Fix container build fail test #691

singhd789 · 2025-12-16T16:31:07Z

Describe your changes

was previously appending lines to createContainer.sh instead of overwriting
also addressed some pylint messages

Issue ticket number and link (if applicable)

n/a

Checklist before requesting a review

I ran my code
I tried to make my code readable
I tried to comment my code
I wrote a new test, if applicable
I wrote new instructions/documentation, if applicable
I ran pytest and inspected it's output
I ran pylint and attempted to implement some of it's feedback
No print statements; all user-facing info uses logging module

- was previously appending lines to createContainer.sh instead of overwriting - also addressed some pylint messages

codecov · 2025-12-16T16:43:50Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.30%. Comparing base (f7ec1c6) to head (fe61609).
⚠️ Report is 7 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #691      +/-   ##
==========================================
- Coverage   85.34%   85.30%   -0.05%     
==========================================
  Files          68       68              
  Lines        4498     4498              
==========================================
- Hits         3839     3837       -2     
- Misses        659      661       +2

Flag	Coverage Δ
unittests	`85.30% <ø> (-0.05%)`	⬇️

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ilaflott · 2025-12-16T18:17:35Z

This is closer! Now instead of test_run_fremake_container_build_notransfer and test_run_fremake_container_build_fail failing within fre/make/tests/compilation/test_run_fremake_builds.py, i just have test_run_fremake_container_build_notransfer failing. It seems to fail with:

============================================= FAILURES 
_____________________________________________ test_run_fremake_container_build_notransfer 

    @pytest.mark.skipif(not has_podman, reason="missing podman")
    def test_run_fremake_container_build_notransfer():
        ''' checks image creation with the .sif transfer turned off '''
        if Path("createContainer.sh").exists():
            os.remove("createContainer.sh")
>       run_fremake_script.fremake_run(YAMLPATH, CONTAINER_PLATFORM, TARGET,
            nparallel=False, njobs=1, no_parallel_checkout=True,
            no_format_transfer=True, execute=True, verbose=VERBOSE)

fre/make/tests/compilation/test_run_fremake_builds.py:102: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
fre/make/run_fremake_script.py:103: in fremake_run
    dockerfile_create(yamlfile, container_platforms, target, execute, no_format_transfer)
fre/make/create_docker_script.py:116: in dockerfile_create
    subprocess.run(args=[dockerBuild.userScriptPath], check=True)

................................
... CLIPPED "USELESS" OUTPUT ...
................................


             subprocess.CalledProcessError: Command '['/home/Ian.Laflotte/Working/fre-cli/createContainer.sh']' returned non-zero exit status 1.

../../conda/envs/fre-cli/lib/python3.11/subprocess.py:571: CalledProcessError
--------------------------------------------- Captured stdout call

COMBINED YAML VALID

COMBINED YAML VALID

COMBINED YAML VALID

COMBINED YAML VALID
STEP 1/19: FROM ghcr.io/rem1776/hpc-mini:alpine3gcc14.2 AS builder
-------------------------------------------------------------------------------------------------------------- Captured stderr call --------------------------------------------------------------------------------------------------------------
+ podman build -f Dockerfile -t null_model_full:debug
time="2025-12-16T13:12:17-05:00" level=warning msg="Network file system detected as backing store.  Enforcing overlay option `force_mask=\"700\"`.  Add it to storage.conf to silence this warning"
Trying to pull ghcr.io/rem1776/hpc-mini:alpine3gcc14.2...
Getting image source signatures
Copying blob sha256:750cdedbeac62fc688a081dc47cabedc7c668c010dc571178595e7524f4fa4b7
Copying blob sha256:210a2ae1a75e9e998739647b797326a97064eb38a1557d9191ff2f0ce0bef86c
Error: creating build container: writing blob: adding layer with blob "sha256:210a2ae1a75e9e998739647b797326a97064eb38a1557d9191ff2f0ce0bef86c": processing tar file(lsetxattr /bin: operation not supported): exit status 1
--------------------------------------------------------------------------------------------------------------- Captured log call ----------------------------------------------------------------------------------------------------------------
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:166 initializing a compile yaml instance...
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:61 Combining yaml files into one dictionary: 
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:84    model yaml: fre/make/tests/null_example/null_model.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:114    compile yaml: fre/make/tests/null_example/compile.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:146    platforms yaml: fre/make/tests/null_example/platforms.yaml
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:175 Combined yaml information saved as dictionary
INFO     fre.make.run_fremake_script:run_fremake_script.py:74 Running fre make: calling checkout_create
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:166 initializing a compile yaml instance...
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:61 Combining yaml files into one dictionary: 
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:84    model yaml: fre/make/tests/null_example/null_model.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:114    compile yaml: fre/make/tests/null_example/compile.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:146    platforms yaml: fre/make/tests/null_example/platforms.yaml
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:175 Combined yaml information saved as dictionary
INFO     fre.make.create_checkout_script:create_checkout_script.py:147 
Checkout script created at tmp/hpcmini.2025/checkout.sh 

