Automated testing

[dafyddstephenson]

Hi all, This PR allows automated testing when code is pushed to GitHub. You can see an example here. This primarily involves the addition of files used by the GitHub runner (VM) handling the testing, but also includes some modifications to the test cases themselves.

Modifications related to CI

• Examples/*/code_check:
  • input_data symlink has been converted to a relative path
  • benchmark.result_github : output log to be compared with when run by GitHub
• Examples/bgc_real/code_check : added this directory to include bgc_real in the test suite
• Examples/bgc_real/code_check/do_test_roms.sh : a modified version of Examples/code_check/do_test_roms.sh which loops over BGC_MODEL in {"BEC","MARBL"} , testing the bgc_real example with either BGC model.
• Examples/bgc_real/code_check/cppdefs_{BEC,MARBL}.opt : for compiling and running the test with either BGC model.
• Examples/bgc_real/marbl_in : configuration file for when running test with MARBL
• Examples/code_check/do_test_all.sh : Added bgc_real case, added exit codes, added github to argument list
• Examples/code_check/do_test_roms.sh : Added github to argument list

New files related to CI

• .github/workflows/automated_testing_workflow.yml : contains step-by-step commands to compile ROMS and run its test suite on a GitHub runner with Ubuntu
• ci/environment.yml : used to create a conda environment on the GitHub runner in which to compile ROMS
• ci/get_input_files.sh : used by the GitHub runner to fetch input_data files for Example cases. In particular, line 10: URL_PREFIX="https://github.com/dafyddstephenson/ucla_roms_examples_input_data/raw/main" points to a location where I've hosted (using git lfs) the files such that they can be accessed with wget and curl. I can transfer ownership of this repo to CESR-lab or we can change URL_PREFIX after finding somewhere else suitable to host the data. Please note that the bgc input files have been modified to ensure compatibility with both BEC and MARBL. In the forcing file, I have set a constant NOx forcing at 1e-13 kg/m2/s and a constant NHy forcing at 1e-12 kg/m2/s, and added pco2_air_alt to take the same values as pco2_air. In the initial and boundary files I have created and set any variables required by MARBL but not BEC to be 0 everywhere.
• ci/set_environ.sh : can be used for testing on GitHub codespaces, VMs hosted by GitHub that are similar to interactive GitHub runners
• ci/ci_makefiles : alternative Makefiles that allow the GitHub runner to compile using gfortran

Unrelated bugfix

• main.F : Lastly, there is a bugfix in main.F setting the call order of init_tracers and init_scalars based on whether the user is running with BEC. If init_scalars comes first then the various BGC tracer indices (e.g. iPO4) are at their default value of 0, causing a runtime error. The output is otherwise unaffected.

Appreciate that there's a lot here so happy to discuss in the comments! Dafydd

[dafyddstephenson]

Hi again @nmolem , I finally got what we discussed yesterday working. The logs are now printed in a separate step of the Actions workflow, but only in the case where the tests fail. The trimmed down input data are at https://github.com/dafyddstephenson/ucla_roms_examples_input_data . Again, I can transfer ownership of this repository to CESR-lab, but I imagine using github to host the files will just be a temporary measure. I think we're ready to merge.