patchworks 0.11.3__tar.gz → 0.11.5__tar.gz

{patchworks-0.11.3 → patchworks-0.11.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.11.3
+Version: 0.11.5
 Summary: Tiled processing of arbitrarily large images with globally consistent labels
 Project-URL: Homepage, https://github.com/imcf/patchworks
 Project-URL: Issues, https://github.com/imcf/patchworks/issues

{patchworks-0.11.3 → patchworks-0.11.5}/docs/guide/snakemake.md

@@ -102,11 +102,14 @@ known after `prepare` decides which tiles are non-empty.)
 ## 5a. Run locally (single machine)
 
 ```bash
-python -m snakemake -s Snakefile --configfile config/config.yaml --cores 8
+python -m snakemake -s Snakefile --configfile config/config.yaml \
+    --rerun-triggers mtime --cores 8
 ```
 
 Tiles run on the local machine (one at a time on the GPU). Good for a small
-image or a smoke test.
+image or a smoke test. `--rerun-triggers mtime` re-runs only steps whose output
+is missing/stale — so upgrading patchworks won't redo the conversion (the SLURM
+profile sets this for you).
 
 ## 5b. Run on SLURM (one GPU job per tile)
 
@@ -185,6 +188,12 @@ The OME-ZARR conversion is **not redone** once `image.zarr` exists: the
 on every later run. To force a fresh conversion, delete `image.zarr` or run
 `snakemake --forcerun convert`.
 
+This relies on `--rerun-triggers mtime` (set in the SLURM profile and the pixi
+tasks; add it on the command line for ad-hoc local runs). Without it, Snakemake
+also re-runs a step when its **code, params or software environment** change —
+so upgrading patchworks would re-do the conversion and overwrite an existing
+result. Keep `mtime` and reruns happen only when an output is missing or stale.
+
 ## pixi (instead of conda)
 
 Conda is **not** required — Snakemake runs in whatever environment launches it.

{patchworks-0.11.3 → patchworks-0.11.5}/workflow/README.md

@@ -56,10 +56,11 @@ account, GPU request).
 ## Run
 
 ```bash
-# locally (single machine)
-snakemake --cores 8 --configfile config/config.yaml
+# locally (single machine) — mtime triggers => upgrades don't redo conversion
+snakemake --cores 8 --configfile config/config.yaml --rerun-triggers mtime
 
 # on SLURM — one GPU job per tile, up to `jobs:` in parallel
+# (the profile already sets --rerun-triggers mtime)
 snakemake --workflow-profile profile/slurm --configfile config/config.yaml
 ```
 

{patchworks-0.11.3 → patchworks-0.11.5}/workflow/pixi.toml

@@ -19,6 +19,8 @@ python = "3.12.*"
 patchworks = { version = "*", extras = ["workflow", "cellpose", "imaris", "bioio"] }
 
 [tasks]
-dry = "snakemake -s Snakefile --configfile config/config.yaml -n -p"
-go = "snakemake -s Snakefile --configfile config/config.yaml --cores 8"
+# --rerun-triggers mtime: don't redo finished steps (e.g. the conversion) just
+# because the patchworks version/code changed — only when an output is missing.
+dry = "snakemake -s Snakefile --configfile config/config.yaml --rerun-triggers mtime -n -p"
+go = "snakemake -s Snakefile --configfile config/config.yaml --rerun-triggers mtime --cores 8"
 slurm = "snakemake --workflow-profile profile/slurm --configfile config/config.yaml"

{patchworks-0.11.3 → patchworks-0.11.5}/workflow/profile/slurm/config.yaml

@@ -8,6 +8,10 @@ executor: slurm
 jobs: 64 # max concurrent SLURM jobs (≈ how many GPUs you can grab at once)
 latency-wait: 60
 rerun-incomplete: true
+# Only re-run when an output is missing/stale — NOT when the patchworks code,
+# params or software env change. Stops an upgrade from re-doing the expensive
+# conversion / re-segmenting an existing image.zarr.
+rerun-triggers: mtime
 printshellcmds: true
 keep-going: true
 

{patchworks-0.11.3 → patchworks-0.11.5}/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):

{patchworks-0.11.3 → patchworks-0.11.5}/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",