Noninteractive run of notebooks and flake8 checks #107
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| @@ -138,8 +125,8 @@ | |||
| "source": [ | |||
| "## Setup data directory\n", | |||
| "\n", | |||
| "You can specify a directory with the `MONAI_DATA_DIRECTORY` environment variable. \n", | |||
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All these blanks in Markdown doc are to make the next sentence in a new line, that's Markdown gramma I think.
Thanks.
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This is going to be tricky to solve, but thanks for pointing it out.
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I've committed a temporary fix f7deb35 pending answer from here: mwouts/jupytext#723.
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OK, could you please update the PR to ignore the blanks?
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I've done that, but I'll have to revert all these accidental changes manually.
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Hi @rijobro , Is this PR OK for review again? Thanks. |
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hi @Nic-Ma , yes it is now! |
* start of automatic and update occ. sens. * current progress * current progress * current progress * current progress * vae * models ensemble * layer_wise_learning_rate * gan * 3d_classification * add 3d_segmentation as well as flake * transform speed * autopep8 * update runner * flake8 support added * max_num_epochs->max_epochs * check that max_epochs exists unless not expected * uncomment executing notebook * check pip install * ignore temp files * no noqa for indented import monai * dont check for indented import monai * flake8 changes * magic pip installs * autofixes * use ! instead of % for pip install * so far * current progress. add black, isort, autoflake * current progress * update class lung lesion notebook * class lung lesion * current progress * current progress * finished * finished * remove pip install of pinned pytorch version * = list() to = [] * [DLMED] fix dyunet notebook issue Signed-off-by: Nic Ma <nma@nvidia.com> * correct faulty import * pep8 for dynunet * all working * add missing quotations * remove personal file path * remove NiftiDataset * dont remove EOL whitespace from comments * 2d_classification * re-add spaces * spaces * last spaces * final changes * notification at end * notification on exit * add github action * data subfolder * make folder if necessary * add flake8 to requirements * change test name Co-authored-by: Nic Ma <nma@nvidia.com>
This uses the python package
papermillto run notebooks.papermillis used instead ofnbconvert --executeas it displays a progress bar. Without some sort of progress update, it's impossible to tell if execution is slow or is hanging.Use
sedto change some variables to 1 to reduce time (e.g.,max_epochs = 180->max_epochs = 1).Use jupytext to internally convert from notebook (
*.ipynb) into script (*.py). From here,flake8is used for checking PEP8 compliance, andautopep8,isort,blackandautoflakeare used for autofixes.This PR also contains all the changes to make the notebooks PEP8 compliant.
The most important file to review here is the
runner.shscript. All other files are hopefully only PEP8 changes, but I would be grateful for any checks to make sure I haven't done anything silly.Example usage: