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4 <meta name="title" content="Version Control With Subversion" />
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9 <li><a href="#s:basics">Basic Use</a></li>
10 <li><a href="#s:merge">Merging Conflicts</a></li>
11 <li><a href="#s:rollback">Recovering Old Versions</a></li>
12 <li><a href="#s:setup">Setting up a Repository</a></li>
13 <li><a href="#s:provenance">Provenance</a></li>
14 <li><a href="#s:summary">Summing Up</a></li>
18 Wolfman and Dracula have been hired by Universal Missions
19 (a space services spinoff from Euphoric State University)
20 to figure out where the company should send its next planetary lander.
21 They want to be able to work on the plans at the same time,
22 but they have run into problems doing this in the past.
24 each one will spend a lot of time waiting for the other to finish.
26 if they work on their own copies and email changes back and forth
27 they know that things will be lost, overwritten, or duplicated.
31 The right solution is to use a
32 <a href="glossary.html#version-control-system">version control system</a>
34 Version control is better than mailing files back and forth because:
40 It's hard (but not impossible) to accidentally overlook or overwrite someone's changes,
41 because the version control system highlights them automatically.
45 It keeps a record of who made what changes when,
46 so that if people have questions later on,
52 Nothing that is committed to version control is ever lost.
53 This means it can be used like the "undo" feature in an editor,
54 and since all old versions of files are saved
55 it's always possible to go back in time to see exactly who wrote what on a particular day,
56 or what version of a program was used to generate a particular set of results.
62 The rest of this chapter will explore how to use
63 a popular open source version control system called Subversion.
64 It does not have all the features of some newer systems,
65 such as <a href="git.html">Git</a>,
66 but it is still widely used,
67 and is simpler to pick up than those more advanced alternatives.
68 No matter which system you use,
69 the most important thing to learn is not the details of their more obscure commands,
70 but the workflow that they encourage.
74 <h2>For Instructors</h2>
77 Version control is the most important practical skill we introduce.
78 As the last paragraph of the introduction above says,
79 the workflow matters more than the ins and outs of any particular tool.
80 By the end of 90 minutes,
81 the instructor should be able to get learners to chant,
82 "Update, edit, merge, commit," in unison,
83 and have them understand what those terms mean
84 and why that's a good way to structure their working day.
88 Provided there aren't network problems,
89 this entire lesson can be covered in <span class="duration">90 minutes</span>.
90 The example at the end
91 showing how to use Subversion keywords to track provenance
92 is the "ah ha!" moment for many learners.
94 skip the material on recovering old versions of files
95 in order to get to this section instead.
96 (The fact that provenance is harder in Git,
97 both mechanically and conceptually,
98 is one reason to keep teaching Subversion.)
102 <h3>Prerequisites</h3>
104 Basic shell concepts and skills
105 (<code>ls</code>, <code>cd</code>, <code>mkdir</code>,
107 basic shell scripting
108 (for the discussion of <a href="#s:provenance">provenance</a>).
113 <h3>Teaching Notes</h3>
116 Make sure the network is working <em>before</em> starting this lesson.
119 Give learners a ten-minute overview of what version control does for them
120 before diving into the watch-and-do practicals.
121 Most of them will have tried to co-author papers by emailing files back and forth,
122 or will have biked into the office
123 only to realize that the USB key with last night's work
124 is still on the kitchen table.
125 Instructors can also make jokes about directories with names like
127 "final version revised",
128 "final version with reviewer three's corrections",
129 "really final version",
131 "come on this really has to be the last version"
132 to motivate version control as a better way to collaborate
133 and as a better way to back work up.
136 Version control is typically taught after the shell,
137 so collect learners' names during that session
138 and create a repository for them to share
139 with their names as both their IDs and their passwords.
140 The easiest way to create the repository is to use
141 a server managed by an ISP such as Dreamhost,
142 or on SourceForge, Google Code, or some other "forge" site,
143 all of which provide web interfaces for repository creation and management.
144 If your learners are advanced enough to be using SSH,
145 you can instead create it on any server they can access,
146 and connect with the <code>svn+ssh</code> protocol instead of HTTPS.
149 Be very clear what files learners are to edit
150 and what user IDs they are to use
151 when giving instructions.
152 It is common for them to edit the instructor's biography,
153 or to use the instructor's user ID and password when committing.
154 Be equally clear <em>when</em> they are to edit things:
155 it's also common for someone to edit the file the instructor is editing
156 and commit changes while the instructor is explaining what's going on,
157 so that a conflict occurs when the instructor comes to commit the file.
160 Learners could do most exercises with repositories on their own machines,
161 but it's hard for them to see how version control helps collaboration
162 unless they're sharing a repository with other learners.
164 showing learners who changed what using <code>svn blame</code>
165 is only compelling if a file has been edited by at least two people.
168 If some learners are using Windows,
169 there will inevitably be issues merging files with different line endings.
170 <code>svn diff -x -w</code> is supposed to suppress differences in whitespace,
171 but we have found that it doesn't always work as advertised.
178 <section id="s:basics">
181 <div class="understand">
182 <h3>Learning Objectives</h3>
184 <li>Draw a diagram showing the places version control stores information.</li>
185 <li>Check out a working copy of a repository.</li>
186 <li>View the history of changes to a project.</li>
187 <li>Explain why working copies of different projects should not overlap.</li>
188 <li>Add files to a project.</li>
189 <li>Commit changes made to a working copy to a repository.</li>
190 <li>Update a working copy to get changes from the repository.</li>
191 <li>Compare the current state of a working copy to the last update from the repository, and to the current state of the repository.</li>
192 <li>Explain what "version 123 of <code>xyz.txt</code>" actually means.</li>
195 <span class="duration">20 minutes</span>.
200 A version control system keeps the master copy of a file
201 in a <a href="glossary.html#repository">repository</a>
202 located on a <a href="glossary.html#server">server</a>—a computer
203 that is never used directly by people,
204 but only by their programs
205 (<a href="#f:repository">Figure 1</a>).
206 No-one ever edits the master copy directly.
208 Wolfman and Dracula each have a <a href="glossary.html#working-copy">working copy</a>
209 on their own machines.
210 They can each edit their working copies whenever and however they want.
213 <figure id="f:repository">
214 <img src="svn/repository.png" alt="Repositories and Working Copies" />
215 <figcaption>Figure 1: Repositories and Working Copies</figcaption>
219 When Wolfman is ready to share his changes with Dracula,
220 he <a href="glossary.html#commit">commits</a> his work to the repository
221 (<a href="#f:workflow">Figure 2</a>).
222 Dracula can then <a href="glossary.html#update">update</a> his working copy
223 to get those changes when he's ready for them.
225 when Dracula finishes working on something,
226 he can commit and so that Wolfman can update.
229 <figure id="f:workflow">
230 <img src="svn/workflow.png" alt="Sharing Files Through Version Control" />
231 <figcaption>Figure 2: Sharing Files Through Version Control</figcaption>
235 If this is all there was to version control,
236 it would be no better than FTP or Dropbox.
237 But what if Dracula and Wolfman change their working copies at the same time?
238 If Wolfman commits first,
239 his changes are simply copied to the repository
240 (<a href="#f:merge_first_commit">Figure 3</a>):
243 <figure id="f:merge_first_commit">
244 <img src="svn/merge_first_commit.png" alt="Wolfman Commits First" />
245 <figcaption>Figure 3: Wolfman Commits First</figcaption>
249 If Dracula now tries to commit something that would overwrite Wolfman's changes
250 the version control system detects the <a href="glossary.html#conflict">conflict</a>,
252 and tells Dracula that there's a problem
253 (<a href="#f:merge_second_commit">Figure 4</a>):
256 <figure id="f:merge_second_commit">
257 <img src="svn/merge_second_commit.png" alt="Dracula Has a Conflict" />
258 <figcaption>Figure 4: Dracula Has a Conflict</figcaption>
262 Dracula must <a href="glossary.html#resolve">resolve</a> that conflict
263 before the version control system will allow him to commit his work.
264 He can accept what Wolfman did,
265 replace it with what he has done,
266 or write something new that combines the two—that's up to him
267 (<a href="#f:merge_resolve">Figure 5</a>).
