update `fre.make` tests to avoid `getcwd`, and light `pylint` cleanup by Copilot · Pull Request #808 · NOAA-GFDL/fre-cli

Copilot · 2026-03-27T22:16:41Z

Describe your changes

test_run_fremake_container_build_fail fails in CI across all Python versions with:

FileNotFoundError: [Errno 2] No such file or directory: PosixPath('createContainer.sh')

Root cause: Path("./createContainer.sh") normalizes to PosixPath('createContainer.sh'), stripping the ./ directory separator. Without it, subprocess.run searches $PATH instead of CWD.

# Before — Path strips "./" → bare filename → $PATH search → FileNotFoundError
run = subprocess.run(Path("./createContainer.sh"), capture_output=True, check=False)

# After — plain string preserves "./" → executes from CWD
run = subprocess.run("./createContainer.sh", capture_output=True, check=False)

This was introduced by the earlier commit converting os.getcwd()-based absolute paths to relative paths for #738. The original code used f"{currPath}/createContainer.sh" which always had a directory component.

Issue ticket number and link (if applicable)

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

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…e/tests - Fix test_checkout_execute: use no_parallel_checkout=True to avoid shell-backgrounding race conditions (parallel syntax is already tested by test_checkout_script_exists) - Break monolithic assert all([...]) into individual assertions with descriptive messages for better failure diagnostics - Create conftest.py with shared fixtures for TEST_BUILD_DIR and output directory cleanup - Replace bare os.environ with monkeypatch.setenv() across all make tests for proper environment variable isolation between tests - Move module-level side effects (directory creation, shutil.rmtree) into pytest fixtures in test_create_compile.py, test_create_makefile.py, and test_run_fremake.py - Remove unused imports (os from test_create_compile.py, shutil.rmtree from test_run_fremake.py) Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/ced8734b-77f0-49eb-b4aa-0a029397548c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/ced8734b-77f0-49eb-b4aa-0a029397548c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

ilaflott · 2026-03-28T01:57:52Z

@copilot try again

…r all files The test created files with different datetimes (19900101 and 19900201). make_simple_varlist uses iglob to pick one file, extracts its datetime, then globs for all files matching that datetime. When iglob picked the 19900201 file first, the pattern *19900201*.nc only matched that one file, missing the salt file - causing intermittent assertion failures. Fix: use the same datetime (19900101) for the duplicate temp file so the glob pattern matches all files regardless of iglob ordering. Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/67d662d6-4df4-4e44-8e4e-cc6525f140ed Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot · 2026-03-28T02:01:44Z

@copilot try again

Fixed in 8258e69. The CI failure was in test_make_simple_varlist_deduplicates — it created files with different datetimes (19900101 vs 19900201), but make_simple_varlist uses iglob to pick one file and builds a glob pattern from its datetime. When iglob picked the 19900201 file first, the pattern *19900201*.nc only matched that one file, missing the salt file entirely. Changed the duplicate to use the same datetime so all files are found regardless of filesystem ordering.

ilaflott · 2026-03-28T02:06:47Z

oh, right... 🙃

codecov · 2026-03-30T13:07:57Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.12%. Comparing base (836559e) to head (dcf950f).
⚠️ Report is 10 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #808   +/-   ##
=======================================
  Coverage   84.12%   84.12%           
=======================================
  Files          71       71           
  Lines        4944     4944           
=======================================
  Hits         4159     4159           
  Misses        785      785

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…etime for all files" This reverts commit 8258e69. The failure was fixed in a different PR, better

ilaflott · 2026-03-30T16:18:20Z

@copilot additionally, address issue #738, which may be related to the issue this PR was created to solve, #807

#738) All test files in fre/make/tests/ now use Path(__file__).resolve().parent instead of os.getcwd() or hardcoded "fre/make/tests/..." strings. This ensures tests work correctly when pytest is run from any directory, not just the repository root. Files changed: - conftest.py, test_create_checkout.py, test_create_compile.py, test_create_makefile.py: Path("fre/make/tests") → Path(__file__).resolve().parent - test_create_dockerfile.py: YAMLDIR uses __file__-relative path; removed os.getcwd() - test_run_fremake.py: all paths use __file__-relative; os.environ → monkeypatch; removed os.getcwd() and unused import os - compilation/test_run_fremake_builds.py: currPath=os.getcwd() → _TEST_DIR = Path(__file__).resolve().parent Note: container output paths (tmp/, createContainer.sh, Dockerfile) remain CWD-relative since the production code creates them in CWD by design. Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/93d0cce5-40bc-46a1-89c8-ada3eed3265a Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot · 2026-03-30T16:31:35Z

@copilot additionally, address issue #738, which may be related to the issue this PR was created to solve, #807

Addressed in b5de105. All test files in fre/make/tests/ now use Path(__file__).resolve().parent instead of os.getcwd() or hardcoded "fre/make/tests/..." strings. This covers conftest.py, test_create_checkout.py, test_create_compile.py, test_create_makefile.py, test_create_dockerfile.py, test_run_fremake.py, and compilation/test_run_fremake_builds.py.

Container output paths (tmp/, createContainer.sh, Dockerfile) remain CWD-relative since the production code creates them in CWD by design — those aren't input/config paths, they're outputs from the fre make container workflow.