INFO     fre.make.run_fremake_script:run_fremake_script.py:79 Running fre make: calling makefile_create
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:166 initializing a compile yaml instance...
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:61 Combining yaml files into one dictionary: 
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:84    model yaml: fre/make/tests/null_example/null_model.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:114    compile yaml: fre/make/tests/null_example/compile.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:146    platforms yaml: fre/make/tests/null_example/platforms.yaml
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:175 Combined yaml information saved as dictionary
INFO     fre.make.create_makefile_script:create_makefile_script.py:118 
Makefile created at ./tmp/hpcmini.2025/Makefile

INFO     fre.make.run_fremake_script:run_fremake_script.py:102 Running fre make: calling dockerfile_create
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:166 initializing a compile yaml instance...
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:61 Combining yaml files into one dictionary: 
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:84    model yaml: fre/make/tests/null_example/null_model.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:114    compile yaml: fre/make/tests/null_example/compile.yaml
INFO     fre.yamltools.info_parsers.compile_info_parser:compile_info_parser.py:146    platforms yaml: fre/make/tests/null_example/platforms.yaml
INFO     fre.yamltools.combine_yamls_script:combine_yamls_script.py:175 Combined yaml information saved as dictionary
INFO     fre.make.create_docker_script:create_docker_script.py:109 
tmpDir created in /home/Ian.Laflotte/Working/fre-cli/tmp
INFO     fre.make.create_docker_script:create_docker_script.py:110 Dockerfile created in /home/Ian.Laflotte/Working/fre-cli

INFO     fre.make.create_docker_script:create_docker_script.py:111 Container build script created at /home/Ian.Laflotte/Working/fre-cli/createContainer.sh
============================================================================================================ short test summary info =============================================================================================================
FAILED fre/make/tests/compilation/test_run_fremake_builds.py::test_run_fremake_container_build_notransfer - subprocess.CalledProcessError: Command '['/home/Ian.Laflotte/Working/fre-cli/createContainer.sh']' returned non-zero exit status 1.

singhd789 · 2025-12-16T18:31:15Z

test_run_fremake_container_build_notransfer

Huh, ok so this one passes for me

ilaflott · 2025-12-23T18:02:52Z

@rem1776 did you test this on PPAN? my problem was visible on PPAN.

i would test it myself but i'm on a plane on my phone.

singhd789 · 2026-01-13T16:54:03Z

@ilaflott are you still seeing that one failure here?

ilaflott · 2026-01-13T17:47:32Z

looks good to me

ilaflott · 2026-01-13T18:55:46Z

ah, yeah, environment problems

edit: that aren't the fault of this PR

- have to generalize null model so unit tests not reliant on actual FMS code

Fix container build fail test

e10c367

- was previously appending lines to createContainer.sh instead of overwriting - also addressed some pylint messages

singhd789 requested a review from ilaflott December 16, 2025 16:31

Add skip if podman not available

ca62296

Dana Singh added 2 commits December 16, 2025 14:04

Fix nparallel options - change to default number for clarity

d80e492

Add apptainer skip to test

3a40b3b

singhd789 requested review from kiihne-noaa and rem1776 December 17, 2025 21:28

ilaflott removed their request for review December 18, 2025 16:04

rem1776 approved these changes Dec 23, 2025

View reviewed changes

Merge branch 'main' into fix-fre-make-run-test

22455fc

Skip test for now

20ebb9e

singhd789 mentioned this pull request Jan 14, 2026

674.force checkout option #679

Open

8 tasks

singhd789 added 2 commits January 15, 2026 13:27

Change FMS checkout to previous tag for now

4a1bf8c

- have to generalize null model so unit tests not reliant on actual FMS code

Update to string

fe61609

singhd789 requested a review from ilaflott January 15, 2026 19:22

ilaflott merged commit 982868f into main Jan 15, 2026
5 of 6 checks passed

ilaflott deleted the fix-fre-make-run-test branch January 15, 2026 19:28

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singhd789 commented Dec 16, 2025

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