refactor(workflow): ♻️ guard the stage store with a touch() sentinel (#29)

Replace the prepare rule's directory(STAGE) output with a touch()ed
STAGE_OK marker (sopa's sentinel discipline). Snakemake then tracks a
tiny leaf file instead of a directory, so it no longer deletes/recreates
(or "moves") the stage store on a re-run and is immune to directory-mtime
quirks. segment depends on the sentinel; scripts open the store by path.

With this + marker outputs + rerun-triggers: mtime, touching any script
yields "Nothing to be done", and losing one tile re-runs only that tile
and the merge — convert/prepare stay cached.

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

Author: lguerard

workflow/rules/common.smk

@@ -9,6 +9,10 @@ IMAGE = f"{WORK}/image.zarr"
 IMAGE_OK = f"{IMAGE}/zarr.json"
 TILES = f"{WORK}/tiles.json"
 STAGE = f"{WORK}/stage.zarr"
+# Completion sentinel for the stage store. Tracking a touch()ed marker instead
+# of directory(STAGE) keeps Snakemake from deleting/recreating the store on a
+# re-run and avoids directory-mtime quirks (same touch() discipline as sopa).
+STAGE_OK = f"{STAGE}.done"
 
 
 def occupied_done(wildcards):

workflow/rules/segment.smk

@@ -5,7 +5,7 @@ checkpoint prepare:
         IMAGE_OK,
     output:
         tiles=TILES,
-        stage=directory(STAGE),
+        stage=touch(STAGE_OK),
     script:
         "../scripts/prepare_tiles.py"
 
@@ -14,7 +14,7 @@ rule segment:
     """Segment one tile on a GPU and write it into the stage store."""
     input:
         tiles=TILES,
-        stage=STAGE,
+        stage=STAGE_OK,
         image=IMAGE_OK,
     output:
         f"{WORK}/seg/{{index}}.done",