Closed matthew-brett closed 8 months ago
Once merged to your default branch, Codecov will compare your coverage reports and display the results in this comment.
Thanks for integrating Codecov - We've got you covered :open_umbrella:
LMK if you want comments on anything specific. Just browsing to get my head around what y'all have been up to so far.
LMK if you want comments on anything specific. Just browsing to get my head around what y'all have been up to so far.
Thanks - the key current stuff is in experiements/scripting_again.py
- I'm just trying to put that into the tests. Any thoughts you have there would be very good. Are you around in the next few days to discuss?
Currently staying with family. If the last couple days are an indication, I'll have about 6-7am CST (UTC-6) between when I'm lucid and others get up. Shall we try tomorrow?
Currently staying with family. If the last couple days are an indication, I'll have about 6-7am CST (UTC-6) between when I'm lucid and others get up. Shall we try tomorrow?
:) - sounds good - speak to you then.
I sent a Zoom invite.
The submodules as written (without a trailing /.git
) don't work for me (git version 2.39.2, datalad 0.18.1)
Submodule 'src/xibabel/testing/ds000009' (https://datasets.datalad.org/openneuro/ds000009) registered for path 'src/xibabel/testing/ds000009' Cloning into '/data/pi/fmri/xib2/src/xibabel/testing/ds000009'... fatal: repository 'https://datasets.datalad.org/openneuro/ds000009/' not found fatal: clone of 'https://datasets.datalad.org/openneuro/ds000009' into submodule path '/data/pi/fmri/xib2/src/xibabel/testing/ds000009' failed Failed to clone 'src/xibabel/testing/ds000009'. Retry scheduled Cloning into '/data/pi/fmri/xib2/src/xibabel/testing/ds000105'... fatal: repository 'https://datasets.datalad.org/openneuro/ds000105/' not found fatal: clone of 'https://datasets.datalad.org/openneuro/ds000105' into submodule path '/data/pi/fmri/xib2/src/xibabel/testing/ds000105' failed Failed to clone 'src/xibabel/testing/ds000105'. Retry scheduled
I see that the actions running here use git 2.43.0, so I wonder if that's the only difference
[INFO] Attempting a clone into /Users/runner/work/xibabel/xibabel/src/xibabel/testing/ds000105 [INFO] Attempting to clone from https://datasets.datalad.org/openneuro/ds000105 to /Users/runner/work/xibabel/xibabel/src/xibabel/testing/ds000105 [INFO] Attempting to clone from https://datasets.datalad.org/openneuro/ds000105/.git to /Users/runner/work/xibabel/xibabel/src/xibabel/testing/ds000105
had to rerun a test, apparently fetching minimal data can be flaky (failed on macos this time)
- Run python -m xibabel.testing minimal CommandError: 'git -c diff.ignoreSubmodules=none -c core.quotepath=false annex get -c annex.retry=3 --json --json-error-messages --json-progress -c annex.dotfiles=true -- sub-07/anat/sub-07_T1w.nii.gz' failed with exitcode 139 under /Users/runner/.xibabel/data/ds000009 [info keys: stdout_json] error: git-annex died of signal 11 Traceback (most recent call last): File "
", line 198, in _run_module_as_main File " ", line 88, in _run_code File "/Users/runner/work/xibabel/xibabel/src/xibabel/testing/main.py", line 26, in main() File "/Users/runner/work/xibabel/xibabel/src/xibabel/testing/main.py", line 22, in main fetcher.get_set(test_set) File "/Users/runner/work/xibabel/xibabel/src/xibabel/testing/fetcher.py", line 124, in get_set out_paths.add(self.get_file(path_str)) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/runner/work/xibabel/xibabel/src/xibabel/testing/fetcher.py", line 113, in get_file return self._get_datalad_file(path_str, source['repo']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/runner/work/xibabel/xibabel/src/xibabel/testing/fetcher.py", line 96, in _get_datalad_file check_call(['datalad', 'get', file_str], cwd=repo_path) File "/usr/local/miniconda/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['datalad', 'get', 'sub-07/anat/sub-07_T1w.nii.gz']' returned non-zero exit status 139. Error: Process completed with exit code 1.
anyway, that's just for posterity, well done here, merging!
I've started with the testing machinery, to debug. Next maybe think about getting test files via datalad.