Add --doi and --conda_requirements to shed_lint

[jmchilton]

Adds --doi and --conda_requirements to planemo shed_lint, closing an eight-year-old gap
between it and planemo lint.

The gap

peterjc reported in #667 that shed_lint was missing options lint has, so checking a repository
meant running both commands. --biocontainer was added independently in 2023 (2c1bbff), without
reference to the issue; the other two were still missing on master:

flag	lint	shed_lint (before)
--urls	yes	yes
--biocontainer	yes	yes
--doi	yes	no
--conda_requirements	yes	no

planemo shed_lint --tools --doi . failed with Error: No such option '--doi'.

Why it was only ever a plumbing gap

The 2017 diagnosis on the issue was that only the click options were missing. That still held:

• shed_lint.lint_repository already calls build_tool_lint_args(ctx, **kwds) (shed_lint.py:72)
  and forwards extra_modules into lint_tool_source_with (shed_lint.py:143) - the same path
  lint uses.
• _lint_extra_modules keys off kwds["doi"] and kwds["conda_requirements"]
  (tool_lint.py:60-73).

Since the click endpoint never put those keys in kwds, the linters silently never loaded. No
downstream change was needed.

Change

Rather than a third copy of each @click.option block, both are extracted into options.py
factories beside the existing lint_biocontainers_option(), and used from both commands.
docs/commands/lint.rst regenerates byte-identical, confirming lint's interface is untouched.

Tests

Two tests in tests/test_shed_lint.py, both reusing existing fixtures (single_tool_required_files,
tests/data/tools/bwa_without_requirements.xml) - no new test data.

• test_tool_linting_doi - asserts the DOI diagnostic is absent without the flag and present with
  it. Offline and deterministic: doi.org and the Tool Shed repositories API are stubbed with
  responses, as tests/test_trs_id.py already does. Worth noting doi.org currently answers 403
  to an unauthenticated requests GET, so an unmocked version of this test would be flaky.
• test_tool_linting_conda_requirements - marked slow, matching the equivalents in test_lint.py.
  It pins the linter's own message as well as the exit code, since a usage error is also non-zero
  and would otherwise pass.

Verified red-to-green: with only the planemo/ changes reverted, both fail (No such option '--doi'); restored, the full tests/test_shed_lint.py passes (9 tests), as does
tests/test_lint.py (8 passed, 5 skipped). flake8, black and mypy clean on the changed files.

Note

--urls is still defined inline and identically in both commands. Folding it into a factory too
would be a one-line change each, but it is outside this issue - happy to include it if preferred.

Fixes #667

🤖 Generated with Claude Code