268 Once he has cleaned things up, he can go ahead and try committing again.
269 If all of the conflicts have been resolved,
270 the version control will accept it this time.
273 <figure id="f:merge_resolve">
274 <img src="svn/merge_resolve.png" alt="Resolving the Conflict" />
275 <figcaption>Figure 5: Resolving the Conflict</figcaption>
279 <h3>Forgiveness vs. Permission</h3>
282 Old-fashioned version control systems prevented conflicts from happening
283 by <a href="glossary.html#lock">locking</a> the master copy
284 whenever someone was working on it.
285 This <a href="glossary.html#pessimistic-concurrency">pessimistic</a> strategy
286 guaranteed that a second person (or monster)
287 could never make changes to the same file at the same time,
288 but it also meant that people had to take turns editing files.
292 Most of today's version control systems use
293 an <a href="glossary.html#optimistic-concurrency">optimistic</a> strategy instead:
294 people are always allowed to edit their working copies,
295 and if a conflict occurs,
296 the version control system helps them sort it out after the fact.
301 To see how this actually works,
302 let's assume that the Mummy
303 (Dracula and Wolfman's boss)
304 has already put some notes in a version control repository
305 whose URL is <code>https://universal.software-carpentry.org/explore</code>.
306 Every repository has an address like this that uniquely identifies the location of the master copy.
310 <h3>There's More Than One Way To Do It</h3>
313 We will drive Subversion from the command line in our examples,
314 but if you prefer using a GUI,
315 there are many for you to choose from.
316 Please see the <a href="ref.html#s:svn:gui">reference</a> for links.
322 and Dracula has just joined the project.
323 In order to get a working copy on his computer,
324 Dracula has to <a href="glossary.html#check-out">check out</a> a copy of the repository.
325 He only has to do this once per project:
326 once he has a working copy,
327 he can update it over and over again to get other people's work.
331 While in his home directory,
332 Dracula types the command:
336 $ <span class="in">svn checkout https://universal.software-carpentry.org/explore</span>
340 This creates a new directory called <code>explore</code>
341 and fills it with a copy of the repository's contents
342 (<a href="#f:example_repo">Figure 6</a>).
346 <span class="out">A explore/jupiter
348 A explore/mars/mons-olympus.txt
349 A explore/mars/cydonia.txt
351 A explore/earth/himalayas.txt
352 A explore/earth/antarctica.txt
353 A explore/earth/carlsbad.txt
354 Checked out revision 6.</span>
357 <figure id="f:example_repo">
358 <img src="svn/example_repo.png" alt="Example Repository" />
359 <figcaption>Figure 6: Example Repository</figcaption>
363 Dracula can then go into this directory
364 and use regular shell commands to view the files:
368 $ <span class="in">cd explore</span>
369 $ <span class="in">ls</span>
370 <span class="out">earth jupiter mars</span>
371 $ <span class="in">ls *</span>
372 <span class="out">earth:
373 antarctica.txt carlsbad.txt himalayas.txt
378 cydonia.txt mons-olympus.txt</span>
382 <h3>Don't Let the Working Copies Overlap</h3>
385 It's very important that the working copies of different project do not overlap;
387 we should never try to check out one project inside a working copy of another project.
388 The reason is that Subversion stories information about
389 the current state of a working copy
390 in special sub-directories called <code>.svn</code>:
394 $ <span class="in">pwd</span>
395 <span class="out">/home/dracula/explore</span>
396 $ <span class="in">ls -a</span>
397 <span class="out">. .. .svn earth jupiter mars</span>
398 $ <span class="in">ls -F .svn</span>
399 <span class="out">entries prop-base/ props/ text-base/ tmp/</span>
403 If two working copies overlap,
404 the files in the <code>.svn</code> directories for one repository
405 will be clobbered by the other repository's <code>.svn</code> files,
406 and Subversion will become hopelessly confused.
411 Dracula can find out more about the history of the project
412 using Subversion's <code>log</code> command:
416 $ <span class="in">svn log</span>
417 <span class="out">------------------------------------------------------------------------
418 r6 | mummy | 2010-07-26 09:21:10 -0400 (Mon, 26 Jul 2010) | 1 line
420 Damn the budget---the Jovian moons would be a _perfect_ place to explore.
421 ------------------------------------------------------------------------
422 r5 | mummy | 2010-07-26 09:19:39 -0400 (Mon, 26 Jul 2010) | 1 line
424 The budget might not even stretch to the Arctic :-(
425 ------------------------------------------------------------------------
426 r4 | mummy | 2010-07-26 09:17:46 -0400 (Mon, 26 Jul 2010) | 1 line
428 Budget cuts may force us to do another dry run in the Arctic.
429 ------------------------------------------------------------------------
430 r3 | mummy | 2010-07-26 09:14:14 -0400 (Mon, 26 Jul 2010) | 1 line
432 Converting document to wiki-formatted text.
433 ------------------------------------------------------------------------
434 r2 | mummy | 2010-07-26 09:11:55 -0400 (Mon, 26 Jul 2010) | 1 line
436 Or put it down near the Face of Cydonia?
437 ------------------------------------------------------------------------
438 r1 | mummy | 2010-07-26 09:08:23 -0400 (Mon, 26 Jul 2010) | 1 line
440 Send the probe to Mons Olympus?
441 ------------------------------------------------------------------------</span>
445 Subversion displays a summary of all the changes made to the project so far.
446 This list includes the
447 <a href="glossary.html#revision-number">revision number</a>,
448 the name of the person who made the change,
449 the date the change was made,
450 and whatever comment the user provided when the change was submitted.
452 the <code>explore</code> project is currently at revision 6,
453 and all changes so far have been made by the Mummy.
457 Notice how detailed the comments on the updates are.
458 Good comments are as important in version control as they are in coding.
459 Without them, it can be very difficult to figure out who did what, when, and why.
460 We can use comments like "Changed things" and "Fixed it" if we want,
461 or even no comments at all,
462 but we'll only be making more work for our future selves.
466 <h3>Numbering Versions</h3>
469 Another thing to notice is that the revision number applies to the whole repository,
470 not to a particular file.
471 When we talk about "version 61" we mean
472 "the state of all files and directories at that point."
473 Older version control systems like CVS gave each file a new version number when it was updated,
474 which meant that version 38 of one file could correspond in time to version 17 of another
475 (<a href="#f:version_numbering">Figure 7</a>).
476 Experience shows that
477 global version numbers that apply to everything in the repository
478 are easier to manage than
479 per-file version numbers,
480 so that's what Subversion uses.
483 <figure id="f:version_numbering">
484 <img src="svn/version_numbering.png" alt="Version Numbering Schemes" />
485 <figcaption>Figure 7: Version Numbering Schemes</figcaption>
490 A couple of cubicles away,
491 Wolfman also runs <code>svn checkout</code>
492 to get a working copy of the repository.
493 He also gets version 6,
494 so the files on his machine are the same as the files on Dracula's.
495 While he is looking through the files,
496 Dracula decides to add some information to the repository about Jupiter's moons.
497 Using his favorite editor,
498 he creates a file in the <code>jupiter</code> directory called <code>moons.txt</code>,
499 and fills it with information about Io, Europa, Ganymede, and Callisto:
502 <pre src="svn/moons_initial.txt">
503 Name Orbital Radius Orbital Period Mass Radius
504 Io 421.6 1.769138 893.2 1821.6
505 Europa 670.9 3.551181 480.0 1560.8
506 Ganymede 1070.4 7.154553 1481.9 2631.2
507 Calisto 1882.7 16.689018 1075.9 2410.3
511 After double-checking his data,
512 he wants to commit the file to the repository so that everyone else on the project can see it.
513 The first step is to add the file to his working copy using <code>svn add</code>:
517 $ <span class="in">svn add jupiter/moons.txt</span>
518 <span class="out">A jupiter/moons.txt</span>
522 Adding a file is not the same as creating it—he has already done that.
524 the <code>svn add</code> command tells Subversion to add the file to
525 the list of things it's supposed to manage.
527 particularly in programming projects,
528 to have backup files or intermediate files in a directory
529 that aren't worth storing in the repository.
