index.html 28.8 KB
Newer Older
1
---
2
layout: workshop      # DON'T CHANGE THIS.
Greg Wilson's avatar
Greg Wilson committed
3
root: .               # DON'T CHANGE THIS EITHER.  (THANK YOU.)
Greg Wilson's avatar
Greg Wilson committed
4
carpentry: "FIXME"    # what kind of Carpentry (must be either "dc" or "swc")
5
venue: "FIXME"        # brief name of host site without address (e.g., "Euphoric State University")
6
7
8
9
10
11
12
13
14
15
16
17
18
address: "FIXME"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "FIXME"      # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "FIXME"     # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "FIXME"       # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "FIXME"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "FIXME"    # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: FIXME      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: FIXME        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["FIXME"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["FIXME"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: "FIXME"      # contact email address for host, lead instructor, or whoever else is handling questions
etherpad:             # optional: URL for the workshop Etherpad if there is one
eventbrite:           # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
19
---
20
21
22

<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->

23
<!--
24
25
  HEADER

26
27
28
29
  Edit the values in the block above to be appropriate for your workshop.
  If the value is not 'true', 'false', 'null', or a number, please use
  double quotation marks around the value, unless specified otherwise.
  And run 'tools/check' *before* committing to make sure that changes are good.
30
31
32
-->

<!--
33
34
  EVENTBRITE

35
36
37
38
39
  This block includes the Eventbrite registration widget if
  'eventbrite' has been set in the header.  You can delete it if you
  are not using Eventbrite, or leave it in, since it will not be
  displayed if the 'eventbrite' field in the header is not set.
-->
40
41
{% if page.eventbrite %}
<iframe
42
  src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
43
  frameborder="0"
44
  width="100%"
45
  height="248px"
46
47
48
49
  scrolling="auto">
</iframe>
{% endif %}

Tom Wright's avatar
Tom Wright committed
50
51
52
<h4>This is the workshop template.  Use it to create your own website.
Delete this line and email the link to your workshop page to admin@software-carpentry.org.
If this is a self organized workshop, please be sure to include any other details
53
Software Carpentry staff may need to know in your email.</h4>
54
55


56
<h2 id="general">General Information</h2>
57

58
<!--
59
60
  INTRODUCTION

61
62
63
  Edit the general explanatory paragraph below if you want to change
  the pitch.
-->
64
65
66
67
68
69
70
71
72
73
<p>
  <a href="{{site.swc_site}}">Software Carpentry</a>'s mission
  is to help scientists and engineers get more research done in less
  time and with less pain by teaching them basic lab skills for
  scientific computing.  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>
74
75
76
77
78
79
80
<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>
81

82
<!--
83
84
  AUDIENCE

85
86
87
  Explain who your audience is.  (In particular, tell readers if the
  workshop is only open to people from a particular institution.
-->
88
<p id="who">
89
90
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers.
91
92
  <strong>You don't need to have any previous knowledge of the tools that will
    be presented at the workshop.</strong>
93
94
</p>

95
<!--
96
97
  LOCATION

98
99
100
101
102
  This block displays the address and links to maps showing directions
  if the latitude and longitude of the workshop have been set.  You
  can use http://itouchmap.com/latlong.html to find the lat/long of an
  address.
-->
103
{% if page.latlng %}
104
<p id="where">
105
  <strong>Where:</strong>
106
  {{page.address}}.
107
  Get directions with
108
  <a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
109
  or
110
  <a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
111
112
113
</p>
{% endif %}

114
<!--
115
116
  SPECIAL REQUIREMENTS

117
118
  Modify the block below if there are any special requirements.
-->
119
<p id="requirements">
Tom Wright's avatar
Tom Wright committed
120
  <strong>Requirements:</strong> Participants must bring a laptop with a
121
122
  Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. They should have a few specific software packages installed (listed
123
124
  <a href="#setup">below</a>). They are also required to abide by
  Software Carpentry's
125
126
127
  <a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.
</p>

Tom Wright's avatar
Tom Wright committed
128
129
130
131
132
133
134
<!--
  ACCESSIBILITY

