update workflows (#17)

* Delete .github/workflows/conventional-prs.yml
* update test workflow based on scattr
* limit to python 3.11, since 3.12 was failing tests
* add dev dependencies with updated snakefmt (needed for github action)
* formatting with updated snakefmt

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+---
+name: Lint and test workflow
+on:
+  push:
+    branches: ['*', '!push-action/*']
+  pull_request:
+    branches: ['*', '!push-action/*']
+jobs:
+  quality:
+    name: Lint code
+    if: github.event.pull_request.merged == false
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python environment
+        uses: khanlab/actions/.github/actions/[email protected]
+        with:
+          python-version: '3.11'
+      - name: snakemake lint
+        run: poetry run snakemake --lint
+      - name: snakefmt
+        run: poetry run snakefmt --check workflow
+  test:
+    runs-on: ubuntu-latest
+    needs: [quality]
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - name: Setup Python environments
+        uses: khanlab/actions/.github/actions/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+          install-library: true
+      - name: Integration dry-run test
+        run: poetry run snakemake -np

pyproject.toml

@@ -7,11 +7,14 @@ readme = "README.md"
 packages = []
 
 [tool.poetry.dependencies]
-python = ">=3.11,<3.13"
+python = ">=3.11,<3.12"
 snakemake = "<8.0.0"
 pulp = "2.7.0"
 snakebids = "0.11.0"
 
+[tool.poetry.group.dev.dependencies]
+snakefmt = "^0.10.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

workflow/rules/common.smk

@@ -18,9 +18,9 @@ def get_all_targets():
                 subject=datasets.loc[i, "subject"],
                 sample=datasets.loc[i, "sample"],
                 acq=datasets.loc[i, "acq"],
-                extension="ome.zarr.zip"
-                if config["ome_zarr"]["use_zipstore"]
-                else "ome.zarr",
+                extension=(
+                    "ome.zarr.zip" if config["ome_zarr"]["use_zipstore"] else "ome.zarr"
+                ),
             )
         )
         targets.extend(