fix: json validation error with markdown cells#1986
Merged
johanneskoester merged 3 commits intosnakemake:mainfrom Dec 6, 2022
Merged
fix: json validation error with markdown cells#1986johanneskoester merged 3 commits intosnakemake:mainfrom
johanneskoester merged 3 commits intosnakemake:mainfrom
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Setting a null execution count makes it easier to manage the saved notebook in a SCM repository.
johanneskoester
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Dec 2, 2022
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It looks like tests are failing due to a failed deployment of slurm. I don't really know what to do about that. |
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Should be fixed with the merge I just did |
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Kudos, SonarCloud Quality Gate passed!
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johanneskoester
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Dec 13, 2022
🤖 I have created a release *beep* *boop* --- ## [7.19.0](v7.18.2...v7.19.0) (2022-12-13) ### Features * add keyword to gridftp remote provide to specify the number or disable usage of multiple data stream ([#1974](#1974)) ([3e6675d](3e6675d)) * provide information about temp, pipe, and service files in --summary ([#1977](#1977)) ([c7c7776](c7c7776)) * native SLURM support (--slurm, see docs) ([#1015](#1015)) ([c7ea059](c7ea059)) ### Bug Fixes * avoid logfile writing in case of dryrun; better hints in case of incomplete checkpoints ([#1994](#1994)) ([a022705](a022705)) * handle case where zenodo deposition does not return files ([#2004](#2004)) ([b63c4a7](b63c4a7)) * issue [#1882](#1882) WorkflowError: Metadata can't be created as it already exists (Windows) ([#1971](#1971)) ([d4484e6](d4484e6)) * json validation error with markdown cells ([#1986](#1986)) ([6c26f75](6c26f75)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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Description
This should fix #718. The cleanup routine after editing a notebook would add the
"outputs"attribute to all cells in the notebook, which would cause the JSON validation of nbconvert to fail for cells where no output is expected.I've also added a cleanup of the
"execution_count"property, which should make SCM management of the notebook easier (execution count of cells is prompt to frequent changes in interactive sessions). I can remove it if that change is superfluous.Finally, I think #1032 can be safely closed, I have not encountered it with recent versions of snakemake.
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).