This talk describes my journey adding continuous integration to the open-source genomics toolkit Tripal.

1. Building Continuous Integration
Testing Standards for an Open-
source community
Bradford Condon, PhD
Co-Maintainer, Tripal
Web and mobile developer, Data
Scientist, Bioinformatician
@bradfordcondon
www.bradfordcondon.com
tripal.info
www.hardwoodgenomics.org

2. Code Styling,
Sniffing,
coverage, and
documentation
.
Continuous
Integration
Testing
Who am I and
what is Tripal?
THE TALK

3. Bench scientist to developer
@bradfordcondon
www.bradfordcondon.com
tripal.info
www.hardwoodgenomics.org
treesnap.org
Confocal microscopy of iron deficient
fungal mutants infecting corn leaf
Condon, B. J., Oide, S., Gibson, D. M., Krasnoff, S. B., & Turgeon, B. G. (2014). Reductive iron
assimilation and intracellular siderophores assist extracellular siderophore-driven iron
homeostasis and virulence. MPMI, 27(8), 793–808. doi:10.1094/MPMI-11-13-0328-R

4. What is Tripal?
1

5. Biological Database?

6. Drupal & Tripal
https://www.drupal.org/
tripal.info
● A Drupal module
● Open-source Biological CMS
● Modest set of community contributed modules
● Provides features that Biologists need
● Adhere to dating sharing principles important
for funding agencies
○ https://www.force11.org/group/fairgroup/fair
principles
Tripal
● Open-source CMS
● Rich community contributed
modules
● Provides basic site
functionality
Drupal

7. https://www.drupal.org/
tripal.info
Funding databases to
develop independently
Funding databases to
develop cooperatively

8. Community Challenges
Academia
Underlying data model highly specialized
Drupal
https://github.com/GMOD/Chado
Core code and extension modules

9. CI Testing Workflow
2

10. Continuous…
integration/delivery/deployment?
https://www.atlassian.com/continuous-delivery/principles/continuous-
integration-vs-delivery-vs-deployment
Integration Delivery Deployment
Merge every day
(automate testing)
Automate release
process
Automate deployment

11. Benefits of CI
● Tests!
● Identify problems earlier
● Reduce merge conflicts
● Release more often
● Tests!
● Organizational culture
● Warning/error overload

12. Code Climate
reads in the
coverage
report and
runs the style
sniffer.
PR is reviewed and
merged on GitHub.
Docs rebuilt.
Travis-CI runs
PHPUnit and
generates
coverage
reports.
Code written
on local
developer
instance and
pushed to
GitHub.
THE WORKFLOW

13. Unit Testing
3
https://phpunit.de/

14. i
Tripal, Drupal, and Testing
BDFL -> PMC
● No means of evaluating PRs
● BDFL PRs not tested
● New users were downloading
broken software
● Many bugs discovered and
introduced live
● Tripal had 0 tests in 2018
● Drupal 7 and under
encouraged SimpleTest
● SimpleTest vs PHPUnit…
● Cons of SimpleTest
○ PHP version support is low
○ No/poor IDE integration
○ Doesn't have simple test log
output

15. Descriptive Test Name
Pack it in/Pack it out
(database, environment, dependencies)
Multiple Assertions/Test
i
If A Test Fails, Will I know Why?

16. i
Setting up PHPUnit with Drupal

17. Tripal Test Suite
Automates configuration of PHPUnit for a
Drupal/Tripal module
https://tripaltestsuite.readthedocs.io/en/latest/

18. Tripal Test Suite
https://tripaltestsuite.readthedocs.io/en/latest/
● Single command setup of PHPUnit environment
● Bootstraps Drupal site
● Provides db transactions
● Provides factories
○ Really helpful for complicated objects
● Stub files for Travis CI!

19. Code Sniffing and
Styling
4

20. PHPCodeSniffer
https://github.com/squizlabs/PHP_CodeSniffer

21. PR OF DOOM

22. PHP CodeSniffer
https://tripaltestsuite.readthedocs.io/en/latest/
● Drupal style standards are intense
● Proper styling facilitates building automated
documentation
● Code smells vs style

23. Code Smell Examples
● Duplicated Code
● Contrived Complexity
● Code too long/complex to understand
● Identifiers too long, short, ambiguous
● Too many parameters
● God Object
● Feature Envy
● Inappropriate Intimacy
● Data clump

24. PHP Beautifier
● Automatically reformat your code
● Great for fixing styling
● Some sniffs can be refactored
automatically

25. INTEGRATE OR DIE
● PHPSTORM
● ATOM
● … Or your IDE of choice

26. Continuous
Integration
5

27. CI Platforms
● Integration with your version
control
● Features
● Guides
● Configurability
● Complexity/Learning Curve
● Price!

28. Travis CI
https://travis-ci.org/
● Build in Travis environment allows matrix
testing of variables, versions
● Build in Docker allows rapid testing
○ For Tripal core, we test upgrade
process by launching docker containers
for each release and running the
upgrade.

29. Travis CI
https://travis-ci.org/
● Environment Setup
● Test installing and
upgrading
● Run PHPUnit
● Send code coverage
report
● Why no deployment?
● Matrix builds

30. Code Climate
Alternatives:
Codacity
Git Prime
Code Cov
https://codeclimate.com/

31. FILE BY FILE TEST COVERAGE

32. STYLE REPORTS
TICKET SYSTEM
FOR STYLE ISSUES
IGNORE ISSUES!

33. GITHUB INTEGRATION
Browser Extension or Chattiest Bot Ever
Microsoft Office, Clippy

34. STUFF DESIGNED FOR ACTUAL TEAMS?

35. GitHub
Integrations

36. DOCUMENTATION
http://www.sphinx-doc.org/en/master/index.html
https://readthedocs.org/
https://tripal.readthedocs.io/en/latest/
RST -> SPHINX -> RTD

37. What is RST
http://api.tripal.info/api/tripal/tripal%21api%21tripal.fields.api.inc/function/hook_field_storage_tqu
ery/3.x

38. DOXYGEN
http://api.tripal.info/api/tripal/tripal%21api%21tripal.fields.api.inc/function/hook_field_storage_tqu
ery/3.x

39. RTD Stack
● RTD server runs Doxygen to generate
documentation from In-code
documentation
● Breathe integrates Doxygen with Sphinx
● RTD runs Sphinx build
● Versioned, continuous documentation
hosted!

40. QC
Fresh Docs
Test
Code
THE WORKFLOW

41. Microsoft Office, Clippy
Thanks for listening!
Any questions?

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