  Modify the block below if there are any barriers to accessibility or
  special instructions.
-->
<p id="accessibility">
Greg Wilson's avatar
Greg Wilson committed
135
136
137
138
139
140
141
142
143
144
145
146
147
  <strong>Accessibility:</strong> We are committed to making this workshop
  accessible to everybody.
  The workshop organisers have checked that:
</p>
<ul>
  <li>The room is wheelchair / scooter accessible.</li>
  <li>Accessible restrooms are available.</li>
</ul>
<p>
  Materials will be provided in advance of the workshop and
  large-print handouts are available if needed by notifying the
  organizers in advance.  If we can help making learning easier for
  you (e.g. sign-language interpreters, lactation facilities) please
Greg Wilson's avatar
Greg Wilson committed
148
149
  <a href="mailto:{{page.contact}}">get in touch</a> and we will
  attempt to provide them.
Tom Wright's avatar
Tom Wright committed
150
151
</p>

152
<!--
153
154
  CONTACT EMAIL ADDRESS

Greg Wilson's avatar
Greg Wilson committed
155
  Display the contact email address set in the configuration file.
156
-->
157
<p id="contact">
158
159
  <strong>Contact</strong>:
  Please mail
Greg Wilson's avatar
Greg Wilson committed
160
161
  <a href="mailto:{{page.contact}}">{{page.contact}}</a> for more
  information.
162
163
164
165
</p>

<hr/>

166
<!--
167
168
  SCHEDULE

169
170
171
172
  Show the workshop's schedule.  Edit the items and times in the table
  to match your plans.  You may also want to change 'Day 1' and 'Day
  2' to be actual dates or days of the week.
-->
173
<h2 id="schedule">Schedule</h2>
174

175
<!-- DO NOT EDIT SURVEY LINKS -->
176
177
<p><em>Surveys</em></p>
<p>Please be sure to complete these surveys before and after the workshop.</p>
Greg Wilson's avatar
Greg Wilson committed
178
179
<p><a href="{{ site.pre_survey }}{{ site.github.project_title }}">Pre-workshop Survey</a></p>
<p><a href="{{ site.post_survey }}{{ site.github.project_title }}">Post-workshop Survey</a></p>
180

181
182
<div class="row">
  <div class="col-md-6">
183
184
    <h3>Day 1</h3>
    <table class="table table-striped">
185
      <tr> <td>09:00</td>  <td>Automating tasks with the Unix shell</td> </tr>
186
      <tr> <td>10:30</td> <td>Coffee</td> </tr>
187
188
189
190
      <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>
191
192
    </table>
  </div>
193
  <div class="col-md-6">
194
195
    <h3>Day 2</h3>
    <table class="table table-striped">
196
197
198
199
200
201
      <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>
202
203
204
205
    </table>
  </div>
</div>

206
<!--
207
208
  ETHERPAD

Raniere Silva's avatar
Raniere Silva committed
209
210
  At `_misc/etherpad.txt` you will find a template for the etherpad.

211
212
213
  Display the Etherpad for the workshop.  You can set this up in
  advance or on the first day; either way, make sure you push changes
  to GitHub after you have its URL.  To create an Etherpad, go to
214

215
      http://pad.software-carpentry.org/YYYY-MM-DD-site
216

217
218
  where 'YYYY-MM-DD-site' is the identifier for your workshop,
  e.g., '2015-06-10-esu'.
219
220
-->
{% if page.etherpad %}
221
<p id="etherpad">
222
223
224
225
226
227
  <strong>Etherpad:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
  <br/>
  We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
</p>
{% endif %}

228
229
<hr/>

230
<!--
231
232
  SYLLABUS

233
234
235
236
237
238
239
  Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment
     around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
     intend to teach.
240
241
  4. You may need to move the div's with class="col-md-6" around inside
     the div's with class="row" to balance the multi-column layout.
242
243
244
245
246

  This is one of the places where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
247
<h2 id="syllabus">Syllabus</h2>
248