530 This is why version control requires us to explicitly tell it which files are to be managed.
534 Once he has told Subversion to add the file,
535 Dracula can go ahead and commit his changes to the repository.
536 He uses the <code>-m</code> flag to provide a one-line message explaining what he's doing;
538 Subversion would open his default editor
539 so that he could type in something longer.
543 $ <span class="in">svn commit -m "Some basic facts about the Galilean moons of Jupiter." jupiter/moons.txt</span>
544 <span class="out">Adding jupiter/moons.txt
545 Transmitting file data .
546 Committed revision 7.</span>
550 When Dracula runs the <code>svn commit</code> command,
551 Subversion establishes a connection to the server,
552 copies over his changes,
553 and updates the revision number from 6 to 7
554 (<a href="#f:updated_repo">Figure 8</a>).
557 <figure id="f:updated_repo">
558 <img src="svn/updated_repo.png" alt="Updated Repository" />
559 <figcaption>Figure 8: Updated Repository</figcaption>
563 <h3>When <em>Not</em> to Use Version Control</h3>
566 Despite the rapidly decreasing cost of storage,
567 it is still possible to run out of disk space.
569 people can easy go through 2 TB/month if they're not careful.
570 Since version control tools usually store revisions in terms of lines,
571 with binary data files,
572 they end up essentially storing every revision separately.
574 (it's what we'd be doing anyway),
575 but it means version control isn't doing what it likes to do,
576 and the repository can get very large very quickly.
577 Another concern is that if very old data will no longer be used,
578 it can be nice to archive or delete old data files.
579 This is not possible if our data is version controlled:
580 information can only be added to a repository,
581 so it can only ever increase in size.
586 <p id="a:define-head">
588 Wolfman uses <code>svn update</code> to update his working copy.
589 It tells him that a new file has been added
590 and brings his working copy up to date with version 7 of the repository,
591 because this is now the most recent revision
592 (also called the <a href="glossary.html#head">head</a>).
593 <code>svn update</code> updates an existing working copy,
594 rather than checking out a new one.
595 While <code>svn checkout</code> is usually only run once per project per machine,
596 <code>svn update</code> may be run many times a day.
600 Looking in the new file <code>jupiter/moons.txt</code>,
601 Wolfman notices that Dracula has misspelled "Callisto"
602 (it is supposed to have two L's.)
603 Wolfman edits that line of the file:
606 <pre src="svn/moons_spelling.txt">
607 Name Orbital Radius Orbital Period Mass Radius
608 Io 421.6 1.769138 893.2 1821.6
609 Europa 670.9 3.551181 480.0 1560.8
610 Ganymede 1070.4 7.154553 1481.9 2631.2
611 <span class="highlight">Callisto 1882.7 16.689018 1075.9 2410.3</span>
615 He also adds a line about Amalthea,
616 which he thinks might be an interesting place to send a probe
617 despite its small size:
620 <pre src="svn/moons_amalthea.txt">
621 Name Orbital Radius Orbital Period Mass Radius
622 <span class="highlight">Amalthea 181.4 0.498179 0.075 125.0</span>
623 Io 421.6 1.769138 893.2 1821.6
624 Europa 670.9 3.551181 480.0 1560.8
625 Ganymede 1070.4 7.154553 1481.9 2631.2
626 Callisto 1882.7 16.689018 1075.9 2410.3
631 he uses the <code>svn status</code> command to check that he hasn't accidentally changed anything else:
635 $ <span class="in">svn status</span>
636 <span class="out">M jupiter/moons.txt</span>
640 and then runs <code>svn commit</code>.
641 Since has hasn't used the <code>-m</code> flag to provide a message on the command line,
642 Subversion launches his default editor and shows him:
647 --This line, and those below, will be ignored--
653 He changes this to be
657 1. Fixed typo in moon's name: 'Calisto' -> 'Callisto'.
658 2. Added information about Amalthea.
659 --This line, and those below, will be ignored--
665 When he saves this temporary file and exits the editor,
666 Subversion commits his changes:
670 <span class="out">Sending jupiter/moons.txt
671 Transmitting file data .
672 Committed revision 8.</span>
676 Note that since Wolfman didn't specify a particular file to commit,
677 Subversion commits <em>all</em> of his changes.
678 This is why he ran the <code>svn status</code> command first.
682 <h3>Which Editor?</h3>
684 If you don't have a default editor set up,
685 Subversion will probably open an editor called Vi.
687 type escape-colon-w-q-! to exit
688 and hope it never happens again.
692 <div class="box" id="b:basics:transaction">
693 <h3>Working With Multiple Files</h3>
696 Our example only includes one file,
697 but version control can work on any number of files at once.
699 if Wolfman noticed that a dozen data files had the same incorrect header,
700 he could change it in all 12 files,
701 then commit all those changes at once.
702 This is actually the best way to work:
703 every logical change to the project should be a single commit,
704 and every commit should include everything involved in one logical change.
711 Dracula wants to synchronize with Wolfman's work.
712 Before updating his working copy with <code>svn update</code>,
714 he checks to see if he has made any changes locally
715 by running <code>svn diff</code>.
717 it compares what's in his working copy to what he got the last time he updated.
718 There are no differences,
719 so there's no output:
723 $ <span class="in">svn diff</span>
728 To compare his working copy to the master,
729 Dracula uses <code>svn diff -r HEAD</code>.
730 The <code>-r</code> flag is used to specify a revision,
731 while <code>HEAD</code> means
732 "<a href="#a:define-head">the latest version of the master</a>".
736 $ <span class="in">svn diff -r HEAD</span>
737 <span class="out">--- moons.txt(revision 8)
738 +++ moons.txt(working copy)
740 Name Orbital Radius Orbital Period Mass Radius
741 +Amalthea 181.4 0.498179 0.075 125.0
742 Io 421.6 1.769138 893.2 1821.6
743 Europa 670.9 3.551181 480.0 1560.8
744 Ganymede 1070.4 7.154553 1481.9 2631.2
745 -Calisto 1882.7 16.689018 1075.9 2410.3
746 +Callisto 1882.7 16.689018 1075.9 2410.3
751 After looking over the changes,
752 Dracula goes ahead and does the update.
756 <h3>Reading a Diff</h3>
759 The output of <code>diff</code> is cryptic even by Unix standards.
764 --- moons.txt(revision 9)
765 +++ moons.txt(working copy)
769 signal that '-' will be used to show content from revision 9
770 and '+' to show content from the user's working copy.
771 The next line, with the '@' markers,
772 indicates where lines were inserted or removed.
773 This isn't really intended for human consumption:
774 editors and other tools can use this information
775 to replay a series of edits against a file.
779 The most important parts of what follows are the lines marked with '+' and '-',
780 which show insertions and deletions respectively.
782 we can see that the line for Amalthea was inserted,
783 and that the line for Callisto was changed
784 (which is indicated by an add and a delete right next to one another).
785 Many editors and other tools can display diffs like this in a two-column display,
786 highlighting changes.
792 <h3>Nothing's Perfekt</h3>
795 Version control systems do have one important shortcoming.
796 While it is easy for them to find, display, and merge differences in text files,
797 images, MP3s, PDFs, or Microsoft Word or Excel files aren't stored as text—they
798 use specialized binary data formats.
799 Most version control systems don't know how to deal with these formats,
800 so all they can say is, "These files differ."
801 Reconciling those differences will probably require use of an auxiliary tool,
802 such as an audio editor
803 or Microsoft Word's "Compare and Merge" utility.
808 <h3>Diffing Other Files</h3>
811 <code>svn diff</code> mimics the behavior of
812 the Unix <code>diff</code> command,
813 which can be used to compare any two files.
814 Given these two files:
819 <th><code>left.txt</code></th>
820 <th><code>right.txt</code></th>
842 <code>diff</code>'s output is:
845 $ <span class="in">diff left.txt right.txt</span>
846 <span class="out">2a3
853 > strontium</span>
858 This is a very common workflow,
859 and is the basic heartbeat of most developers' days.
866 Update our working copy
867 so that we have any changes other people have committed.
875 Commit our changes to the repository
876 so that other people can get them.
882 It's worth noticing here how important Wolfman's comments about his changes were.
883 It's hard to see the difference between "Calisto" with one 'L' and "Callisto" with two,
884 even if the line containing the difference has been highlighted.
