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Commit 70f0909b authored by Toby Hodges's avatar Toby Hodges
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Merge branch 'style-polishing' into 'master' 

Style polishing

Closes #56, #48, and #24

See merge request !44
parents 97ad7ab4 b303c9f2
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AUTHORS deleted 100644 → 0
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FIXME: list authors' names and email addresses.
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---
layout: page
title: Authors
---
This material is the product of contributions from the following people:
* Aliaksandr Halavatyi
* Jean-Karim Hériché
* Toby Hodges
* Julius Hossain
* Dominik Kutra
* Constantin Pape
* Christian Tischer
The material also owes much to [The Carpentries](https://carpentries.org):
the site theme is based on
[The Carpentries lesson style](https://github.com/carpentries/styles/)
and the concept-focussed style of the modules is inspired by material taught in
[The Carpentries Instructor Training](https://carpentries.github.io/instructor-training/).
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FIXME: describe how to cite this lesson.
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---
layout: page
title: Citation
---
Citation info coming soon.
CONTRIBUTING.md
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---
layout: default
layout: page
title: Guidelines for Contributing
---
# Guidelines for Contributing
Contributions to this project are very welcome.
Changes should be submitted by merge request from a new branch to `master`.
......
LICENSE.md
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---
layout: page
title: License
---
This material is made available under the [Creative Commons Attribution license][cc-by-human].
The following is a human-readable summary of (and not a substitute for)
the [full legal text of the CC BY 4.0 license][cc-by-legal].
......@@ -35,7 +40,7 @@ Notices:
permissions necessary for your intended use. For example, other
rights such as publicity, privacy, or moral rights may limit how you
use the material.
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
[our-gitlab-repo]: https://git.embl.de/grp-bio-it/image-analysis-training-resources/
\ No newline at end of file
[our-gitlab-repo]: https://git.embl.de/grp-bio-it/image-analysis-training-resources/
TEACHING.md deleted 100644 → 0
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# Teaching tips
## White-boards
- Try to frequently use white-board, because:
- It makes teaching more interactive.
- It slows down teaching, because you have to draw.
- Make sure you have good pens with high contrast.
- Have two white-boards:
- One for tidy concept maps.
- One for messy notes.
## Stand
- Try not to sit, because:
- Teaching will be more dynamic.
- People can see and hear you better.
- Construct something to have your computer up, such that you can stand in front of it.
_config.yml
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......@@ -19,6 +19,7 @@ life_cycle: "pre-alpha"
kind: "lesson"
# Sites
repository: "https://git.embl.de/grp-bio-it/image-analysis-training-resources"
repo_url: "https://git.embl.de/grp-bio-it/image-analysis-training-resources"
cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
......
_extras/about.md
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---
layout: page
title: About
---
{% include carpentries.html %}
TODO
{% include links.md %}
_extras/figures.md
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---
layout: page
title: Figures
---
......@@ -6,17 +7,17 @@ title: Figures
<script>
window.onload = function() {
var lesson_episodes = [
{% for episode in site.episodes %}
"{{ episode.url }}"{% unless forloop.last %},{% endunless %}
var lesson_modules = [
{% for module in site.modules %}
"{{ module.url }}"{% unless forloop.last %},{% endunless %}
{% endfor %}
];
var xmlHttp = []; /* Required since we are going to query every episode. */
for (i=0; i < lesson_episodes.length; i++) {
for (i=0; i < lesson_modules.length; i++) {
xmlHttp[i] = new XMLHttpRequest();
xmlHttp[i].episode = lesson_episodes[i]; /* To enable use this later. */
xmlHttp[i].module = lesson_modules[i]; /* To enable use this later. */
xmlHttp[i].onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
......@@ -24,7 +25,7 @@ title: Figures
var htmlDoc = parser.parseFromString(this.responseText,"text/html");
var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
var article_here = document.getElementById(this.episode);
var article_here = document.getElementById(this.module);
var images = htmlDocArticle.getElementsByTagName("img");
if (images.length > 0) {
......@@ -52,17 +53,17 @@ title: Figures
}
}
}
episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
xmlHttp[i].open("GET", episode_url);
module_url = "{{ relative_root_path }}" + lesson_modules[i];
xmlHttp[i].open("GET", module_url);
xmlHttp[i].send(null);
}
}
</script>
{% comment %}
Create anchor for each one of the episodes.