249
250
<div class="row">
  <div class="col-md-6">
251
    <h3 id="syllabus-shell">The Unix Shell</h3>
252
    <ul>
253
      <li>Files and directories</li>
254
255
256
257
      <li>History and tab completion</li>
      <li>Pipes and redirection</li>
      <li>Looping over files</li>
      <li>Creating and running shell scripts</li>
258
      <li>Finding things</li>
259
      <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
260
261
    </ul>
  </div>
262
  <div class="col-md-6">
263
    <h3 id="syllabus-python">Programming in Python</h3>
264
265
266
267
268
    <ul>
      <li>Using libraries</li>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
269
      <li>Loops and conditionals</li>
270
271
      <li>Defensive programming</li>
      <li>Using Python from the command line</li>
272
      <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
273
274
    </ul>
  </div>
275
276
  <!--
  <div class="col-md-6">
277
    <h3 id="syllabus-r">Programming in R</h3>
278
279
280
281
    <ul>
      <li>Working with vectors and data frames</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
282
      <li>Loops and conditionals</li>
283
      <li>Using R from the command line</li>
284
      <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Reference...</a></li>
285
286
    </ul>
  </div>
287
  -->
288
289
  <!--
  <div class="col-md-6">
290
    <h3 id="syllabus-matlab">Programming in MATLAB</h3>
291
292
293
294
295
296
    <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>
297
      <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Reference...</a></li>
298
299
300
     </ul>
   </div>
   -->
301
302
</div>

303
304
<div class="row">
  <div class="col-md-6">
305
    <h3 id="syllabus-git">Version Control with Git</h3>
306
307
308
309
310
311
312
313
314
    <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>
315
      <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></li>
316
317
    </ul>
  </div>
318
  <div class="col-md-6">
319
    <h3 id="syllabus-sql">Managing Data with SQL</h3>
320
321
322
323
324
325
326
327
328
    <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>
329
      <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Reference...</a></li>
330
331
332
333
334
335
    </ul>
  </div>
</div>

<hr/>

336
<!--
337
338
  SETUP

339
340
341
  Delete irrelevant sections from the setup instructions.  Each
  section is inside a 'div' without any classes to make the beginning
  and end easier to find.
342

343
344
345
346
  This is the other place where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
347

348
<h2 id="setup">Setup</h2>
349

350
<p>
351
352
  To participate in a Software Carpentry workshop, you will need
  access to the software described below. In addition, you will
353
  need an up-to-date web browser.
354
355
</p>
<p>
David LeBauer's avatar
David LeBauer committed
356
357
  We maintain a list of common issues that occur during installation as a reference for instructors
  that may be useful on the
358
  <a href = "{{site.swc_github}}/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
359
360
</p>

361
<div id="shell"> <!-- Start of 'shell' section. -->
362
  <h3>The Bash Shell</h3>
363

364
365
366
367
  <p>
    Bash is a commonly-used shell that gives you the power to do simple
    tasks more quickly.
  </p>
368

