12 | We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTRIBUTING.md) and have a look at
13 | the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
14 | how to write new episodes.
15 |
16 | Please see the current list of [issues][FIXME] for ideas for contributing to this
17 | repository. For making your contribution, we use the GitHub flow, which is
18 | nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git
19 | by Scott Chacon.
20 | Look for the tag . This indicates that the maintainers will welcome a pull request fixing this issue.
21 |
22 |
23 | ## Maintainer(s)
24 |
25 | Current maintainers of this lesson are
26 |
27 | * FIXME
28 | * FIXME
29 | * FIXME
30 |
31 |
32 | ## Authors
33 |
34 | A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
35 |
36 | ## Citation
37 |
38 | To cite this lesson, please consult with [CITATION](CITATION)
39 |
40 | [lesson-example]: https://carpentries.github.io/lesson-example
41 |
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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 | carpentry: "swc"
11 |
12 | # Overall title for pages.
13 | title: "Lesson Title"
14 |
15 | # Life cycle stage of the lesson
16 | # See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html
17 | # Possible values: "pre-alpha", "alpha", "beta", "stable"
18 | life_cycle: "pre-alpha"
19 |
20 | #------------------------------------------------------------
21 | # Generic settings (should not need to change).
22 | #------------------------------------------------------------
23 |
24 | # What kind of thing is this ("workshop" or "lesson")?
25 | kind: "lesson"
26 |
27 | # Magic to make URLs resolve both locally and on GitHub.
28 | # See https://help.github.com/articles/repository-metadata-on-github-pages/.
29 | # Please don't change it: 10 | 11 | 12 | 13 |
14 | 15 | 16 | 17 | 18 | {% comment %} This is a comment in Liquid {% endcomment %} 19 | 20 | > ## Prerequisites 21 | > 22 | > A computer with Docker installed on it 23 | {: .prereq} 24 | 25 | {% include links.md %} 26 | -------------------------------------------------------------------------------- /reference.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: reference 3 | --- 4 | 5 | ## Glossary 6 | 7 | {% include links.md %} 8 | -------------------------------------------------------------------------------- /setup.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Setup 3 | --- 4 | To install Docker Community Edition on your Linux, Mac, or Windows machine follow the [instructions in the Docker docs](https://docs.docker.com/install/). 5 | 6 | 7 | {% include links.md %} 8 | --------------------------------------------------------------------------------