Fix/update template to match latest Greene Lab template #46
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…improvements (#127) - temporarily track which plugin source came from with `_plugin` and `_input`, then ignore `exit()` when it is a metasource to address #121. delete these keys before exporting. - better error catching for various error-prone points - make logging and `.get()` fallbacks better - make `exit()`s happen at end of loop with `will_exit` flags, instead of stopping in the middle so users can see all entries that cause problems at once - rerun auto-cite and regenerate cache keys due to renaming of internal `_plugin` and `_input` keys - change "message" in exception catching to "e" to match convention - update docs to reflect above
- add the ability to run auto-cite workflow periodically, or on demand (through the github website interface), but comment out - increase timeout for auto-cite workflow - better citation date handling and fallbacks - truncate non-rich citation authors
See changelog for high level, user-facing changes. - docker python install changes. pin watchdog version, turn off unneeded caching. - docker entrypoint changes. run cite process immediately, ensure no simultaneous runs. - first time setup fixes. don't parse config.yaml as yaml, instead customize with string replacement to preserve key order and comments. - add title and link fallbacks to citation component - fix start/end markers for blog post excerpts, and remove special characters from hidden search attribute - change member page from col layout to float - add multi-line option to regex_scan liquid plugin (to support start/end marker bug above) - add new regex_strip liquid plugin to strip all special characters from string - card, code, portrait, post excerpt css fixes - fix testbed image links - (re)include user pr template - fix versioning workflow to correctly parse and split changelog - add show-title and show-subtitle site config options - include site subtitle in description meta tag
See greenelab/lab-website-template#177 . v1.1.1 introduced a regression in `first-time-setup.yaml` when clearing the `gh-pages` branch. I wanted to make the command simpler -- to simply delete everything in the folder -- but I didn't think it through enough. [There is a safeguard to prevent the command from working](https://unix.stackexchange.com/questions/369530/rm-refusing-to-remove-or-directory-skipping), and also even if it did work it would delete the `.git` folder which would break things. Thus, this version reverts the command to how it was before, manually specifying each `.` folder.
Closes #181 and #180 Closes #179 - fix typo in first-time-setup.yaml - fix versioning workflow tag/release - tweak some cite.py and _plugins comments - add commented out `continue` for if user wants to discard sources that have ids that can't be cited by Manubot, per #186 discussion - clean Manubot title/authors/publisher/etc output. trim whitespace and filter. - fix citation, portrait, and float css The tagging/releasing step is now reverted to [how I had it in v1.1.0](https://github.com/greenelab/lab-website-template/pull/166/files#diff-67cc7f4d3d06063e6239e59de699c4a2c768ba544777ded6aa22ab45aa0ad24a), just using `ncipollo/release-action` for both the tag and the release, and removing `mathieudutour/github-tag-action`. Idk why I keep going back and forth. I guess the last time I tried using just `ncipollo` it didn't work? But it seems to be working now (links ephemeral): https://github.com/vincerubinetti/lwt-test/pull/2 https://github.com/vincerubinetti/lwt-test/releases/tag/v1.1.4 --------- Co-authored-by: vincerubinetti <[email protected]>
- explicitly list cite process cache files in gitignore - add default values for all `.get()` calls for extra safety and also to indicate expected type - change `id` to `_id` in plugins. this was done in the main `cite.py` script in v1.1.1 but i missed it in the plugins. - fix dangerous memoize/cache bug where cache key doesn't include the id of the metasource currently being cited, which affects the output - orcid plugin: update api to v3 - orcid plugin: fix bug where all ids for single source were being included. instead, find most recent doi, and fallback to other id type if not available. - orcid plugin: keep a few details from api for ids that aren't citable by manubot - allow `format_date` util func to accept numeric timestamp (returned from orcid api) - tweak member bio page
- various cite process tweaks - add traceback logging of running plugins - change variable names for clarity and consistency - add generic "safe get" function as suggested by Faisal last pr - use generic safe get in place all of all gets. helps fix bug due to orcid api sometimes returning none types for certain fields, and other future bugs.
Unpins all cite process python packages from their exact versions, pins them to **major versions**. This ensures users will be on the latest versions of packages, without breaking changes (assuming the packages follow semver properly), and without having to constantly update their template version (which can be a pain). Closes #210 Addresses #211 FOR THE TEMPLATE MAINTAINER(S) New template version checklist: - [x] I have updated CITATION and CHANGELOG as appropriate. - [x] I have updated lab-website-template-docs as appropriate. - [x] I have checked the testbed as appropriate. --------- Co-authored-by: vincerubinetti <[email protected]>
- add discussion templates. be more aggressive requiring fields. - update to latest version of all github actions (checking for breaking changes) - add debug step to each workflow to allow ssh access in - fix site.location vs page.url bug (see issue) - add html-proofer plugin to check for broken images and links, disabled by default because it adds a lot of time to hot-reload, but set explicitly as false in config so users can easily flip it on - update bundler version and re-bundle gems - add "remove" option for cite-process that allows a user to remove a source from a metasource. e.g., an ORCID returns a source that the user doesn't want on their site, so in their sources.yaml they put the id and remove: true. - by default, ignore sources that manubot can't cite if they're from metasources (see changelog) - add markdownify to more component params - fix bug in citation (and other) components where when lookup is blank, first entry in list is always chosen - make use of newly widely available CSS container queries - remove compilation-time wrapping of tables because it breaks nested tables, and is not (practically) possible to support them in the same way. replace with run-time js plugin for wrapping. - upgrade font awesome and improve loading mechanism - fix header title/subtitle CSS bug reported by @Maruuka - add "image" param to post excerpt component, so blog posts can have thumbnails - fix bug that prevents manual passing of tags to tag component - add heading 5/6 styles/support - tweak dark mode plugin - various style tweaks New template version checklist: - [x] I have updated CITATION and CHANGELOG as appropriate. - [x] I have updated lab-website-template-docs as appropriate. - [x] I have checked the testbed as appropriate. - [x] I have tested changed workflows on a freshly generated and forked repo.
- fix bug where literal yaml date object doesn't get parsed correctly - fixes addition of site.url by gh-actions workflow New template version checklist: - [x] I have updated CITATION and CHANGELOG as appropriate. - [x] I have updated lab-website-template-docs as appropriate. - [x] I have checked the testbed as appropriate.
Closes #250 Closes #256 Closes #260 Closes #258 - adds `affiliation` to member portrait component - simplify portrait component code/css - make tag de-dupe behavior the same as search de-dupe. normalize to lower-kebab-case. - expand list of manubot-supported id types for falling back to orcid api details - change order and type of preferred ids from orcid --------- Co-authored-by: Faisal Alquaddoomi <[email protected]> Co-authored-by: vincerubinetti <[email protected]>
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Update to the latest version of the Greene Lab template we are using. This was a hell of a job, manually resolving the merge conflicts.