Fix three bugs in the component tests

[rcannood]

These all run in viash ns test for every component in every task repo.

The required links were not checked when there were none

check_links() returned early on an empty links, before asserting that the required ones are present:

check_links({}, ["documentation", "repository"])                     # passed
check_links({"documentation": ...}, ["documentation", "repository"])  # "Link .links.repository is not defined"

So a method without any links passed, and a method with a partial links block failed -- the wrong way around, since methods are exactly where those links are mandatory.

An optional output crashed the test

The format validation loop in check_output_files() does not filter on required the way the existence check above it does. An optional output argument without a default or example never gets a value assigned, so check_format() fell over with a bare KeyError: 'value' instead of skipping it.

check_url() had no timeout

head() without a timeout waits forever on an unresponsive host, and every component test checks all the links and dois in its config. It now uses a 30 second timeout, and a request that fails outright reports the link as unreachable instead of letting a ConnectionError escape as a traceback.

Also

^10.\d{4,9}/ matched a doi prefix like 10X1038, since the dot was not escaped.

Tests

check_links, check_references and check_url had no tests at all; run_and_check_output had none either. Added a few for the paths touched here -- the link and output ones fail on main.