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microbiomedata / NMDC_documentation

Document workflows, schemas, and portal
https://nmdc-documentation.readthedocs.io
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GitHub Actions: `check-links` job is failing #25

Open eecavanna opened 1 year ago

eecavanna commented 1 year ago

The check-links job is failing.

I checked the "Actions" tab on GitHub to see when the most recent passing run occurred, and did not see any passing runs.

https://github.com/microbiomedata/NMDC_documentation/actions/workflows/link-check.yaml

This section was added on September 7, 2023: Here's the failure list from the latest run. In this list, I manually (via regex replacement) formatted the file:/// links, added šŸ”’ emojis to (at least some) private GitHub links, and added checkboxes.

Summary

Status Count
šŸ” Total 8623
āœ… Successful 7527
ā³ Timeouts 12
šŸ”€ Redirected 0
šŸ‘» Excluded 1022
ā“ Unknown 0
šŸš« Errors 62

Errors per input

Errors in ./docs/reference/metadata/index.md

Errors in ./docs/howto_guides/submit2nmdc.md

Errors in ./docs/reference/metadata/fao_class.md

Errors in ./docs/reference/metadata/growth_facil.md

Errors in ./docs/reference/metadata/combined_schema_docs.md

Errors in ./docs/reference/metadata/Metadata_Documentation_Overview.md

Errors in ./docs/reference/metadata/salinity_category.md

Errors in ./docs/reference/metadata/identifiers.md

Errors in ./docs/reference/metadata/Biosample.md

Errors in ./docs/reference/metadata/plant_growth_med.md

Errors in ./docs/reference/metadata/geo_loc_name.md

Errors in ./docs/reference/metadata/Environment.md

Errors in ./docs/reference/metadata/NMDC_MIxS_Soil_documentation.md

Errors in ./docs/explanation/publications.md

Errors in ./docs/reference/metadata/types/ExternalIdentifier.md

Errors in ./docs/reference/data_portal.md

Errors in ./docs/reference/metadata/README.md

Errors in ./docs/reference/metadata/schema-validation.md

eecavanna commented 1 year ago

Each run takes 1-2 minutes.

image

Here's a link to information about GitHub Actions "minutes" quotas:

https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#included-storage-and-minutes

eecavanna commented 1 year ago

I think at least some of the file:/// link failures could be fixed by using absolute URLs to those files (e.g. https://example.com/path/to/file.png) instead of relative paths (e.g. ../../file.png). For example, here:

https://github.com/microbiomedata/NMDC_documentation/blob/ae70391d84c555d35e41dba0a868aa237f354f5b/docs/reference/metadata/schema-validation.md?plain=1#L31

That might not be what the authors want when the docs are deployed to a different server, though. With that in mind, I wonder whether lychee (the link checker) can be configured to interpret these particular links differently (e.g. preprocessing them by adding a prefix before checking them).

eecavanna commented 1 year ago

I think the failing https://pypi.org/proje../_static/jsonschema/ hyperlink contains a typo (i.e. a copy/paste error):

https://github.com/microbiomedata/NMDC_documentation/blob/ae70391d84c555d35e41dba0a868aa237f354f5b/docs/reference/metadata/combined_schema_docs.md?plain=1#L1397