patchworks 0.11.0__tar.gz → 0.11.1__tar.gz

{patchworks-0.11.0 → patchworks-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 0.11.0
+Version: 0.11.1
 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-0.11.1}/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 +174,24 @@ 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).
 
+## 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-0.11.0 → patchworks-0.11.1}/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-0.11.1/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"