Collaborating with others

Using version control systems to collaborate with others is essentially no different to working solo on multiple machines, except that you perhaps have less knowledge of exactly what changes have been made by others.

Suppose my colleague Barbara has also been working on the same code: she cloned my repository at version 0, and since then has been working independently. I’m a little wary of pulling in her changes, so first I can take a look at what she’s changed:

First I add Barbara’s repository as a “remote”:

Then I can fetch her changes to look at them, without merging them into my code.

Looks like there may be some problems, since I’ve also changed parameters in CUBA.py, and I’m saving figures to PNG format, not postscript. Oh, well, deep breath, let’s plunge in:

$ git pull /Users/barbara/our_network_model
remote: Counting objects: 13, done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 6 (delta 3), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
From /Users/barbara/our_network_model
 * branch            HEAD       -> FETCH_HEAD
Auto-merging CUBA.py
CONFLICT (content): Merge conflict in CUBA.py
Auto-merging COBAHH.py
CONFLICT (content): Merge conflict in COBAHH.py
Automatic merge failed; fix conflicts and then commit the result.

Doing the pull in SourceTree gives a similar message:

Unlike last time, when our changes were in different parts of the file, and so could be merged automatically, here Barbara has changed some of the same lines as me, and Git can’t choose which changes to keep.

Dealing with conflicting changes

If we now look at CUBA.py, we can see the conflicts marked with <<<<<<< and >>>>>>>:

...
from brian import *
import time

start_time=time.time()
<<<<<<< HEAD
taum=15*ms
taue=3*ms
taui=5*ms
=======
taum=25*ms
taue=5*ms
taui=10*ms
>>>>>>> 58a6d1659c88502e66e2aa27396a92949be24172
Vt=-50*mV
Vr=-65*mV
El=-49*mV

...

<<<<<<< HEAD
+savefig("CUBA_output.png")
=======
savefig("firing_rate_CUBA.eps")
>>>>>>> 58a6d1659c88502e66e2aa27396a92949be24172

Well, it makes sense for both me and Barbara to explore different parameters, and it makes sense to allow different file formats, so let’s move the parameters into a separate file, and parameterize the file format. The file now looks like this:

...
from brian import *
import time
from parameters import TAU_M, TAU_E, TAU_I, FILE_FORMAT

start_time=time.time()
taum = TAU_M*ms
taue = TAU_E*ms
taui = TAU_I*ms
Vt=-50*mV
Vr=-65*mV
El=-49*mV

...

assert FILE_FORMAT in ('eps', 'png', 'jpg')
savefig("firing_rate_CUBA.%s" % FILE_FORMAT)

After manually editing COBAHH.py as well, I can now do a commit:

$ git add COBAHH.py CUBA.py parameters.py

$ git commit -m "Merged Barbara's changes; moved parameters to separate file"

SourceTree shows us how the graph has changed.

Note

I decided to add the new parameters.py to the repository. This means Barbara and I will still have conflicts in future if we’re using different parameters, but at least the conflicts will be localized to this one file. It might have been better not to have parameters.py under version control, since it changes so often, but then we need another mechanism, in addition to version control, to keep track of our parameters.

I send Barbara an e-mail to tell her what I’ve done. Now all she has to do is run git pull.

(barbara)$ cd ~/our_network_model
(barbara)$ git pull /Volumes/USERS/andrew/my_network_model
remote: Counting objects: 13, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 5 (delta 2), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.
From /Volumes/USERS/andrew/my_network_model
   0d285ea..f02997c  master     -> origin/master
Updating e0a1383..f02997c
Fast-forward
 COBAHH.py     |  4 ++--
 CUBA.py       | 10 ++++++----
 parameters.py |  4 ++++
 3 files changed, 12 insertions(+), 6 deletions(-)
 create mode 100644 parameters.py

Now she has the new file, parameters.py, as well as the modified versions of CUBA.py and COBAHH.py.

Recap #2

You should now be able to use Git for:

• quick and easy backups of your code
• keeping your work in sync between multiple computers
• collaborating with colleagues