feat(18): adopt the shared CLI helpers in screen.py - #25

Follow-up to #24, which migrated the other seven rdkit Jobs but left screen.py
out because of a short-flag collision. Per the decision on that PR, -d is
dropped from --descriptor and screen.py now takes the shared group.

Summary

• --descriptor loses its -d short form, freeing -d for the group's
  --delimiter. The manifest passes --descriptor long-form
  (data-manager/rdkit.yaml:971), so it needs no change. The in-file usage
  example was updated too.
• Adopts rdkit_utils.add_common_molecule_io_args(parser, output_required=True)
  and add_reporting_args(parser), replacing 9 hand-typed options.

Net −15/+10 lines.

⚠️ -d now means --delimiter, silently

This is the cost of the decision and worth being explicit about. -d still
parses — it just binds to a different option:

$ screen.py ... -d rdkit
-d rdkit now parses as: delimiter='rdkit', descriptor='rdkit'

So an existing script or habit passing -d <descriptor> does not error; it
silently sets a nonsense delimiter and falls back to the default descriptor. The
Job manifest is unaffected, but anyone invoking screen.py directly should know.
If that trade is unwelcome, the alternative remains giving the helper a knob to
omit -d.

A latent crash this would have introduced

screen.py's --delimiter defaulted to '\t'; the shared group defaults to
None. The manifest passes --delimiter only conditionally
({% if separatorInputs is defined %}) while --write-header is separately
conditional — so a real invocation with headerOutputs set and
separatorInputs unset would have reached:

outf.write(delimiter.join(headers) + '\n')   # AttributeError: 'NoneType'

parser.set_defaults(delimiter='\t') after the helper call preserves the
existing default exactly. Verified: with no --delimiter, both old and new
parse to '\t'.

ProgressReporter is not used here

This Job's progress message carries a hit count —
"Processed {} records, {} hits" — which report() does not emit. Swapping it
in would have quietly dropped that. The inline loop stays; --interval still
comes from add_reporting_args().

Verification

One scenario fails on both old and new: --queries-file with
--write-header and no --queries-delimiter raises IndexError inside the
query reader. Pre-existing and unrelated to this change.

jote was not run — needs the informaticsmatters/vs-prep image rebuilt.

🤖 Generated with Claude Code