chore: add lock files and top-level check commands (#1)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **Chores**
* Added automated linting checks for Snakemake workflows to the CI
pipeline
  * Enhanced development task automation and configuration

* **Documentation**
* Updated contributor guidelines with current development commands and
procedures

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: ameynert

.github/workflows/python_package.yml

@@ -14,7 +14,8 @@ jobs:
       matrix:
         PYTHON_VERSION: ["3.12", "3.13"]
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - name: Checkout from GitHub
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
 
       - name: Install uv
         uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57  # v8.0.0
@@ -26,5 +27,4 @@ jobs:
 
       - name: Test the library
         run: |
-          uv run --locked poe check-all
-
+          uv run --directory divref --locked poe check-all

.github/workflows/workflow_linting.yml

@@ -0,0 +1,24 @@
+name: Snakemake linting check
+
+on: 
+  push:
+
+env:
+  PIXI_VERSION: v0.65.0
+
+jobs:
+  Tests:
+    runs-on: ubuntu-latest
+    environment: github-actions-snakemake-linting
+    steps:
+      - name: Checkout from GitHub
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961  # v0.8.10
+        with:
+          pixi-version: ${{ env.PIXI_VERSION }}
+          cache: true
+
+      - name: Run linting
+        run: pixi run lint --check

CONTRIBUTING.md

@@ -5,71 +5,77 @@
 To check and resolve linting issues in the codebase, run:
 
 ```console
-uv run ruff check --fix
+uv run --directory divref ruff check --fix
 ```
 
 To check and resolve formatting issues in the codebase, run:
 
 ```console
-uv run ruff format
+uv run --directory divref ruff format
 ```
 
 To check the unit tests in the codebase, run:
 
 ```console
-uv run pytest
+uv run --directory divref pytest
 ```
 
 To check the typing in the codebase, run:
 
 ```console
-uv run mypy
+uv run --directory divref mypy
 ```
 
 To generate a code coverage report after testing locally, run:
 
 ```console
-uv run coverage html
+uv run --directory divref coverage html
 ```
 
-To check the lock file is up to date:
+To check the `uv` lock file is up to date:
 
 ```console
-uv lock --check
+uv lock --directory divref --check
+```
+
+To check the `pixi` lock file is up to date:
+
+```console
+pixi run check-lock
 ```
 
 ## Shortcut Task Commands
 
-###### For Running Individual Checks
+###### For Running Individual Toolkit Checks
 
 ```console
-uv run poe check-format
-uv run poe check-lint
-uv run poe check-tests
-uv run poe check-typing
+uv run --directory divref poe check-format
+uv run --directory divref poe check-lint
+uv run --directory divref poe check-tests
+uv run --directory divref poe check-typing
 ```
 
-###### For Running All Checks
+###### For Running All Toolkit Checks
 
 ```console
-uv run poe check-all
+pixi run check-toolkit
 ```
 
 ###### For Running Individual Fixes
 
 ```console
-uv run poe fix-format
-uv run poe fix-lint
+uv run --directory divref poe fix-format
+uv run --directory divref poe fix-lint
 ```
 
 ###### For Running All Fixes
 
 ```console
-uv run poe fix-all
+uv run --directory divref poe fix-all
 ```
 
 ###### For Running All Fixes and Checks
 
 ```console
-uv run poe fix-and-check-all
+pixi run fix-and-check-all
 ```

divref/uv.lock

@@ -8,6 +8,7 @@ version = "0.1.0"
 [feature.snakemake.dependencies]
 python = ">=3.12.8,<3.13"
 snakemake-minimal = ">=8.28.0,<9.0"
+snakefmt = ">=1.0.0,<2"
 
 [pypi-dependencies]
 divref = { path = "./divref", editable = true }
@@ -16,4 +17,20 @@ divref = { path = "./divref", editable = true }
 default = { features = ["snakemake"] }
 
 [tasks]
+check-toolkit = "uv run --directory divref poe check-all"
+fix-and-check-toolkit = "uv run --directory divref poe fix-and-check-all"
+
+check-lock   = "pixi lock --check"
+
+check-all = [
+    { task = "check-toolkit" },
+    { task = "check-lock" },
+]
+
+fix-and-check-all = [
+    { task = "fix-and-check-toolkit" },
+    { task = "check-lock" },
+]
+
+lint = "snakefmt --line-length 100 workflows/*.smk"
 download = "snakemake -j1 -s workflows/download.smk"

pixi.lock

@@ -1,7 +1,9 @@
 from snakemake.utils import validate
 
+
 configfile: os.path.join(workflow.basedir, "config", "config.yml")
 
+
 validate(config, os.path.join(workflow.basedir, "config", "config_schema.yml"))
 
 SAMPLES = config["samples"]