885 Without Wolfman's comments,
886 Dracula might have wasted time wondering what the difference was.
891 Wolfman should probably have committed his two changes separately,
892 since there's no logical connection between
893 fixing a typo in Callisto's name
894 and adding information about Amalthea to the same file.
895 Just as a function or program should do one job and one job only,
896 a single commit to version control should have a single logical purpose so that it's easier to find,
898 and if necessary undo later on.
902 <h3>Who Did What?</h3>
905 One other very useful command is <code>svn blame</code>,
906 which shows when each line in the file was last changed
911 $ <span class="in">svn blame moons.txt</span>
912 <span class="out"> 14 dracula Name Orbital Radius Orbital Period Mass Radius
913 14 dracula (10**3 km) (days) (10**20 kg) (km)
914 14 dracula Amalthea 181.4 0.498179 0.075 131 x 73 x 67
915 9 mummy Io 421.6 1.769138 893.2 1821.6
916 9 mummy Europa 670.9 3.551181 480.0 1560.8
917 9 mummy Ganymede 1070.4 7.154553 1481.9 2631.2
918 14 dracula Callisto 1882.7 16.689018 1075.9 2410.3
919 14 dracula Himalia 11460 250.5662 0.095 85.0
920 14 dracula Elara 11740 259.6528 0.008 40.0</span>
924 If you are ever wondering who to talk to about a change,
926 <code>svn blame</code> is a good place to start.
930 <div class="keypoints">
933 <li>Version control is a better way to manage shared files than email or shared folders.</li>
934 <li>The master copy is stored in a repository.</li>
935 <li>Nobody ever edits the master directory: instead, each person edits a local working copy.</li>
936 <li>People share changes by committing them to the master or updating their local copy from the master.</li>
937 <li>The version control system prevents people from overwriting each other's work by forcing them to merge concurrent changes before committing.</li>
938 <li>It also keeps a complete history of changes made to the master so that old versions can be recovered reliably.</li>
939 <li>Version control systems work best with text files, but can also handle binary files such as images and Word documents.</li>
940 <li>Every repository is identified by a URL.</li>
941 <li>Working copies of different repositories may not overlap.</li>
942 <li>Each changed to the master copy is identified by a unique revision number.</li>
943 <li>Revisions identify snapshots of the entire repository, not changes to individual files.</li>
944 <li>Each change should be commented to make the history more readable.</li>
945 <li>Commits are transactions: either all changes are successfully committed, or none are.</li>
946 <li>The basic workflow for version control is update-change-commit.</li>
947 <li><code>svn add <em>things</em></code> tells Subversion to start managing particular files or directories.</li>
948 <li><code>svn checkout <em>url</em></code> checks out a working copy of a repository.</li>
949 <li><code>svn commit -m "<em>message</em>" <em>things</em></code> sends changes to the repository.</li>
950 <li><code>svn diff</code> compares the current state of a working copy to the state after the most recent update.</li>
951 <li><code>svn diff -r HEAD</code> compares the current state of a working copy to the state of the master copy.</li>
952 <li><code>svn history</code> shows the history of a working copy.</li>
953 <li><code>svn status</code> shows the status of a working copy.</li>
954 <li><code>svn update</code> updates a working copy from the repository.</li>
958 <div class="challenges">
964 Using the repository URL, user ID, and password provided by the instructor,
965 perform the following actions:
968 Check out a working copy of the repository.
971 Create a text file called <em>your_id</em>.txt
972 (using your user ID instead of <em>your_id</em>)
973 and write a three-line biography of yourself in it.
976 Add this file to your working copy.
979 Commit your changes to the repository.
982 Update your working copy to get other people's biographies.
985 Examine the change log to see
986 the order in which people added their biographies
993 What does the command <code>svn diff -r 14</code> do?
994 What does it do if there have only been 10 changes to the repository?
999 Unix <code>diff</code> and <code>svn diff</code> compare files line by line.
1000 Why doesn't this work for MP3 audio files?
1008 <section id="s:merge">
1009 <h2>Merging Conflicts</h2>
1011 <div class="understand">
1012 <h3>Learning Objectives</h3>
1014 <li>Explain what causes conflicts to occur and how to tell when one has occurred.</li>
1015 <li>Resolve a conflict.</li>
1016 <li>Identify the auxiliary files created when a conflict occurs.</li>
1019 <span class="duration">20 minutes</span>.
1024 Dracula and Wolfman have both synchronized their working copies of <code>explore</code>
1025 with version 8 of the repository.
1026 Dracula now edits his copy to change Amalthea's radius
1027 from a single number to a triple to reflect its irregular shape:
1030 <pre src="svn/moons_dracula_triple.txt">
1031 Name Orbital Radius Orbital Period Mass Radius
1032 <span class="highlight">Amalthea 181.4 0.498179 0.075 131 x 73 x 67</span>
1033 Io 421.6 1.769138 893.2 1821.6
1034 Europa 670.9 3.551181 480.0 1560.8
1035 Ganymede 1070.4 7.154553 1481.9 2631.2
1036 Callisto 1882.7 16.689018 1075.9 2410.3
1039 <p class="continue">
1040 He then commits his work,
1041 creating revision 9 of the repository
1042 (<a href="#f:after_dracula_commits">Figure 9</a>).
1045 <figure id="f:after_dracula_commits">
1046 <img src="svn/after_dracula_commits.png" alt="After Dracula Commits" />
1047 <figcaption>Figure 9: After Dracula Commits</figcaption>
1051 But while he is doing this,
1052 Wolfman is editing <em>his</em> copy
1053 to add information about two other minor moons,
1057 <pre src="svn/moons_wolfman_extras.txt">
1058 Name Orbital Radius Orbital Period Mass Radius
1059 Amalthea 181.4 0.498179 0.075 131
1060 Io 421.6 1.769138 893.2 1821.6
1061 Europa 670.9 3.551181 480.0 1560.8
1062 Ganymede 1070.4 7.154553 1481.9 2631.2
1063 Callisto 1882.7 16.689018 1075.9 2410.3
1064 <span class="highlight">Himalia 11460 250.5662 0.095 85.0
1065 Elara 11740 259.6528 0.008 40.0</span>
1069 When Wolfman tries to commit his changes to the repository,
1070 Subversion won't let him:
1074 $ <span class="in">svn commit -m "Added data for Himalia, Elara"</span>
1075 <span class="out">Sending jupiter/moons.txt
1076 svn: Commit failed (details follow):
1077 svn: File or directory 'moons.txt' is out of date; try updating
1078 svn: resource out of date; try updating</span>
1081 <p class="continue">
1083 Wolfman's changes were based on revision 8,
1084 but the repository is now at revision 9,
1085 and the file that Wolfman is trying to overwrite
1086 is different in the later revision.
1088 one of version control's main jobs is to make sure that
1089 people don't trample on each other's work.)
1090 Wolfman has to update his working copy to get Dracula's changes before he can commit.
1092 Dracula edited a line that Wolfman didn't change,
1093 so Subversion can merge the differences automatically.
1097 This does <em>not</em> mean that Wolfman's changes have been committed to the repository:
1098 Subversion only does that when it's ordered to.
1099 Wolfman's changes are still in his working copy,
1100 and <em>only</em> in his working copy.
1101 But since Wolfman's version of the file now includes
1102 the lines that Dracula added,
1103 Wolfman can go ahead and commit them as usual to create revision 10
1104 (<a href="#f:merge_without_conflict">Figure 10</a>).
1107 <figure id="f:merge_without_conflict">
1108 <img src="svn/merge_without_conflict.png" alt="Merging Without Conflict" />
1109 <figcaption>Figure 10: Merging Without Conflict</figcaption>
1113 Wolfman's working copy is now in sync with the master,
1114 but Dracula's is one behind at revision 9.
1116 they independently decide to add measurement units
1117 to the columns in <code>moons.txt</code>.
