patchworks 0.11.0__tar.gz → 0.11.2__tar.gz

{patchworks-0.11.0 → patchworks-0.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.11.0
+Version: 0.11.2
 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-0.11.0 → patchworks-0.11.2}/docs/guide/snakemake.md

@@ -34,8 +34,9 @@ pip install "patchworks[workflow,cellpose,imaris,bioio]"
 - `cellpose` → the segmentation model
 - `imaris` / `bioio` → read your input format (`.ims`, `.czi`, `.lif`, …)
 
-On a cluster, do this inside a conda/venv that the compute nodes can see, or let
-each rule activate a conda env (see *Conda*, below).
+On a cluster, do this inside a conda/venv/pixi env that the compute nodes can
+see, or let each rule activate a conda env. Prefer pixi? Skip this step — the
+workflow ships a `pixi.toml`; see *pixi (instead of conda)*, below.
 
 ## 3. Configure the run
 
@@ -173,6 +174,29 @@ Snakemake is resumable — if jobs fail or you cancel, just relaunch the same
 command and it picks up only the missing tiles. To force a clean rerun, delete
 `work_dir` (or the relevant outputs).
 
+The OME-ZARR conversion is **not redone** once `image.zarr` exists: the
+`convert` rule's output is a marker file inside the store, so Snakemake skips it
+on every later run. To force a fresh conversion, delete `image.zarr` or run
+`snakemake --forcerun convert`.
+
+## pixi (instead of conda)
+
+Conda is **not** required — Snakemake runs in whatever environment launches it.
+The workflow ships a `pixi.toml`, so the whole thing is:
+
+```bash
+cd workflow
+pixi install          # builds the env (patchworks + snakemake + readers)
+pixi run dry          # dry-run
+pixi run go           # run locally (8 cores)
+pixi run slurm        # submit to SLURM (edit profile/slurm/config.yaml first)
+```
+
+`pixi run …` activates the env, so the rule scripts execute in that env — do
+**not** pass `--use-conda`. On a cluster, keep the `workflow/` directory on a
+shared filesystem the compute nodes can read: the SLURM executor re-launches
+Snakemake from this env's interpreter on each compute node.
+
 ## Conda (optional)
 
 To have each rule run in a named conda env instead of the active one, add

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvbGFiZWxzLmRvbmU=

@@ -0,0 +1 @@
+{"rule": "merge", "input": ["/tmp/pw_wf/out/seg/0.done", "/tmp/pw_wf/out/seg/1.done", "/tmp/pw_wf/out/seg/2.done", "/tmp/pw_wf/out/seg/3.done", "/tmp/pw_wf/out/seg/4.done", "/tmp/pw_wf/out/seg/5.done", "/tmp/pw_wf/out/seg/6.done", "/tmp/pw_wf/out/seg/7.done"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/merge.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289946198395, "starttime": 1782306826.05809, "endtime": 1782306826.057891, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/seg/0.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/1.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/2.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/3.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/4.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/5.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/6.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/pw_wf/out/seg/7.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzAuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938895482, "starttime": 1782306823.2564273, "endtime": 1782306823.255227, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzEuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938895635, "starttime": 1782306823.2361996, "endtime": 1782306823.2352273, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzIuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938895788, "starttime": 1782306820.7251186, "endtime": 1782306820.724245, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzMuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938792521, "starttime": 1782306820.8450873, "endtime": 1782306820.8442442, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzQuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938792674, "starttime": 1782306820.7828398, "endtime": 1782306820.7822447, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzUuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938792827, "starttime": 1782306823.5588164, "endtime": 1782306823.558225, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzYuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938792980, "starttime": 1782306823.0890763, "endtime": 1782306823.0882282, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc2VnLzcuZG9uZQ==

@@ -0,0 +1 @@
+{"rule": "segment", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json", "/tmp/pw_wf/out/stage.zarr", "/tmp/pw_wf/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289938793133, "starttime": 1782306821.0048127, "endtime": 1782306821.0042431, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/tiles.json": "sha256:d5abe0a9301e6274b02cdae545a8b5e414d3b51c1396d18ae9bcb1ea935bfe67", "/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvc3RhZ2UuemFycg==

@@ -0,0 +1 @@
+{"rule": "prepare", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/prepare_tiles.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289946375343, "starttime": 1782306818.2703326, "endtime": 1782306818.2701185, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

patchworks-0.11.2/workflow/.snakemake/metadata/L3RtcC9wd193Zi9vdXQvdGlsZXMuanNvbg==

@@ -0,0 +1 @@
+{"rule": "prepare", "input": ["/tmp/pw_wf/out/image.zarr/zarr.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/prepare_tiles.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 8289946375343, "starttime": 1782306818.2703326, "endtime": 1782306818.2692626, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/pw_wf/out/image.zarr/zarr.json": "sha256:8baa9bb439818b6e4a5358464300e6239dae6fddb2b31fa26717a7c56eaf1458"}}

