bug report - "table-reader" plugin is not installed

[adeans]

I got this error when I tried updating my ontology: 'ERROR - Config value 'plugins': The "table-reader" plugin is not installed' https://github.com/adeans/gallont/actions/runs/8266804231/job/22615690162

Reporting it here as suggested by @matentzn here: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/2541#discussion_r1524647207

[matentzn]

@adeans thank you for reporting this here.

@pfabry you have added the table-reader plugin through https://github.com/INCATools/ontology-development-kit/issues/857.

Can you test that it actually works with the

https://github.com/INCATools/ontology-development-kit/blob/7e33922efa475da437e6790dfb7f5160340c3e49/template/_dynamic_files.jinja2#L1843

Workflow, in particular the

https://github.com/INCATools/ontology-development-kit/blob/7e33922efa475da437e6790dfb7f5160340c3e49/template/_dynamic_files.jinja2#L1865

action we use to deploy the docs? If not, we should remove it from:

https://github.com/INCATools/ontology-development-kit/blob/7e33922efa475da437e6790dfb7f5160340c3e49/template/_dynamic_files.jinja2#L1806

[pfabry]

The plugin works in local repositories but not in the github actions whether it is brand new repo made with ODK 1.5 or an updated repo.

[matentzn]

@pfabry there seems to be a way to do this somehow by installing an additional plugin based on the instructions here: https://github.com/mhausenblas/mkdocs-deploy-gh-pages?tab=readme-ov-file#installing-mkdocs-plugins

Would you be willing to test this so we get this working?

[pfabry]

@matentzn Thank you for the information. It seems to work when doing the following steps:

• adding a requirements.txt file at the root of the repository with the line: mkdocs-table-reader-plugin
• adding the line REQUIREMENTS: requirements.txtat the end of the docs.yml workflow
• removing src/ontology/reports/* from the .gitignore file (if you don't want to have to copy .csv file in the /docs folder)

A test repository is available here I wrote "seems" because I still have an error when running the docs workflow, but it's now a permission error that seems to be on my side.

EDIT: Thanks @anitacaron (Slack, ODK channel). The last issue was a repository permission issue easily solved by modifying the repository actions workflow permissions. So, the table-reader is functional after the following steps:

• adding a requirements.txt file at the root of the repository with the line: mkdocs-table-reader-plugin
• adding the line REQUIREMENTS: requirements.txtat the end of the docs.yml workflow
• removing src/ontology/reports/* from the .gitignore file (if you don't want to have to copy .csv file in the /docs folder)
• In the repository settings, go to: Actions > General > Workflow permissions and check: Read and write permissions

[matentzn]

@pfabry thanks for the investigation.

Before we can make this decision: #1039 I think its better to comment out the plugin by default: https://github.com/INCATools/ontology-development-kit/pull/1040

Do you agree?

[pfabry]

@pfabry thanks for the investigation.

Before we can make this decision: #1039 I think its better to comment out the plugin by default: #1040

Do you agree?

Yes!