1118 Wolfman is quicker off the mark this time;
1119 he adds a line to the file:
1122 <pre src="svn/moons_wolfman_units.txt">
1123 Name Orbital Radius Orbital Period Mass Radius
1124 <span class="highlight"> (10**3 km) (days) (10**20 kg) (km)</span>
1125 Amalthea 181.4 0.498179 0.075 131 x 73 x 67
1126 Io 421.6 1.769138 893.2 1821.6
1127 Europa 670.9 3.551181 480.0 1560.8
1128 Ganymede 1070.4 7.154553 1481.9 2631.2
1129 Callisto 1882.7 16.689018 1075.9 2410.3
1130 Himalia 11460 250.5662 0.095 85.0
1131 Elara 11740 259.6528 0.008 40.0
1134 <p class="continue">
1135 and commits it to create revision 11.
1136 While he is doing this,
1138 Dracula inserts a different line at the top of the file:
1141 <pre src="svn/moons_dracula_units.txt">
1142 Name Orbital Radius Orbital Period Mass Radius
1143 <span class="highlight"> * 10^3 km * days * 10^20 kg * km</span>
1144 Amalthea 181.4 0.498179 0.075 131 x 73 x 67
1145 Io 421.6 1.769138 893.2 1821.6
1146 Europa 670.9 3.551181 480.0 1560.8
1147 Ganymede 1070.4 7.154553 1481.9 2631.2
1148 Callisto 1882.7 16.689018 1075.9 2410.3
1149 Himalia 11460 250.5662 0.095 85.0
1150 Elara 11740 259.6528 0.008 40.0
1155 when Dracula tries to commit,
1156 Subversion tells him he can't.
1158 when Dracula does updates his working copy,
1159 he doesn't just get the line Wolfman added to create revision 11
1160 (<a href="#f:merge_with_conflict">Figure 11</a>).
1163 <figure id="f:merge_with_conflict">
1164 <img src="svn/merge_with_conflict.png" alt="Merge With Conflict" />
1165 <figcaption>Figure 11: Merge With Conflict</figcaption>
1169 There is an actual conflict in the file,
1170 so Subversion asks Dracula what he wants to do:
1173 <pre src="svn/moons_dracula_conflict.txt">
1174 $ <span class="in">svn update</span>
1175 <span class="out">Conflict discovered in 'jupiter/moons.txt'.
1176 Select: (p) postpone, (df) diff-full, (e) edit,
1177 (mc) mine-conflict, (tc) theirs-conflict,
1178 (s) show all options:</span>
1182 Dracula choose <code>p</code> for "postpone",
1183 which tells Subversion that he'll deal with the problem later.
1184 Once the update is finished,
1185 he opens <code>moons.txt</code> in his editor and sees:
1189 Name Orbital Radius Orbital Period Mass
1190 +<<<<<<< .mine
1191 + * 10^3 km * days * 10^20 kg
1193 + (10**3 km) (days) (10**20 kg)
1194 +>>>>>>> .r11
1195 Amalthea 181.4 0.498179 0.074
1196 Io 421.6 1.769138 893.2
1197 Europa 670.9 3.551181 480.0
1198 Ganymede 1070.4 7.154553 1481.9
1199 Callisto 1882.7 16.689018 1075.9
1202 <p class="continue">
1204 Subversion has inserted
1205 <a href="glossary.html#conflict-marker">conflict markers</a>
1206 in <code>moons.txt</code>
1207 wherever there is a conflict.
1208 The line <code><<<<<<< .mine</code> shows the start of the conflict,
1209 and is followed by the lines from the local copy of the file.
1210 The separator <code>=======</code> is then
1211 followed by the lines from the repository's file that are in conflict with that section,
1212 while <code>>>>>>>> .r11</code> marks the end of the conflict.
1216 Before he can commit,
1217 Dracula has to edit his copy of the file to get rid of those markers.
1221 <pre src="svn/moons_dracula_resolved.txt">
1222 Name Orbital Radius Orbital Period Mass Radius
1223 <span class="highlight"> (10^3 km) (days) (10^20 kg) (km)</span>
1224 Amalthea 181.4 0.498179 0.075 131 x 73 x 67
1225 Io 421.6 1.769138 893.2 1821.6
1226 Europa 670.9 3.551181 480.0 1560.8
1227 Ganymede 1070.4 7.154553 1481.9 2631.2
1228 Callisto 1882.7 16.689018 1075.9 2410.3
1229 Himalia 11460 250.5662 0.095 85.0
1230 Elara 11740 259.6528 0.008 40.0
1233 <p class="continue">
1234 then uses the <code>svn resolved</code> command to tell Subversion that
1235 he has fixed the problem.
1236 Subversion will now let him commit to create revision 12.
1240 <h3>Auxiliary Files</h3>
1243 When Dracula did his update and Subversion detected the conflict in <code>moons.txt</code>,
1244 it created three temporary files to help Dracula resolve it.
1245 The first is called <code>moons.txt.r9</code>;
1246 it is the file as it was in Dracula's local copy
1247 before he started making changes,
1248 i.e., the common ancestor for his work
1249 and whatever he is in conflict with.
1253 The second file is <code>moons.txt.r11</code>.
1254 This is the most up-to-date revision from the repository—the
1255 file as it is including Wolfman's changes.
1256 The third temporary file, <code>moons.txt.mine</code>,
1257 is the file as it was in Dracula's working copy before he did the Subversion update.
1261 Subversion creates these auxiliary files primarily
1262 to help people merge conflicts in binary files.
1263 It wouldn't make sense to insert <code><<<<<<<</code>
1264 and <code>>>>>>>></code> characters into an image file
1265 (it would almost certainly result in a corrupted image).
1266 The <code>svn resolved</code> command deletes these three extra files
1267 as well as telling Subversion that the conflict has been taken care of.
1273 Some power users prefer to work with interpolated conflict markers directly,
1274 but for the rest of us,
1275 there are several tools for displaying differences and helping to merge them,
1276 including <a href="http://diffuse.sourceforge.net/">Diffuse</a> and <a href="http://winmerge.org/">WinMerge</a>.
1277 If Dracula launches Diffuse,
1278 it displays his file,
1279 the common base that he and Wolfman were working from,
1280 and Wolfman's file in a three-pane view
1281 (<a href="#f:diff_viewer">Figure 12</a>):
1284 <figure id="f:diff_viewer">
1285 <img src="svn/diff_viewer.png" alt="A Difference Viewer" />
1286 <figcaption>Figure 12: A Difference Viewer</figcaption>
1289 <p class="continue">
1290 Dracula can use the buttons to merge changes from either of the edited versions
1291 into the common ancestor,
1292 or edit the central pane directly.
1295 he uses <code>svn resolved</code> and <code>svn commit</code>
1296 to create revision 12 of the repository.
1300 In this case, the conflict was small and easy to fix.
1301 However, if two or more people on a team are repeatedly creating conflicts for one another,
1302 it's usually a signal of deeper communication problems:
1303 either they aren't talking as often as they should, or their responsibilities overlap.
1305 the version control system can help the team find and fix these issues
1306 so that it will be more productive in future.
1310 <h3>Working With Multiple Files</h3>
1313 As mentioned <a href="#a:transaction">earlier</a>,
1314 every logical change to a project should result in a single commit,
1315 and every commit should represent one logical change.
1316 This is especially true when resolving conflicts:
1317 the work done to reconcile one person's changes with another are often complicated,
1318 so it should be a single entry in the project's history,
1319 with other, later, changes coming after it.
1324 <div class="keypoints">
1327 <li>Conflicts must be resolved before a commit can be completed.</li>
1328 <li>Subversion puts markers in text files to show regions of conflict.</li>
1329 <li>For each conflicted file, Subversion creates auxiliary files containing the common parent, the master version, and the local version.</li>
1330 <li><code>svn resolve <em>files</em></code> tells Subversion that conflicts have been resolved.</li>
1334 <div class="challenges">
1338 If you are working in a group,
1339 partner with someone who has also wrote a biography for themselves
1340 for the previous section's challenges.
1345 Both partners use <code>svn update</code>
1346 to make sure their working copies are up to date
1347 and that there are no local changes.
1350 The first partner edits her biography and commits the changes.
1353 The second partner edits her copy of the file
1354 (<em>without</em> having updated to get the first partner's changes),
1355 then tries to <code>svn commit</code>.
1358 Once the second partner has resolved the conflict,
1359 she commits her changes.