369
370
  <div class="row">
    <div class="col-md-4">
371
      <h4 id="shell-windows">Windows</h4>
Sarah Stevens's avatar
Sarah Stevens committed
372
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
373
374
375
376
      <ol>
        <li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
        <li>Run the installer and follow the steps bellow:
          <ol>
bhjolly's avatar
bhjolly committed
377
            <!-- Git 2.8.2 Setup -->
378
379
380
381
382
383
384
            <!-- Information -->
            <li>Click on "Next".</li>
            <!-- Select Components -->
            <li>Click on "Next".</li>
            <!-- Adjusting your PATH environment -->
            <li>
              <strong>
bhjolly's avatar
bhjolly committed
385
                Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
386
387
388
389
              </strong>
                If you forgot to do this programs that you need for the workshop will not work properly.
                If this happens rerun the installer and select the appropriate option.
            </li>
bhjolly's avatar
bhjolly committed
390
391
            <!-- Choosing the SSH executable -->
            <li>Click on "Next".</li>
392
            <!-- Configuring the line ending conversions -->
393
394
            <li>
              <strong>
bhjolly's avatar
bhjolly committed
395
                Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
396
397
              </strong>
            </li>
398
            <!-- Configuring the terminal emulator to use with Git Bash -->
399
400
            <li>
              <strong>
bhjolly's avatar
bhjolly committed
401
                Keep "Use Windows' default console window" selected and click on "Next".
402
403
              </strong>
            </li>
404
            <!-- Configuring experimental performance tweaks -->
bhjolly's avatar
bhjolly committed
405
            <li>Click on "Install".</li>
406
407
408
409
410
            <!-- Installing -->
            <!-- Completing the Git Setup Wizard -->
            <li>Click on "Finish".</li>
          </ol>
        </li>
411
412
413
414
415
416
417
418
419
420
421
422
        <li>
          If your "HOME" environment variable is not set (or you don't know what this is):
          <ol>
            <li>Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
            <li>
              Type the following line into the command prompt window exactly as shown:
              <p><code>setx HOME "%USERPROFILE%"</code></p>
            </li>
            <li>Press [Enter], you should see <code>SUCCESS: Specified value was saved.</code></li>
            <li>Quit command prompt by typing <code>exit</code> then pressing [Enter]</li>
          </ol>
        </li>
423
424
      </ol>
      <p>This will provide you with both Git and Bash in the Git Bash program.</p>
425
    </div>
426
    <div class="col-md-4">
427
      <h4 id="shell-macosx">Mac OS X</h4>
428
      <p>
429
430
        The default shell in all versions of Mac OS X is Bash, so no
        need to install anything.  You access Bash from the Terminal
431
        (found in
Sarah Stevens's avatar
Sarah Stevens committed
432
433
434
435
        <code>/Applications/Utilities</code>).
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open the Terminal.
        You may want to keep
436
        Terminal in your dock for this workshop.
437
438
      </p>
    </div>
439
    <div class="col-md-4">
440
      <h4 id="shell-linux">Linux</h4>
441
      <p>
442
443
444
445
        The default shell is usually Bash, but if your
        machine is set up differently you can run it by opening a
        terminal and typing <code>bash</code>.  There is no need to
        install anything.
446
447
      </p>
    </div>
448
  </div>
Raniere Silva's avatar
Raniere Silva committed
449
</div> <!-- End of 'shell' section. -->
450

Greg Wilson's avatar
Greg Wilson committed
451
<div id="git"> <!-- Start of 'Git' section. GitHub browser compatability
452
           is given at https://help.github.com/articles/supported-browsers/-->
453
454
455
456
457
  <h3>Git</h3>
  <p>
    Git is a version control system that lets you track who made changes
    to what when and has options for easily updating a shared or public
    version of your code
458
    on <a href="https://github.com/">github.com</a>. You will need a
459
460
    <a href="https://help.github.com/articles/supported-browsers/">supported</a>
    web browser (current versions of Chrome, Firefox or Safari,
461
    or Internet Explorer version 9 or above).
462
  </p>
463
464
  <p>
    You will need an account at <a href="https://github.com/">github.com</a>
Jan T. Kim's avatar
Jan T. Kim committed
465
466
    for parts of the Git lesson. Basic GitHub accounts are free. We encourage
    you to create a GitHub account if you don't have one already.
467
468
469
    Please consider what personal information you'd like to reveal. For
    example, you may want to review these
    <a href="https://help.github.com/articles/keeping-your-email-address-private/">instructions
Jan T. Kim's avatar
Jan T. Kim committed
470
    for keeping your email address private</a> provided at GitHub.
471
  </p>
472