… PATH search subprocess.run() with a bare filename (no directory separator) searches $PATH instead of looking in CWD. The original code used an absolute path via os.getcwd() which had a directory component. After switching to relative paths for #738, we need './' prefix so subprocess finds the CWD file directly. Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/2adfb38f-005c-4d4f-84ce-d74925588f9d Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

ilaflott · 2026-03-30T17:11:21Z

Container output paths (tmp/, createContainer.sh, Dockerfile) remain CWD-relative since the production code creates them in CWD by design — those aren't input/config paths, they're outputs from the fre make container workflow.

notable caveat

Path("./createContainer.sh") normalizes to PosixPath("createContainer.sh"), stripping the "./" directory separator. Without it, subprocess.run searches $PATH instead of looking in the current working directory, causing FileNotFoundError in CI. Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/3cf04c93-09b4-45a1-ae96-d20489b8c309 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/3cf04c93-09b4-45a1-ae96-d20489b8c309 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

…json files) Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/3cf04c93-09b4-45a1-ae96-d20489b8c309 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

…e, CMOR json files)" This reverts commit 141ffde.

This reverts commit 93ce73d.

ilaflott · 2026-03-30T18:10:11Z

this should now close #738 and #807

…ecks via with pytest.raises(...)

Initial plan

ca2c53d

Copilot AI assigned Copilot and ilaflott Mar 27, 2026

Copilot started work on behalf of ilaflott March 27, 2026 22:19 View session

Copilot AI linked an issue Mar 27, 2026 that may be closed by this pull request

some unit tests are confusingly flakey #807

Open

Copilot AI and others added 2 commits March 27, 2026 22:28

Add clarifying documentation to conftest.py fixture docstrings

baee6a8

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/ced8734b-77f0-49eb-b4aa-0a029397548c Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Fix flakey unit tests in test_create_checkout~~ Fix flaky test_checkout_execute and improve test isolation in fre/make/tests Mar 27, 2026

Copilot finished work on behalf of ilaflott March 27, 2026 22:31

Copilot AI requested a review from ilaflott March 27, 2026 22:31

Copilot started work on behalf of ilaflott March 28, 2026 01:57 View session

Copilot AI changed the title ~~Fix flaky test_checkout_execute and improve test isolation in fre/make/tests~~ Fix flaky tests in test_create_checkout and test_cmor_finder, improve test isolation in fre/make/tests Mar 28, 2026

Copilot finished work on behalf of ilaflott March 28, 2026 02:03

ilaflott and others added 2 commits March 30, 2026 11:13

Revert "Fix flaky test_make_simple_varlist_deduplicates: use same dat…

68c0e25

…etime for all files" This reverts commit 8258e69. The failure was fixed in a different PR, better

Merge branch 'main' into copilot/fix-flakey-unit-tests

ce38782

ilaflott changed the title ~~Fix flaky tests in test_create_checkout and test_cmor_finder, improve test isolation in fre/make/tests~~ Fix flaky tests in test_create_checkout, improve test isolation in fre/make/tests Mar 30, 2026

Copilot started work on behalf of ilaflott March 30, 2026 16:18 View session

Copilot AI changed the title ~~Fix flaky tests in test_create_checkout, improve test isolation in fre/make/tests~~ Fix flaky tests, improve test isolation, and use __file__-relative paths in fre/make/tests Mar 30, 2026

Copilot finished work on behalf of ilaflott March 30, 2026 16:33

Copilot started work on behalf of ilaflott March 30, 2026 16:56 View session

Copilot AI changed the title ~~Fix flaky tests, improve test isolation, and use __file__-relative paths in fre/make/tests~~ Fix flaky tests, use __file__-relative paths in fre/make/tests (#738, #807) Mar 30, 2026

Copilot finished work on behalf of ilaflott March 30, 2026 17:02

Copilot started work on behalf of ilaflott March 30, 2026 17:27 View session

Copilot AI and others added 3 commits March 30, 2026 17:32

verified: all fre make tests pass locally in conda environment

93ce73d

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/3cf04c93-09b4-45a1-ae96-d20489b8c309 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

revert: remove test artifacts accidentally committed (Makefile, CMOR …

141ffde

…json files) Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/3cf04c93-09b4-45a1-ae96-d20489b8c309 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Copilot AI changed the title ~~Fix flaky tests, use __file__-relative paths in fre/make/tests (#738, #807)~~ fix(tests): use string not Path for subprocess.run to preserve ./ prefix Mar 30, 2026

Copilot finished work on behalf of ilaflott March 30, 2026 17:47

ilaflott added 2 commits March 30, 2026 13:55

Revert "revert: remove test artifacts accidentally committed (Makefil…

6ddedd1

…e, CMOR json files)" This reverts commit 141ffde.

Revert "verified: all fre make tests pass locally in conda environment"

7dc8ade

This reverts commit 93ce73d.

ilaflott marked this pull request as ready for review March 30, 2026 18:09

ilaflott linked an issue Mar 30, 2026 that may be closed by this pull request

fre make tests use getcwd #738

Open

ilaflott requested review from ceblanton, laurenchilutti and singhd789 March 30, 2026 18:10

ilaflott added bug Something isn't working clean up labels Mar 30, 2026

ilaflott and others added 2 commits March 30, 2026 14:14

Fix URL formatting in README.md

762bab4

pylint touch ups and change xfails that are testing for failure to ch…

933cd98

…ecks via with pytest.raises(...)

ilaflott changed the title ~~fix(tests): use string not Path for subprocess.run to preserve ./ prefix~~ update fre.make tests to avoid getcwd, and light pylint cleanup Mar 30, 2026

fix a rogue tab and adjust indentation

4753c95

ceblanton mentioned this pull request Mar 31, 2026

Use pytest fixtures for temporary paths to fix cwd dependency in fre make tests #793

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singhd789 added the beta1 label Apr 1, 2026

ilaflott mentioned this pull request Apr 7, 2026

preview of future fre.cmor #842

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Merge branch 'main' into copilot/fix-flakey-unit-tests

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update `fre.make` tests to avoid `getcwd`, and light `pylint` cleanup#808

update `fre.make` tests to avoid `getcwd`, and light `pylint` cleanup#808
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