1362 Repeat these four steps with roles reversed.
1367 If you are working on your own,
1368 you can simulate the steps above
1369 by checking out a second copy of the project into a new directory.
1371 this cannot overlap any existing checked-out copies.)
1372 Edit your biography in one copy and commit those changes,
1373 then switch to the other copy and edit the same file
1380 <section id="s:rollback">
1381 <h2>Recovering Old Versions</h2>
1383 <div class="understand">
1384 <h3>Learning Objectives</h3>
1386 <li>Discard changes made to a working copy.</li>
1387 <li>Recover an old version of a file.</li>
1388 <li>Explain what branches are and when they are used.</li>
1391 <span class="duration">20 minutes</span>.
1396 Now that we have seen how to merge files and resolve conflicts,
1397 we can look at how to use version control as an "infinite undo".
1398 Suppose that when Wolfman starts work late one night,
1399 his copy of <code>explore</code> is in sync with the head at revision 12.
1400 He decides to edit the file <code>moons.txt</code>;
1401 unfortunately, he forgot that there was a full moon,
1402 so his changes don't make a lot of sense:
1405 <pre src="svn/poetry.txt">
1406 Just one moon can make me growl
1407 Four would make me want to howl
1412 When he's back in human form the next day,
1413 he wants to undo his changes.
1414 Without version control, his choices would be grim:
1415 he could try to edit them back into their original state by hand
1416 (which for some reason hardly ever seems to work),
1417 or ask his colleagues to send him their copies of the files
1418 (which is almost as embarrassing as chasing the neighbor's cat when in wolf form).
1422 Since he's using Subversion, though,
1423 and hasn't committed his work to the repository,
1424 all he has to do is <a href="glossary.html#revert">revert</a> his local changes.
1425 <code>svn revert</code> simply throws away local changes to files
1426 and puts things back the way they were before those changes were made.
1427 This is a purely local operation:
1428 since Subversion stores the history of the project inside every working copy,
1429 Wolfman doesn't need to be connected to the network to do this.
1434 Wolfman uses <code>svn diff</code> <em>without</em> the <code>-r HEAD</code> flag
1435 to take a look at the differences between his file
1436 and the master copy in the repository.
1437 Since he doesn't want to keep his changes,
1438 his next command is <code>svn revert moons.txt</code>.
1442 $ <span class="in">cd jupiter</span>
1443 $ <span class="in">svn revert moons.txt</span>
1444 <span class="out">Reverted moons.txt</span>
1448 What if someone <em>has</em> committed their changes,
1449 but still wants to undo them?
1451 suppose Dracula decides that the numbers in <code>moons.txt</code> would look better with commas.
1452 He edits the file to put them in:
1455 <pre src="svn/moons_commas.txt">
1456 Name Orbital Radius Orbital Period Mass Radius
1457 (10^3 km) (days) (10^20 kg) (km)
1458 Amalthea 181.4 0.498179 0.075 131 x 73 x 67
1459 Io 421.6 1.769138 893.2 1<span class="highlight">,</span>821.6
1460 Europa 670.9 3.551181 480.0 1<span class="highlight">,</span>560.8
1461 Ganymede 1<span class="highlight">,</span>070.4 7.154553 1<span class="highlight">,</span>481.9 2<span class="highlight">,</span>631.2
1462 Callisto 1<span class="highlight">,</span>882.7 16.689018 1<span class="highlight">,</span>075.9 2<span class="highlight">,</span>410.3
1463 Himalia 11<span class="highlight">,</span>460 250.5662 0.095 85.0
1464 Elara 11<span class="highlight">,</span>740 259.6528 0.008 40.0
1467 <p class="continue">
1468 then commits his changes to create revision 13.
1469 A little while later,
1470 the Mummy sees the change and orders Dracula to put things back the way they were.
1471 What should Dracula do?
1475 We can draw the sequence of events leading up to revision 13
1476 as shown in <a href="#f:before_undoing">Figure 13</a>:
1479 <figure id="f:before_undoing">
1480 <img src="svn/before_undoing.png" alt="Before Undoing" />
1481 <figcaption>Figure 13: Before Undoing</figcaption>
1484 <p class="continue">
1485 Dracula wants to erase revision 13 from the repository,
1486 but he can't actually do that:
1487 once a change is in the repository,
1489 What he can do instead is merge the old revision with the current revision
1490 to create a new revision
1491 (<a href="#f:merging_history">Figure 14</a>).
1494 <figure id="f:merging_history">
1495 <img src="svn/merging_history.png" alt="Merging History" />
1496 <figcaption>Figure 14: Merging History</figcaption>
1499 <p class="continue">
1500 This is exactly like merging changes made by two different people;
1501 the only difference is that the "other person" is his past self.
1506 Dracula must merge revision 12 (the one before his change)
1507 with revision 13 (the current head revision)
1508 using <code>svn merge</code>:
1512 $ <span class="in">svn merge -r HEAD:12 moons.txt</span>
1513 <span class="out">-- Reverse-merging r13 into 'moons.txt'
1517 <p class="continue">
1518 The <code>-r</code> flag specifies the range of revisions to merge:
1519 to undo the changes from revision 12 to revision 13,
1520 he uses either <code>13:12</code> or <code>HEAD:12</code>
1521 (since he is going backward in time from the most recent revision to revision 12).
1522 This is called a <a href="glossary.html#reverse-merge">reverse</a> merge
1523 because he's going backward in time.
1527 After he runs this command,
1528 he must run <code>svn commit</code> to save the changes to the repository.
1529 This creates a new revision, number 14,
1530 rather than erasing revision 13.
1532 the changes he made to create revision 13 are still there
1533 if he can ever convince the Mummy that numbers should have commas.
1537 <h3>Another Way to Do It</h3>
1540 Another way to recover a particular version of a particular file
1541 is to use the <code>svn copy</code> command.
1542 If the URL of our repository is
1543 <code>https://universal.software-carpentry.org/explore</code>,
1548 $ <span class="in">svn copy https://universal.software-carpentry.org/explore/mission.txt@120 ./mission.txt</span>
1551 <p class="continue">
1552 copies the file <code>mission.txt</code> as it was in revision 120
1553 into our working directory
1554 (overwriting whatever <code>mission.txt</code> file we currently have,
1557 using <code>svn copy</code> brings along the file's history as well,
1558 so that future <code>svn log</code> operations will show
1559 how <code>mission.txt</code> was resurrected.
1564 Merging can be used to recover older revisions of files,
1565 not just the most recent,
1566 and to recover many files or directories at a time.
1567 The most frequent use, though,
1568 is to manage parallel streams of development in large projects.
1569 This is outside the scope of this chapter,
1570 but the basic idea is simple.
1574 Suppose that Universal Missions has just released a new program
1575 for designing interplanetary voyages.
1576 Dracula and Wolfman are supposed to add some features
1577 that were left out of the first release because time ran short.
1579 Frankenstein and the Mummy are doing technical support:
1580 their job is to fix any bugs that users find.
1584 All sorts of things could go wrong
1585 if both teams tried to work on the same code at the same time.
1587 Dracula and Wolfman might want to make large changes
1588 to the structure of the code
1589 in order to make it easier to add new features,
1590 while Frankenstein and the Mummy want to make as few changes as possible
1591 so as not to introduce new bugs while fixing old ones.
1595 The usual way to handle this situation is
1596 to create a <a href="glossary.html#branch">branch</a>
1597 in the repository for each major sub-project
1598 (<a href="#f:branch_merge">Figure 15</a>).
1599 While Wolfman and Dracula work on
1600 the <a href="glossary.html#main-line">main line</a>,
1601 Frankenstein and the Mummy create a branch,
1602 which is just another copy of the repository's files and directories
1603 that is also under version control.
1604 They can work in their branch without disturbing Wolfman and Dracula and vice versa:
1607 <figure id="f:branch_merge">
1608 <img src="svn/branch_merge.png" alt="Branching and Merging" />
1609 <figcaption>Figure 15: Branching and Merging</figcaption>
1613 Branches in version control repositories are often described as "parallel universes".
1614 Each branch starts off as a clone of the project at some moment in time
1615 (typically each time the software is released,
1616 or whenever work starts on a major new feature).