{patchworks-0.11.0 → patchworks-0.11.2}/workflow/README.md

@@ -38,6 +38,15 @@ pip install "patchworks[workflow,cellpose,imaris,bioio]"
 # workflow → snakemake + the SLURM executor plugin
 ```
 
+Prefer pixi? No conda needed — a `pixi.toml` is included:
+
+```bash
+pixi install
+pixi run dry    # dry-run
+pixi run go     # run locally
+pixi run slurm  # submit to SLURM
+```
+
 ## Configure
 
 Edit `config/config.yaml` (input, output dir, channel, tile shape, Cellpose

{patchworks-0.11.0 → patchworks-0.11.2}/workflow/config/config.yaml

@@ -15,6 +15,8 @@ work_dir: "/path/to/results" # everything is written under here
 reuse_pyramid: true # for .ims: copy its own pyramid (fast); else rebuild
 convert_chunks: null # null → patchworks' bounded auto chunks; or [c,z,y,x]
 shard: false # true → pack chunks into shards (zarr v3; fewer files)
+# Re-running reuses an existing image.zarr automatically (skips conversion).
+# To force a rebuild: delete image.zarr, or `snakemake --forcerun convert`.
 
 # ---- tiling -----------------------------------------------------------------
 channel: 0 # channel to segment

patchworks-0.11.2/workflow/pixi.toml

@@ -0,0 +1,24 @@
+# pixi environment for the patchworks Snakemake workflow.
+#   pixi install
+#   pixi run dry      # dry-run (plan only)
+#   pixi run go       # run locally
+#   pixi run slurm    # submit to SLURM (edit profile/slurm/config.yaml first)
+#
+# On a cluster, put this project on a shared filesystem the compute nodes can
+# read: the SLURM jobs re-launch snakemake from this env's interpreter.
+
+[project]
+name = "patchworks-workflow"
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[dependencies]
+python = "3.12.*"
+
+[pypi-dependencies]
+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"
+slurm = "snakemake --workflow-profile profile/slurm --configfile config/config.yaml"

{patchworks-0.11.0 → patchworks-0.11.2}/workflow/rules/common.smk

@@ -2,6 +2,11 @@
 
 WORK = config["work_dir"]
 IMAGE = f"{WORK}/image.zarr"
+# A single file inside the store, used as the convert rule's output and as the
+# dependency marker for downstream rules. Tracking a leaf file (not the
+# directory) lets Snakemake skip conversion when the store already exists and
+# avoids wiping the whole store on a re-run (same trick as imcf/sopa).
+IMAGE_OK = f"{IMAGE}/zarr.json"
 TILES = f"{WORK}/tiles.json"
 STAGE = f"{WORK}/stage.zarr"
 

{patchworks-0.11.0 → patchworks-0.11.2}/workflow/rules/convert.smk

@@ -2,6 +2,7 @@
 
 rule convert:
     output:
-        directory(IMAGE),
+        # marker file inside the store; existence => skip re-conversion.
+        IMAGE_OK,
     script:
         "../scripts/convert.py"

{patchworks-0.11.0 → patchworks-0.11.2}/workflow/rules/segment.smk

@@ -2,7 +2,7 @@
 
 checkpoint prepare:
     input:
-        IMAGE,
+        IMAGE_OK,
     output:
         tiles=TILES,
         stage=directory(STAGE),
@@ -15,7 +15,7 @@ rule segment:
     input:
         tiles=TILES,
         stage=STAGE,
-        image=IMAGE,
+        image=IMAGE_OK,
     output:
         f"{WORK}/seg/{{index}}.done",
     script:

patchworks-0.11.2/workflow/scripts/convert.py

@@ -0,0 +1,21 @@
+"""Snakemake script: convert the input to a pyramidal OME-ZARR.
+
+The rule's output is a marker file inside the store (``image.zarr/zarr.json``),
+so Snakemake skips this step entirely when the store already exists — the
+conversion is not redone. To force a fresh conversion, delete ``image.zarr``
+(or run ``snakemake --forcerun convert``).
+"""
+
+from patchworks.plugins.ome_zarr import to_ome_zarr
+
+cfg = snakemake.config  # noqa: F821  (injected by Snakemake)
+chunks = cfg.get("convert_chunks")
+to_ome_zarr(
+    cfg["input"],
+    str(snakemake.output[0]).removesuffix("/zarr.json"),  # noqa: F821
+    chunks=tuple(chunks) if chunks else None,
+    shard=bool(cfg.get("shard", False)),
+    reuse_pyramid=bool(cfg.get("reuse_pyramid", False)),
+    progress=False,
+    overwrite=True,
+)

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L2ltYWdlLnphcnI=

@@ -1 +0,0 @@
-{"rule": "convert", "input": [], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/convert.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968324357465, "starttime": 1782285191.3091571, "endtime": 1782285191.3090107, "incomplete": false, "external_jobid": null, "input_checksums": {}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L2xhYmVscy5kb25l

