Running Code (Part B)#

In this stage, you will run the code, by using the provided data. The REPLICATION.md is the report!

Signal that you are working on Part B#

To signal that you are starting to run the code, you will now transition the JIRA subtask to “Code is running”.

Move to Part B to Code is running

Principles#

Keep a log of what you do, what you find, and what does not work, in the REPLICATION.md, under Replication Steps.

  • Document if you manually downloaded data from anywhere other than the authors’ deposit.

  • Document any manual changes you made to the deposit structure (renamed file, created directory).

  • If you run into error messages that are not captured by the “log file” (see below), then screenshot, or copy verbatim, into the report.

You should also run code so that it generates an actual “log file”. How to do this depends on the software.

We have an entire section of the manual for this!

Check the software-specific guidelines in the manual’s section on running code, debug the code, and set the code to run.

Note

Sometimes, code can run for a long time. Leave the Jira ticket in Code is running to signal that there is activity there. Remember to come back regularly to check on it, and remember to commit all changes immediately (before running code).

If you appear to be stuck…

then as soon as possible, call on

  • your supervisors (Sofia, Lars)

  • more senior RAs (pre-approvers) or graduate students

  • bring it up in a Monday or Thursday meeting

Do not let yourself be blocked too long!

Once you have run the code, come back here to continue!

Details#

  • If code runs for a long time, record in the Jira issue (as a comment) when you started the code.

  • Use the Computing Environment to record where (CCSS, BioHPC node, etc.) you started the code.

  • It is not unusual for code to run for several days. You can start a new case in the meantime!

Wrapping up#

Once the code has run, error-free and creating the intended output (as far as you can tell), it is time to wrap up this sub-tasks.

  • Review again the Replication steps section, please include all steps that you took.

Note

You, or somebody else, will compare the output to the manuscript in the next step! You may, however, simply check that output exists, regardless of its specific content, before moving forward.

Move to Part B to Code has completed