1617 Changes made to a branch only affect that branch,
1618 just as changes made to the files in one directory don't affect files in other directories.
1620 the branch and the main line are both stored in the same repository,
1621 so their revision numbers are always in step.
1625 If someone decides that a bug fix in one branch should also be made in another,
1626 all they have to do is merge the files in question.
1627 This is exactly like merging an old version of a file with the current one,
1628 but instead of going backward in time,
1629 the change is brought sideways from one branch to another.
1633 Branching helps projects scale up by letting sub-teams work independently,
1634 but too many branches can cause as many problems as they solve.
1635 Karl Fogel's excellent book
1636 <a href="bib.html#fogel-producing-oss"><cite>Producing Open Source Software</cite></a>,
1637 and Laura Wingerd and Christopher Seiwald's paper
1638 "<a href="bib.html#wingerd-seiwald-scm">High-level Best Practices in Software Configuration Management</a>",
1639 talk about branches in much more detail.
1640 Projects usually don't need to do this until they have a dozen or more developers,
1641 or until several versions of their software are in simultaneous use,
1642 but using branches is a key part of switching from software carpentry to software engineering.
1645 <div class="keypoints">
1648 <li>Old versions of files can be recovered by merging their old state with their current state.</li>
1649 <li>Recovering an old version of a file does not erase the intervening changes.</li>
1650 <li>Use branches to support parallel independent development.</li>
1651 <li><code>svn revert</code> undoes local changes to files.</li>
1652 <li><code>svn merge</code> merges two revisions of a file.</li>
1656 <div class="challenges">
1661 Explain what the command:
1663 svn diff -r 240:261 fish.dat
1665 does, and when you might want to run it.
1669 Suppose that a file called <code>mission.txt</code>
1670 existed in revision 90 of a repository,
1671 but had been deleted in revision 91.
1672 What two commands could we use to recover it?
1680 <section id="s:setup">
1681 <h2>Setting Up a Repository</h2>
1683 <div class="understand">
1684 <h3>Learning Objectives</h3>
1686 <li>How to create a repository.</li>
1689 <span class="duration">25 minutes</span>
1690 (mostly discussion about where to host repositories).
1695 It is finally time to see how to create a repository.
1697 we will keep the master copy of our work in a repository
1698 on a server that we can access from other machines on the internet.
1699 That master copy consists of files and directories that no-one ever edits directly.
1700 Instead, a copy of Subversion running on that machine
1701 manages updates for us and watches for conflicts.
1702 Our working copy is a mirror image of the master sitting on our computer.
1703 When our Subversion client needs to communicate with the master,
1704 it exchanges data with the copy of Subversion running on the server.
1708 To make this to work, we need four things:
1714 The repository itself.
1715 It's not enough to create an empty directory and start filling it with files:
1716 Subversion needs to create a lot of other structure
1717 in order to keep track of old revisions, who made what changes, and so on.
1721 The full URL of the repository.
1722 This includes the URL of the server
1723 and the path to the repository on that machine.
1724 (The second part is needed because a single server can,
1726 host many repositories.)
1730 Permission to read or write the master copy.
1731 Many open source projects give the whole world permission to read from their repository,
1732 but very few allow strangers to write to it:
1733 there are just too many possibilities for abuse.
1734 Somehow, we have to set up a password or something like it
1735 so that users can prove who they are.
1739 A working copy of the repository on our computer.
1740 Once the first three things are in place,
1741 this just means running the <code>checkout</code> command.
1747 To keep things simple,
1748 we will start by creating a repository on the machine that we're working on.
1749 This won't let us share our work with other people,
1750 but it <em>will</em> allow us to save the history of our work as we go along.
1754 The command to create a repository is <code>svnadmin create</code>,
1755 followed by the path to the repository.
1756 If we want to create a repository called <code>missions_repo</code>
1757 directly under our home directory,
1758 we just <code>cd</code> to get home
1759 and run <code>svnadmin create missions_repo</code>.
1760 This command creates a directory called <code>missions_repo</code> to hold our repository,
1761 and fills it with various files that Subversion uses
1762 to keep track of the project's history:
1766 $ <span class="in">cd</span>
1767 $ <span class="in">svnadmin create missions_repo</span>
1768 $ <span class="in">ls -F missions_repo</span>
1769 <span class="out">README.txt conf/ db/ format hooks/ locks/</span>
1772 <p class="continue">
1773 We should <em>never</em> edit any of this directly,
1774 since it will almost certainly make the repository unusable.
1776 we should use <code>svn checkout</code>
1777 to get a working copy of this repository.
1778 If our home directory is <code>/users/mummy</code>,
1779 then the full path to the repository we just created is <code>/users/mummy/missions_repo</code>,
1780 so we run <code>svn checkout file:///users/mummy/missions missions_working</code>.
1785 the second argument,
1786 <code>missions_working</code>,
1787 specifies where the working copy is to be put.
1788 The first argument is the URL of our repository,
1789 and it has two parts.
1790 <code>/users/mummy/missions_repo</code> is the path to repository directory.
1791 <code>file://</code> specifies the <a href="glossary.html#protocol">protocol</a>
1792 that Subversion will use to communicate with the repository—in this case,
1793 it says that the repository is part of the local machine's filesystem.
1794 (Notice that the protocol ends in two slashes,
1795 while the absolute path to the repository starts with a slash,
1796 making three in total.
1797 A very common mistake is to type only two, since that's what web URLs normally have.)
1801 When we're doing a checkout,
1802 it is <em>very</em> important that we provide the second argument,
1803 which specifies the name of the directory we want the working copy to be put in.
1805 Subversion will try to use the name of the repository,
1806 <code>missions_repo</code>,
1807 as the name of the working copy.
1808 Since we're in the directory that contains the repository,
1809 this means that Subversion will try to overwrite the repository with a working copy.
1811 there isn't much risk of our sanity being torn to shreds,
1812 but this could ruin our repository.
1816 To avoid this problem,
1817 most people create a sub-directory in their account called something like <code>repos</code>,
1818 and then create their repositories in that.
1820 we could create our repository in <code>/users/mummy/repos/missions</code>,
1821 then check out a working copy as <code>/users/mummy/missions</code>.
1822 This practice makes both names easier to read.
1826 The obvious next step is to put our repository on a server,
1827 rather than on our personal machine.
1829 we should <em>always</em> do this
1830 so that we don't lose the history of our project
1831 if our laptop is damaged or stolen.
1832 A departmental server is also much more likely to be backed up regularly
1833 than our personal machine…
1837 Creating a repository on a server is simple:
1838 just log in and go through the steps described above.
1839 Accessing that repository from another machine
1840 is also straightforward.
1841 If the machine's address is <code>serv.euphoric.edu</code>,
1842 and our user ID is <code>dracula</code>,
1843 the URL of the repository will be something like:
1847 svn+ssh://dracula@serv.euphoric.edu/home/dracula/repos/missions
1851 Reading from left to right:
1856 <code>svn+ssh</code> is the protocol that Subversion uses to connect to the server
1858 a combination of Subversion's own protocol
1859 and <a href="shell.html#s:ssh">SSH</a>);
1862 <code>dracula@serv.euphoric.edu</code> identifies the server and who we are
1863 (just like an email address);
1867 <code>/home/dracula/repos/missions</code> is the absolutely path of the repository
1872 <p id="a:only_user">
1873 That's fine if you are the only person using the repository,
1874 but if you want to share it with others,
1875 you need to worry about security.
1876 As we discuss in the lesson on <a href="web.html">web programming</a>,
1877 as soon as you provide a service on the internet,
1878 there's the possibility that someone may try to attack your system through it.
1879 Rather than trying to learn enough system administration skills
1880 to set things up safely,
1881 it is usually easier to:
1887 ask your department's system administrator to set it up for you;
1891 use a hosting service like <a href="http://www.sf.net">SourceForge</a>,
1892 <a href="http://code.google.com">Google Code</a>,
1893 <a href="https://github.com/">GitHub</a>,
1894 or <a href="https://bitbucket.org/">BitBucket</a>; or
1898 spend a few dollars a month on a commercial hosting service
1899 that provides web-based GUIs for creating and managing repositories.