473
474
  <div class="row">
    <div class="col-md-4">
475
      <h4 id="git-windows">Windows</h4>
476
      <p>
477
478
        Git should be installed on your computer as part of your Bash
        install (described above).
479
480
      </p>
    </div>
481
    <div class="col-md-4">
482
      <h4 id="git-macosx">Mac OS X</h4>
483
      <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">Video Tutorial</a>
484
      <p>
Greg Wilson's avatar
Merging    
Greg Wilson committed
485
486
487
488
        <strong>For OS X 10.9 and higher</strong>, install Git for Mac
        by downloading and running the most recent "mavericks" installer from
        <a href="http://sourceforge.net/projects/git-osx-installer/files/">this list</a>.
        After installing Git, there will not be anything in your <code>/Applications</code> folder,
489
        as Git is a command line program.
Greg Wilson's avatar
Merging    
Greg Wilson committed
490
491
492
        <strong>For older versions of OS X (10.5-10.8)</strong> use the
        most recent available installer labelled "snow-leopard"
        <a href="http://sourceforge.net/projects/git-osx-installer/files/">available here</a>.
493
494
      </p>
    </div>
495
    <div class="col-md-4">
496
      <h4 id="git-linux">Linux</h4>
497
      <p>
498
499
        If Git is not already available on your machine you can try to
        install it via your distro's package manager. For Debian/Ubuntu run
500
501
        <code>sudo apt-get install git</code> and for Fedora run
        <code>sudo yum install git</code>.
502
503
      </p>
    </div>
504
  </div>
505
</div> <!-- End of 'Git' section. -->
506

Raniere Silva's avatar
Raniere Silva committed
507
508
509
510
511
512
513
514
515
<div id="editor"> <!-- Start of 'editor' section. -->
  <h3>Text Editor</h3>

  <p>
    When you're writing code, it's nice to have a text editor that is
    optimized for writing code, with features like automatic
    color-coding of key words.  The default text editor on Mac OS X and
    Linux is usually set to Vim, which is not famous for being
    intuitive.  if you accidentally find yourself stuck in it, try
Raniere Silva's avatar
Raniere Silva committed
516
    typing the escape key, followed by <code>:q!</code> (colon, lower-case 'q',
Raniere Silva's avatar
Raniere Silva committed
517
518
519
520
521
522
    exclamation mark), then hitting Return to return to the shell.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="editor-windows">Windows</h4>
Sarah Stevens's avatar
Sarah Stevens committed
523
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
Raniere Silva's avatar
Raniere Silva committed
524
      <p>
525
        nano is a basic editor and the default that instructors use in the workshop.
526
        To install it,
Raniere Silva's avatar
Raniere Silva committed
527
528
529
530
531
        download the <a href="{{site.swc_installer}}">Software Carpentry Windows installer</a>
        and double click on the file to run it.
        <strong>This installer requires an active internet connection.</strong>
      </p>
      <p>
Raniere Silva's avatar
Raniere Silva committed
532
        Others editors that you can use are
533
534
        <a href="http://notepad-plus-plus.org/">Notepad++</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
Raniere Silva's avatar
Raniere Silva committed
535
536
        <strong>Be aware that you must
          add its installation directory to your system path.</strong>
537
        Please ask your instructor to help you do this.
Raniere Silva's avatar
Raniere Silva committed
538
539
540
541
542
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-macosx">Mac OS X</h4>
      <p>
543
        nano is a basic editor and the default that instructors use in the workshop.
Sarah Stevens's avatar
Sarah Stevens committed
544
545
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open nano.
Raniere Silva's avatar
Raniere Silva committed
546
547
548
        It should be pre-installed.
      </p>
      <p>
Raniere Silva's avatar
Raniere Silva committed
549
        Others editors that you can use are
550
551
        <a href="http://www.barebones.com/products/textwrangler/">Text Wrangler</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
Raniere Silva's avatar
Raniere Silva committed
552
553
554
555
556
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-linux">Linux</h4>
      <p>
557
        nano is a basic editor and the default that instructors use in the workshop.
Raniere Silva's avatar
Raniere Silva committed
558
559
560
        It should be pre-installed.
      </p>
      <p>
Raniere Silva's avatar
Raniere Silva committed
561
        Others editors that you can use are
Raniere Silva's avatar
Raniere Silva committed
562
        <a href="https://wiki.gnome.org/Apps/Gedit">Gedit</a>,
563
564
        <a href="http://kate-editor.org/">Kate</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
Raniere Silva's avatar
Raniere Silva committed
565
566
567
568
569
      </p>
    </div>
  </div>
</div> <!-- End of 'editor' section. -->

