Improve testability of pdb_deposition.py

[tdudgeon]

Context

pdb_deposition.py has one existing test file (test_validate_structure_cif_doc.py) covering only
the validate_structure_cif_doc() function. The main workhorse — process_input() — is a 383-line
function that tangles file discovery, SoakDB reads, CIF manipulation, token substitution, and file
writing with no seams for unit testing. The goal is to extract a small number of focused functions
and add tests that cover the behaviours most likely to regress.

---

Proposed refactoring

1. Extract substitute_tokens() — pure, highest value

The token-replacement logic is scattered across an if/elif/elif block inside the mmcifgen loop.
Extract it into a standalone pure function:

def substitute_tokens(
    template: str,
    xtal_name: str,
    cmpd_code: str,
    cmpd_codes: list[str],
    pose_id_str: str,
) -> str:

Handles $CompoundCode, $CrystalName, $PoseID, $ExternalCodeN (N=1–9) in one place. No side
effects, trivially unit-testable.

2. Extract merge_mmcifgen_into_structure() — CIF-level, integration-testable

The entire for item in mmcifgen_block: loop applies the template block from mmcif-gen to the
per-crystal CIF block. Extract it:

def merge_mmcifgen_into_structure(
    structure_block: cif.Block,
    mmcifgen_block,
    xtal_name: str,
    cmpd_code: str,
    cmpd_codes_dict: dict,
    pose_ids_dict: dict,
) -> None:

Can be tested end-to-end with real or synthetic CIF blocks (gemmi already works well in tests, as
shown by test_validate_structure_cif_doc.py).

3. Make run_mmcifgen() injectable in process_input()

Add a mmcifgen_runner=run_mmcifgen parameter with a default so tests can substitute a stub that
writes a known CIF instead of running the full external tool.

---

Tests to write

New file: tests/test_pdb_deposition.py

Unit tests (no I/O)

test_substitute_tokens

• All four tokens present and substituted correctly
• $ExternalCode3 picks the right column; others are erased
• $PoseID with multiple pose codes, comma-separated
• Crystal with no entry in cmpd_codes_dict or pose_ids_dict — empty substitution, no crash
• Template with no tokens — returned unchanged

test_read_fragalysis_csv

• Happy path: two pose codes for one crystal → {'xtal': ['code_a', 'code_b']}
• Quoted CSV fields parsed correctly (regression from PR Add pose IDs to mmCIF keywords via $PoseID token substitution #82)
• filename=None → empty dict
• Rows with fewer than 3 columns skipped

test_read_cmpd_codes

• Happy path: crystal → list of codes
• filename=None → empty dict

Use tmp_path for CSV fixtures — no checked-in test data files needed.

CIF-level integration tests (uses gemmi, no external processes)

test_merge_mmcifgen_into_structure_title — build minimal mmcifgen CIF block in-memory with
_struct.title loop containing tokens; assert substituted correctly in destination block.

test_merge_mmcifgen_into_structure_keywords — same for _struct_keywords.text with $PoseID.

test_merge_mmcifgen_into_structure_passthrough — items with no tokens added unchanged.

Extend tests/test_validate_structure_cif_doc.py

• Missing required loop category → issue reported
• _refine R-factor out of range → issue reported
• $CompoundCode not substituted in title → issue reported
• Sequential _software.pdbx_ordinal passes validation

---

Files to change

File	Change
src/pdbdepo/pdb_deposition.py	Extract substitute_tokens() and merge_mmcifgen_into_structure(); add mmcifgen_runner param to process_input()
tests/test_pdb_deposition.py	New — unit and CIF-level tests
tests/test_validate_structure_cif_doc.py	Extended validation cases

No new test-data files needed — CSV fixtures use tmp_path, CIF fixtures built in memory.