Create anchor for each one of the modules.
{% endcomment %}
{% for episode in site.episodes %}
<article id="{{ episode.url }}" class="figures"></article>
{% for module in site.modules %}
<article id="{{ module.url }}" class="figures"></article>
{% endfor %}
{% include links.md %}
_extras/guide.md
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---
title: "Instructor Notes"
layout: page
---
FIXME
## White-boards
- Try to frequently use white-board, because:
- It makes teaching more interactive.
- It slows down teaching, because you have to draw.
- Make sure you have good pens with high contrast.
- Have two white-boards:
- One for tidy concept maps.
- One for messy notes.
## Stand
- Try not to sit, because:
- Teaching will be more dynamic.
- People can see and hear you better.
- Construct something to have your computer up, such that you can stand in front of it.
{% include links.md %}
_includes/dc/intro.html deleted 100644 → 0
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<p>
<a href="{{site.dc_site}}">Data Carpentry</a>
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
</p>
<p align="center">
<em>
For more information on what we teach and why,
please see our paper
"<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
</em>
</p>
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<div class="row">
<div class="col-md-6">
<h3>Day 1</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Automating tasks with the Unix shell</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>Building programs with Python</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
<div class="col-md-6">
<h3>Day 2</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Version control with Git</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>Managing data with SQL</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
</div>
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<div class="row">
<div class="col-md-6">
<h3 id="syllabus-shell">The Unix Shell</h3>
<ul>
<li>Files and directories</li>
<li>History and tab completion</li>
<li>Pipes and redirection</li>
<li>Looping over files</li>
<li>Creating and running shell scripts</li>
<li>Finding things</li>
<li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<h3 id="syllabus-python">Programming in Python</h3>
<ul>
<li>Using libraries</li>
<li>Working with arrays</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Defensive programming</li>
<li>Using Python from the command line</li>
<li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-r">Programming in R</h3>
<ul>
<li>Working with vectors and data frames</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Using R from the command line</li>
<li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
<!--
<div class="col-md-6">
<h3 id="syllabus-matlab">Programming in MATLAB</h3>
<ul>
<li>Working with arrays</li>
<li>Reading and plotting data</li>
<li>Creating and using functions</li>
<li>Loops and conditionals</li>
<li>Defensive programming</li>
<li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
</div>
<div class="row">
<div class="col-md-6">
<h3 id="syllabus-git">Version Control with Git</h3>
<ul>
<li>Creating a repository</li>
<li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
<li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
<li>Ignoring files</li>
<li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
<li>Resolving conflicts</li>
<li>Open licenses</li>
<li>Where to host work, and why</li>
<li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-sql">Managing Data with SQL</h3>
<ul>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Calculating new values on the fly</li>
<li>Handling missing values</li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li>Creating, modifying, and deleting data</li>
<li>Programming with databases</li>
<li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
</ul>
</div>
-->
<div class="col-md-6">
<h3 id="syllabus-r">Open Refine</h3>
<ul>
<li>Introduction to OpenRefine</li>
<li>Importing data</li>
<li>Basic functions</li>
<li>Advanced Functions</li>
<li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>
</ul>
</div>
</div>
_includes/dc/who.html deleted 100644 → 0
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<p id="who">
<strong>Who:</strong>
The course is aimed at graduate students and other researchers.