570
<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
571
572
573
           the workshop will teach Python using something other than
           the IPython notebook.
           Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
574
  <h3>Python</h3>
575

576
577
578
579
  <p>
    <a href="http://python.org">Python</a> is a popular language for
    scientific computing, and great for general-purpose programming as
    well.  Installing all of its scientific packages individually can be
580
    a bit difficult, so we recommend
581
    <a href="https://www.continuum.io/anaconda">Anaconda</a>,
582
    an all-in-one installer.
583
  </p>
584

Greg Wilson's avatar
Greg Wilson committed
585
586
    <p>
      Regardless of how you choose to install it,
587
588
      <strong>please make sure you install Python version 3.x</strong>
      (e.g., 3.4 is fine).
Greg Wilson's avatar
Greg Wilson committed
589
    </p>
590

591
592
593
    <p>
      We will teach Python using the IPython notebook, a programming environment
      that runs in a web browser. For this to work you will need a reasonably
594
      up-to-date browser. The current versions of the Chrome, Safari and
Greg Wilson's avatar
Greg Wilson committed
595
596
      Firefox browsers are all
      <a href="http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility">supported</a>
597
      (some older browsers, including Internet Explorer version 9
598
      and below, are not).
599
600
    </p>

601
602
  <div class="row">
    <div class="col-md-4">
603
      <h4 id="python-windows">Windows</h4>
Sarah Stevens's avatar
Sarah Stevens committed
604
      <a href="https://www.youtube.com/watch?v=xxQ0mzZ8UvA">Video Tutorial</a>
605
606
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
607
        <li>Download the Python 3 installer for Windows.</li>
608
609
        <li>Install Python 3 using all of the defaults for installation <em>except</em> make sure to check <strong>Make Anaconda the default Python</strong>.</li>
      </ol>
610
    </div>
611
    <div class="col-md-4">
612
      <h4 id="python-macosx">Mac OS X</h4>
Sarah Stevens's avatar
Sarah Stevens committed
613
      <a href="https://www.youtube.com/watch?v=TcSAln46u9U">Video Tutorial</a>
614
615
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
616
        <li>Download the Python 3 installer for OS X.</li>
617
618
        <li>Install Python 3 using all of the defaults for installation.</li>
      </ol>
619
    </div>
620
    <div class="col-md-4">
621
      <h4 id="python-linux">Linux</h4>
622
      <ol>
623
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
624
        <li>Download the Python 3 installer for Linux.</li>
625
626
627
628
        <li>Install Python 3 using all of the defaults for installation.
        (Installation requires using the shell. If you aren't
        comfortable doing the installation yourself
        stop here and request help at the workshop.)</li>
629
        <li>
630
          Open a terminal window.
631
632
        </li>
        <li>
633
          Type <pre>bash Anaconda3-</pre> and then press
634
635
          tab. The name of the file you just downloaded should
          appear.
636
637
        </li>
        <li>
638
639
640
641
642
643
644
          Press enter. You will follow the text-only prompts.  When
          there is a colon at the bottom of the screen press the down
          arrow to move down through the text. Type <code>yes</code> and
          press enter to approve the license. Press enter to approve the
          default location for the files. Type <code>yes</code> and
          press enter to prepend Anaconda to your <code>PATH</code>
          (this makes the Anaconda distribution the default Python).
645
        </li>
646
647
      </ol>
    </div>
648
  </div>
649
<!--
650
651
652
653
654
  <p>
  Once you are done installing the software listed above,
  please go to <a href="setup/index.html">this page</a>,
  which has instructions on how to test that everything was installed correctly.
  </p>
655
-->
656
</div> <!-- End of 'Python' section. -->
657

658
<div id="r"> <!-- Start of 'R' section. -->
659
  <h3>R</h3>
660

661
662
663
664
665
666
  <p>
    <a href="http://www.r-project.org">R</a> is a programming language
    that is especially powerful for data exploration, visualization, and
    statistical analysis. To interact with R, we use
    <a href="http://www.rstudio.com/">RStudio</a>.
  </p>
667

