fix: use pydantic models for validation (#496)

Co-authored-by: Eric Blanc <[email protected]>
Co-authored-by: Nicolai-vKuegelgen <[email protected]>

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -42,10 +42,9 @@ jobs:
         uses: marocchino/[email protected]
         with:
           message: |
-            - Please format your Python code with [black](https://black.readthedocs.io): `make black`
+            - Please format your Python code with [ruff](https://docs.astral.sh/ruff/): `make fmt`
+            - Please check your Python code with [ruff](https://docs.astral.sh/ruff/): `make check`
             - Please format your Snakemake code with [snakefmt](https://github.com/snakemake/snakefmt): `make snakefmt`
-            - Please organize your imports [isorts](https://isort.readthedocs.io): `make isort`
-            - Please ensure that your code passes [flake8](https://flake8.pycqa.org/en/latest/): `make flake8`
 
             You can trigger all lints locally by running `make lint`
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -58,11 +57,12 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
-            pip install -r requirements/test.txt
+            pip install -r requirements/base.txt -r requirements/test.txt
+            pip install -e .
             pip freeze
 
       - name: Build documentation
@@ -75,7 +75,7 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.10"
+          - "3.12"
           # - "3.11"  # no compatible pysam yet
           # - "3.12"  # no compatible pysam yet
     needs: linting
@@ -95,7 +95,7 @@ jobs:
       - name: Prepare environment.yml file
         run: >
           cp environment.yml /tmp/environment.yml && sed -i -e
-          's/- python/- python=${{ matrix.python-version }}/'
+          's/- python=.*/- python=${{ matrix.python-version }}/'
           /tmp/environment.yml
       - name: Update environment using mamba
         run: mamba env update --name root --file /tmp/environment.yml

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.8
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

.tests/test-workflow/config/cancer_wes/config.yaml.jinja2

@@ -23,9 +23,9 @@ step_config:
 
 
   somatic_variant_calling:
+    path_ngs_mapping: ../ngs_mapping
     tools: [mutect2]
     mutect2:
-      ngs_mapping: ../ngs_mapping
       extra_arguments: []
       window_length: 300000000
       keep_tmpdir: onerror

.tests/test-workflow/workflow/envs/snappy.yaml

@@ -4,7 +4,7 @@ channels:
 dependencies:
 
   # Fundamentals
-  - python >=3.11.0
+  - python >=3.12.0
   - pip =24
   - git-lfs =3.5
   - gcc_linux-64 =13.2

.tests/test-workflow/workflow/rules/common.smk

@@ -23,7 +23,7 @@ def folder_names(pipeline: str) -> list[str]:
 
 def reference_path() -> str:
     if chrom := config["reference"].get("chromosome", None):
-        return f"resources/refs/{chrom}.fa.gz"
+        return "resources/refs/" + chrom + ".fa.gz"
     else:
         return "resources/refs/genome.fa.gz"
 
@@ -33,8 +33,8 @@ def reference_faidx_region_string(wildcards) -> str:
     region = config["reference"].get("region", None)
     match chrom, region:
         case None, None:
-            return f""
+            return ""
         case chrom, None:
-            return f"{chrom}"
+            return chrom
         case chrom, region:
-            return f"{chrom}:{region}"
+            return chrom + ":" + region

Makefile

@@ -4,49 +4,42 @@ default: help
 .PHONY: help
 help:
 	@echo help      -- display this help
-	@echo black     -- apply black code formatter
+	@echo fmt       -- apply code formatter
 	@echo snakefmt  -- apply snakefmt code formatter
 	@echo srcfmt    -- apply black and snakefmt formatters
 	@echo lint      -- run linters
 	@echo test      -- run tests through pytest
-	@echo isort     -- run isort
+	@echo check     -- run code checker
 
-.PHONY: black
-black:
-	black -l 100 .
+.PHONY: fmt
+fmt:
+	ruff format .
 
 .PHONY: snakefmt
 snakefmt:
 	snakefmt -l 100 . --include '(\.smk$$|\.rules$$|^Snakefile)'
 
 .PHONY: srcfmt
-srcfmt: black snakefmt
+srcfmt: fmt snakefmt
 
 .PHONY: lint
-lint: flake8 lint-black lint-snakefmt lint-isort
+lint: check lint-fmt lint-snakefmt
 
-.PHONY: isort
-isort:
-	isort --force-sort-within-sections --profile=black .
+.PHONY: check
+check:
+	ruff check .
 
-.PHONY: flake8
-flake8:
-	flake8
-
-.PHONY: lint-black
-lint-black:
-	black -l 100 --check .
+.PHONY: lint-fmt
+lint-fmt:
+	ruff format --check .
 
 .PHONY: lint-snakefmt
 lint-snakefmt:
 	snakefmt -l 100 . --include '(\.smk$$|\.rules$$|^Snakefile)' --check
 
-.PHONY: lint-isort
-lint-isort:
-	isort --force-sort-within-sections --profile=black --check .
 
 test:
-	py.test
+	pytest
 
 coverage:
 	coverage report