The lonelypages script only has a dictionary of languages, and if an entry exists in the dictionary for the site language, the script runs.
As a result of a very recent i18n change (https://gerrit.wikimedia.org/r/#/c/199579/), this means that the script runs on wikidata using the English configuration, even though this is inappropriate as the template {{Orphan}} in the English configuration is not present on that site (https://www.wikidata.org/wiki/Template:Orphan).
| Status | Subtype | Assigned | Task | ||
|---|---|---|---|---|---|
| Open | None | T94679 scripts that do not check site correctly | |||
| Declined | None | T94680 lonelypages only checks site language, rather than checking template exists |
fwiw, this is currently causing a build breakage - https://travis-ci.org/wikimedia/pywikibot-core/jobs/56654900#L461 . however the problem is larger, as the script would also run on English Wikisource, which the script doesnt support and will behave sub-optimally as {{orphan}} on English Wikisource is implemented differently.
By the way I think it's the other way around: With T94679 fixed this would be a relatively easy task.
Change 201446 had a related patch set uploaded (by XZise):
[FEAT] Load the settings from wiki
lonelypages.py script has been removed. Please file a task if you want to use it; i will be recovered then.