patchworks 2.6.6__tar.gz → 2.6.7__tar.gz

{patchworks-2.6.6 → patchworks-2.6.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: patchworks
-Version: 2.6.6
+Version: 2.6.7
 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-2.6.6 → patchworks-2.6.7}/docs/guide/snakemake.md

@@ -415,6 +415,13 @@ results/image.zarr/labels/cyto_labels/
     up front — mainly useful to keep segmentation itself GPU-efficient
     across configs, not required for the relate step to work.)
 
+!!! tip "The relate step's log"
+    Unlike `prepare`/`segment`/`merge`, the relate step isn't a Snakemake
+    rule, so it doesn't get a `log:` directive for free. It writes its own
+    log to `<work_dir>/logs/relate.log` (override with `relate.py --log`),
+    the same tee-to-file-and-stdout behaviour as the other steps — check
+    there instead of scrolling back through `srun`'s live output.
+
 See [Relating labels across segmentations](label_relations.md) for what
 `label_relations()` returns and how to save it yourself — the cluster
 workflow's own automation is below.

{patchworks-2.6.6 → patchworks-2.6.7}/tests/test_run_multi.py

@@ -188,6 +188,19 @@ def test_relate_script_has_the_real_bookkeeping():
     assert "openpyxl" in src
 
 
+def test_relate_writes_its_own_log():
+    """relate.py runs via srun, not a Snakemake rule -- nothing else wires up
+
+    its logging (see prepare/segment/merge's `log:` directives), so main()
+    has to call start_log() itself or its output only ever streams to
+    whatever invoked srun and is gone once that terminal scrolls past it.
+    """
+    src = (_workflow_dir() / "scripts" / "relate.py").read_text()
+    assert "from _pw import start_log" in src
+    assert "start_log(" in src
+    assert '"logs" / "relate.log"' in src
+
+
 def test_relate_rechunks_mismatched_label_arrays(tmp_path):
     """A chunk-layout mismatch must be rechunked away, not require a re-run.
 

{patchworks-2.6.6 → patchworks-2.6.7}/workflow/scripts/relate.py

@@ -10,6 +10,12 @@ e.g. under srun):
     python scripts/relate.py --work-dir /path/to/work_dir \
         --image-store /path/to/work_dir/image.zarr \
         --relations '[{"a": "nuclei_labels", "b": "cyto_labels", "output": "nuclei_to_cyto.xlsx"}]'
+
+Unlike prepare/segment/merge, this doesn't run as a Snakemake rule, so nothing
+wires up its own logs/<rule>/*.log by default -- srun just streams output to
+whatever invoked it. main() calls start_log() itself instead, writing to
+<work_dir>/logs/relate.log (override with --log), the same tee-to-file-and-
+stdout behaviour the Snakemake-driven scripts get via _pw.start_log.
 """
 
 from __future__ import annotations
@@ -176,7 +182,19 @@ def main() -> None:
             "relations:"
         ),
     )
+    parser.add_argument(
+        "--log",
+        default=None,
+        help="log file path (default: <work-dir>/logs/relate.log)",
+    )
     args = parser.parse_args()
+
+    from _pw import start_log
+
+    log_path = args.log or str(Path(args.work_dir) / "logs" / "relate.log")
+    start_log(log_path)
+    print(f"[relate] logging to {log_path}", flush=True)
+
     run_relations(args.work_dir, args.image_store, json.loads(args.relations))