<strong>
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
</strong>
</p>
_includes/lc/intro.html deleted 100644 → 0
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<p>
<a href="{{site.lc_site}}">Library Carpentry</a>
is made by people working in library- and information-related roles to help you:
</p>
<ul>
<li>automate repetitive, boring, error-prone tasks</li>
<li>create, maintain and analyze sustainable and reusable data</li>
<li>work effectively with IT and systems colleagues</li>
<li>better understand the use of software in research</li>
<li>and much more...</li>
</ul>
<p align="center">
<em>
Library Carpentry introduces you to the fundamentals of computing
and provides you with a platform for further self-directed learning.
For more information on what we teach and why, please see our paper
"<a href="https://doi.org/10.18352/lq.10176">Library Carpentry: software skills training for library professionals</a>".
</em>
</p>
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<div class="row">
<div class="col-md-6">
<h3>Day 1</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Data Intro for Librarians</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>Shell Lessons for Libraries</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
<div class="col-md-6">
<h3>Day 2</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Git Intro for Librarians</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>OpenRefine for Librarians</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
</div>
_includes/lc/syllabus.html deleted 100644 → 0
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<div class="row">
<div class="col-md-6">
<h3 id="syllabus-python">Data Intro</h3>
<ul>
<li>Intro to data</li>
<li>Jargon busting</li>
<li>Keyboard shortcuts</li>
<li>Plain text formats</li>
<li>Naming files</li>
<li>Regular expressions</li>
<li><a href="https://data-lessons.github.io/library-data-intro/reference/">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<h3 id="syllabus-shell">The Unix Shell</h3>
<ul>
<li>Files and directories</li>
<li>History and tab completion</li>
<li>Counting and sorting contents in files</li>
<li>Pipes and redirection</li>
<li>Mining or searching in files</li>
<li><a href="https://data-lessons.github.io/library-shell/reference/">Reference...</a></li>
</ul>
</div>
</div>
<div class="row">
<div class="col-md-6">
<h3 id="syllabus-git">Version Control with Git</h3>
<ul>
<li>Creating a repository</li>
<li>Configuring git</li>
<li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
<li>Viewing state changes with <code>status</code></li>
<li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
<li>Where to host work, and why</li>
<li><a href="https://data-lessons.github.io/library-git/reference">Reference...</a></li>
</ul>
</div>
<div class="col-md-6">
<div class="col-md-6">
<h3 id="syllabus-r">Open Refine</h3>
<ul>
<li>Introduction to OpenRefine</li>
<li>Importing data</li>
<li>Basic functions</li>
<li>Advanced Functions</li>
<li><a href="https://data-lessons.github.io/library-openrefine/reference">Reference...</a></li>
</ul>
</div>
</div>
</div>
<!--div class="row">
<div class="col-md-6">
<h3 id="syllabus-sql">SQL Intro</h3>
<ul>
<li>What is SQL?</li>
<li>Intro to SQLite Manager</li>
<li>Importing a database</li>
<li>Reading and sorting data</li>
<li>Filtering with <code>where</code></li>
<li>Combining values using aggregation</li>
<li>Combining information from multiple tables using <code>join</code></li>
<li><a href="https://data-lessons.github.io//library-sql/reference/">Reference...</a></li>
</ul>
</div>
</div>
-->
_includes/lc/who.html deleted 100644 → 0
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<p id="who">
<strong>Who:</strong>
The course is for people working in library- and information-related roles.
<strong>
You don't need to have any previous knowledge of the tools that
will be presented at the workshop.
</strong>
</p>
_includes/lesson_footer.html
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......@@ -2,7 +2,7 @@
Footer for lesson pages.
{% endcomment %}
{% include gh_variables.html %}
<!-- {% include gh_variables.html %} -->
<footer>
<div class="row">
......@@ -33,14 +33,14 @@
<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
{% endif %}
{% else %}
<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
<a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit source file</a>
{% endif %}
/
<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
<a href="{{ repo_url }}/blob/{{ source_branch }}/contributing" data-checker-ignore>Contributing</a>
/
<a href="{{ repo_url }}/">Source</a>
/
<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
<!-- /
<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a> -->
/
<a href="mailto:{{ site.email }}">Contact</a>
</div>
......
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