@@ -1 +0,0 @@
-{"rule": "merge", "input": ["/tmp/toy/out/seg/0.done", "/tmp/toy/out/seg/1.done", "/tmp/toy/out/seg/3.done", "/tmp/toy/out/seg/4.done"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/merge.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968324177309, "starttime": 1782285198.9120235, "endtime": 1782285198.9118745, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/toy/out/seg/0.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/toy/out/seg/1.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/toy/out/seg/3.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "/tmp/toy/out/seg/4.done": "sha256:e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3N0YWdlLnphcnI=

@@ -1 +0,0 @@
-{"rule": "prepare", "input": ["/tmp/toy/out/image.zarr"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/prepare_tiles.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968324357329, "starttime": 1782285193.0925362, "endtime": 1782285193.0922585, "incomplete": false, "external_jobid": null, "input_checksums": {}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3NlZy80LmRvbmU=

@@ -1 +0,0 @@
-{"rule": "segment", "input": ["/tmp/toy/out/image.zarr", "/tmp/toy/out/stage.zarr", "/tmp/toy/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968316803128, "starttime": 1782285194.9512916, "endtime": 1782285194.9498596, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/toy/out/tiles.json": "sha256:a7ba7de7a100b9eed2f69158d779580251e48da2c4bdb722e28c4d9a79abb411"}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3NlZy8wLmRvbmU=

@@ -1 +0,0 @@
-{"rule": "segment", "input": ["/tmp/toy/out/image.zarr", "/tmp/toy/out/stage.zarr", "/tmp/toy/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968316911209, "starttime": 1782285194.9791708, "endtime": 1782285194.9778593, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/toy/out/tiles.json": "sha256:a7ba7de7a100b9eed2f69158d779580251e48da2c4bdb722e28c4d9a79abb411"}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3NlZy8xLmRvbmU=

@@ -1 +0,0 @@
-{"rule": "segment", "input": ["/tmp/toy/out/image.zarr", "/tmp/toy/out/stage.zarr", "/tmp/toy/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968316911362, "starttime": 1782285196.8732357, "endtime": 1782285196.871846, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/toy/out/tiles.json": "sha256:a7ba7de7a100b9eed2f69158d779580251e48da2c4bdb722e28c4d9a79abb411"}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3NlZy8zLmRvbmU=

@@ -1 +0,0 @@
-{"rule": "segment", "input": ["/tmp/toy/out/image.zarr", "/tmp/toy/out/stage.zarr", "/tmp/toy/out/tiles.json"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/segment_tile.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968316911515, "starttime": 1782285196.9122667, "endtime": 1782285196.9108458, "incomplete": false, "external_jobid": null, "input_checksums": {"/tmp/toy/out/tiles.json": "sha256:a7ba7de7a100b9eed2f69158d779580251e48da2c4bdb722e28c4d9a79abb411"}}

patchworks-0.11.0/workflow/.snakemake/metadata/L3RtcC90b3kvb3V0L3RpbGVzLmpzb24=

@@ -1 +0,0 @@
-{"rule": "prepare", "input": ["/tmp/toy/out/image.zarr"], "log": [], "shellcmd": null, "params": [], "code": "        \"../scripts/prepare_tiles.py\"\n", "record_format_version": 6, "conda_env": null, "container_img_url": null, "software_stack_hash": "d41d8cd98f00b204e9800998ecf8427e", "job_hash": 7968324357329, "starttime": 1782285193.0925362, "endtime": 1782285193.0908728, "incomplete": false, "external_jobid": null, "input_checksums": {}}

patchworks-0.11.0/workflow/scripts/convert.py

@@ -1,15 +0,0 @@
-"""Snakemake script: convert the input to a pyramidal OME-ZARR."""
-
-from patchworks.plugins.ome_zarr import to_ome_zarr
-
-cfg = snakemake.config  # noqa: F821  (injected by Snakemake)
-chunks = cfg.get("convert_chunks")
-to_ome_zarr(
-    cfg["input"],
-    snakemake.output[0],  # noqa: F821
-    chunks=tuple(chunks) if chunks else None,
-    shard=bool(cfg.get("shard", False)),
-    reuse_pyramid=bool(cfg.get("reuse_pyramid", False)),
-    progress=False,
-    overwrite=True,
-)