1905 If you choose the second or third option,
1906 please check with whoever handles intellectual property at your institution
1907 to make sure that putting your work on a commercially-operated machine
1908 that is probably in some other legal jurisdiction
1909 isn't going to cause trouble.
1910 Many people assume that it's "just OK",
1911 while others act as if not having asked will be an acceptable defence later on.
1913 neither is true…
1916 <div class="keypoints">
1919 <li><code>svnadmin create <em>name</em></code> creates a new repository.</li>
1920 <li>Repositories can be hosted locally, on local (departmental) servers, on hosting services, or on their owners' own domains.</li>
1924 <div class="challenges">
1930 Create a Subversion repository called <code>trials_repo</code>
1931 in your home directory.
1932 Check out a working copy in a directory called <code>trials_working</code>
1933 (also in your home directory).
1934 Add a couple of text files,
1936 and then use <code>svn info trials_working</code>
1937 to see what Subversion tells you about your working copy.
1941 We said <a href="#a:only_user">above</a> that
1942 you might be the only person using a particular repository.
1943 When and why is version control worth using
1944 if no-one else is working on a project with you?
1948 There are many ways to organize repositories.
1949 Some of the most common are to create one repository for:
1951 <li>each person</li>
1953 <li>all the work done on one grant</li>
1954 <li>all the work done on one project</li>
1955 <li>the entire lab (which is shared by everyone in the lab)</li>
1956 <li>the entire department (typically with a top-level directory for each person or project in the department)</li>
1958 What activities does each one make easy or hard?
1959 Which of these would you prefer, and why?
1967 <section id="s:provenance">
1970 <div class="understand">
1971 <h3>Learning Objectives</h3>
1973 <li>What data provenance is.</li>
1974 <li>How to embed version numbers and other information in files managed by version control.</li>
1975 <li>How to record version information about a program in its output.</li>
1978 <span class="duration">20 minutes</span>
1979 (without a practical exercise).
1985 the <a href="glossary.html#provenance">provenance</a> of a work
1986 is the history of who owned it, when, and where.
1988 it's the record of how a particular result came to be:
1989 what raw data was processed by what version of what program to create which intermediate files,
1990 what was used to turn those files into which figures of which papers,
1995 One of the big benefits of using version control is that
1996 it lets us track the provenance of scientific data automatically.
1998 suppose we have a text file <code>combustion.dat</code> in a Subversion repository.
1999 Run the following two commands:
2003 $ svn propset svn:keywords Revision combustion.dat
2004 $ svn commit -m "Turning on the 'Revision' keyword" combustion.dat
2007 <p class="continue">
2008 This does nothing by itself,
2009 but now open the file in an editor
2010 and add the following line somewhere near the top:
2018 The <code>$Revision:$</code> string means something special to Subversion.
2019 Save the file, and commit the change:
2023 $ svn commit -m "Inserting the 'Revision' keyword" combustion.dat
2027 When we open the file again,
2028 we'll see that Subversion has changed that line to something like:
2035 <p class="continue">
2036 i.e., it has inserted the version number
2037 after the colon and before the closing <code>$</code>.
2038 If we edit the file again—e.g., add a couple of lines with random numbers—and
2040 the line is updated again to:
2048 Here's what just happened.
2049 First, Subversion allows uss to add
2050 <a href="glossary.html#property-subversion">properties</a>
2051 to files and and directories.
2052 These properties aren't stored in the files or directories themselves,
2053 but in Subversion's database.
2054 One of those properties,
2055 <code>svn:keywords</code>,
2056 tells Subversion to look in files that are being changed
2057 for strings of the form <code>$propertyname: …$</code>,
2058 where <code>propertyname</code> is a string like <code>Revision</code> or <code>Author</code>.
2059 (About half a dozen such strings are supported.)
2063 If it sees such a string,
2064 Subversion rewrites it as the commit is taking place to replace <code>…</code>
2065 with the current version number,
2066 the name of the person making the change,
2067 or whatever else the property's name tells it to do.
2068 We only have to add the string to the file once;
2070 Subversion updates it for you every time the file changes.
2074 Putting the version number in the file this way can be pretty handy.
2075 If you copy the file to another machine,
2077 it carries its version number with it,
2078 so you can tell which version you have even if it's outside version control.
2079 We'll see some more useful things we can do with this information <a href="python.html">later</a>.
2083 We can use this trick with shell scripts too,
2084 or with almost any other kind of program.
2085 Let's go back to Nelle Nemo's data processing from
2086 the lesson on the <a href="shell.html">shell</a>.
2087 Suppose she writes a shell script called <code>gooclean</code>
2088 to tidy up data files.
2089 Her first version looks like this:
2093 # gooclean: clean up a single data file
2094 goonorm -b 0 100 < $1 | goofilter -x --enlarge 2.0 > cleaned-$1
2097 <p class="continue">
2099 it runs <code>goonorm</code> and then <code>goofilter</code> with some fixed parameters
2100 and creates an output file called <code>cleaned-something.dat</code>
2101 (if the input file's name was <code>something.dat</code>).
2102 Assuming that '#' is the comment character for her output files,
2103 she could instead write:
2107 # gooclean: clean up a single data file
2108 <span class="highlight">echo "# gooclean $Revision:$" > cleaned-$1</span>
2109 goonorm -b 0 100 < $1 | goofilter -x --enlarge 2.0 <span class="highlight">>></span> cleaned-$1
2112 <p class="continue">
2113 then set the <code>svn:keywords</code> property
2114 and commit the file to insert the revision number,
2119 # gooclean: clean up a single data file
2120 <span class="highlight">echo "# gooclean $Revision: 487$" > cleaned-$1</span>
2121 goonorm -b 0 100 < $1 | goofilter -x --enlarge 2.0 <span class="highlight">>></span> cleaned-$1
2126 each time this script is run it will:
2133 # gooclean $Revision: 487$
2139 append whatever the pipline containing <code>goonorm</code> and <code>goofilter</code>
2140 would have put in the file originally.
2141 (The double redirection <code>>></code> means "append to" rather than "overwrite".)
2145 <p class="continue">
2147 the output of this shell script will always record
2148 exactly what version of the script produced it.
2149 This isn't enough to reproduce the output—we would need to record
2150 the version numbers of the input files and the <code>goonorm</code> and <code>goofilter</code> programs,
2151 and the values of the parameters those programs used
2152 in order to do that—but it's an important and useful first step.
2155 <div class="keypoints">
2158 <li><code>$Keyword: …$</code> in a file can be filled in with a property value each time the file is committed.</li>
2159 <li>Put version numbers in programs' output to establish provenance for data.</li>
2160 <li><code>svn propset svn:keywords <em>property</em> <em>files</em></code> tells Subversion to start filling in property values.</li>
2164 <div class="challenges">
2170 Add <code>$Id:$</code> to a file,
2171 use <code>svn propset</code> to set the corresponding property,
2172 and then commit a change to the file.
2173 What value does Subversion fill in for this keyword?
2174 When would you use this rather than <code>Revision</code> or <code>Author</code>?
2178 What does the <code>svn:ignore</code> property do when applied to a directory?
2179 When would you use it?
2188 <section id="s:summary">
2193 <a href="bib.html#mccullough-reproducibility">McCullough, McGeary, and Harrison</a>
2194 analyzed several years of
2195 the data and code archive of <cite>Journal of Money, Credit, and Banking</cite>,
2196 a prestigious journal with a mandatory archiving policy.
2197 Of 266 articles published during that time,
2198 193 were empirical and should have had data and code deposited in the archive.
2200 only 69 actually had anything in the archive;
2201 Excluding eleven articles that only had data,
2202 and seven that required software or other resources they did not have,
2203 McCullough et al. were only able to replicate 14 of the remaining 186 articles.
2204 This doesn't mean that the other 92% were wrong,
2205 but it does mean there is no practical way to tell.
2210 version control doesn't making computational research reproducible.
2211 It <em>does</em> help,
2213 and also eliminates the frustration and wasted time caused by
2214 trying to figure out which emailed copy of a file,
2215 or which of a dozen directories or USB drives,
2217 And while correlation doesn't imply causality,
2218 there is certainly a strong correlation between
2219 knowing enough about good computational practices to use version control
2220 and knowing how to do other things right as well.
2224 {% endblock content %}