668
669
  <div class="row">
    <div class="col-md-4">
670
      <h4 id="r-windows">Windows</h4>
Sarah Stevens's avatar
Sarah Stevens committed
671
      <a href="https://www.youtube.com/watch?v=q0PjTAylwoU">Video Tutorial</a>
672
      <p>
673
674
675
676
677
        Install R by downloading and running
        <a href="http://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
        from <a href="http://cran.r-project.org/index.html">CRAN</a>.
        Also, please install the
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
678
679
      </p>
    </div>
680
    <div class="col-md-4">
681
      <h4 id="r-macosx">Mac OS X</h4>
Sarah Stevens's avatar
Sarah Stevens committed
682
      <a href="https://www.youtube.com/watch?v=5-ly3kyxwEg">Video Tutorial</a>
683
      <p>
684
685
686
687
688
        Install R by downloading and running
        <a href="http://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
        from <a href="http://cran.r-project.org/index.html">CRAN</a>.
        Also, please install the
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
689
690
      </p>
    </div>
691
    <div class="col-md-4">
692
      <h4 id="r-linux">Linux</h4>
693
      <p>
694
695
696
697
        You can download the binary files for your distribution
        from <a href="http://cran.r-project.org/index.html">CRAN</a>. Or
        you can use your package manager (e.g. for Debian/Ubuntu
        run <code>sudo apt-get install r-base</code> and for Fedora run
698
        <code>sudo yum install R</code>).  Also, please install the
699
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
700
701
      </p>
    </div>
702
  </div>
703
</div> <!-- End of 'R' section. -->
704

705
<div id="sql"> <!-- Start of 'SQLite' section. -->
706
  <h3>SQLite</h3>
707

708
709
710
711
712
  <p>
    SQL is a specialized programming language used with databases.  We
    use a simple database manager called
    <a href="http://www.sqlite.org/">SQLite</a> in our lessons.
  </p>
713

714
715
  <div class="row">
    <div class="col-md-4">
716
      <h4 id="sql-windows">Windows</h4>
717
      <p>
718
        The <a href="{{site.swc_installer}}">Software Carpentry Windows Installer</a>
719
720
        installs SQLite for Windows.
        If you used the installer to configure nano, you don't need to run it again.
721
722
      </p>
    </div>
723
    <div class="col-md-4">
724
      <h4 id="sql-macosx">Mac OS X</h4>
725
      <p>
726
        SQLite comes pre-installed on Mac OS X.
727
728
      </p>
    </div>
729
    <div class="col-md-4">
730
      <h4 id="sql-linux">Linux</h4>
731
      <p>
732
        SQLite comes pre-installed on Linux.
733
734
      </p>
    </div>
735
  </div>
736
737

  <p><strong>If you installed Anaconda, it also has a copy of SQLite
Raniere Silva's avatar
Raniere Silva committed
738
    <a href="https://github.com/ContinuumIO/anaconda-issues/issues/307">without support to <code>readline</code></a>.
739
    Instructors will provide a workaround for it if needed.</strong></p>
740
</div> <!-- End of 'SQLite' section. -->
741

742
743
<!--
  Uncomment this section if you are using our virtual machine.
744

745
<div id="vm">
746
  <h3>Virtual Machine</h3>
747

748
749
750
751
752
753
754
755
756
757
  <p>
    Some instructors prefer to have learners use a virtual machine (VM)
    rather than install software on their own computers.  If your
    instructors have chosen to do this, please:
  </p>
  <ol>
    <li>
      Install <a href="https://www.virtualbox.org/">VirtualBox</a>.
    </li>
    <li>
758
      Download our <a href="{{site.swc_vm}}">VM image</a>.
759
760
761
762
763
764
765
766
767
768
      <strong>Warning:</strong> this file is 1.7 GByte, so please
      download it <em>before</em> coming to your workshop.
    </li>
    <li>
      Load the VM into VirtualBox by selecting "Import Appliance" and
      loading the <code>.ova</code> file.
    </li>
  </ol>
</div>
-->