add linter

.github/workflows/linter.yml

@@ -0,0 +1,56 @@
+---
+name: Lint Code Base
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  linter:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    permissions:
+      contents: read
+      packages: read
+      # To report GitHub Actions status checks
+      statuses: write
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+          #      - name: Install conda environment dependencies
+          #        uses: conda-incubator/setup-miniconda@v2
+          #        with:
+          #          miniforge-version: latest
+          #          miniforge-variant: Mambaforge
+          #          mamba-version: "*"
+          #          channels: conda-forge,bioconda
+          #          channel-priority: strict
+          #          activate-environment: JupyText
+          #          auto-update-conda: true
+          #          environment-file: tests/conda_snk_env.yaml
+
+  #     - name: Set up Python
+  #       uses: actions/setup-python@v5
+  #       with:
+  #         python-version: '3.12'
+  #         architecture: 'x64'
+
+      - name: Super-linter
+        uses: super-linter/[email protected] 
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+          #VALIDATE_SNAKEMAKE_LINT: true
+          PYTHON_RUFF_CONFIG_FILE: .ruff.toml
+          VALIDATE_PYTHON_RUFF: true
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.ruff.toml

@@ -0,0 +1,77 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.8
+target-version = "py38"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "single"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"

README.md

@@ -1,3 +1,4 @@
 # mixmax
+[![Super-Linter](https://github.com/JohannesGawron/DNA-ADT-analysis/actions/workflows/linter.yml/badge.svg)](https://github.com/marketplace/actions/super-linter)
 
 A python tool to develop cost efficient and robust multiplexing strategies for single-cell genomics and transcriptomics data that allows sample identification after demultiplexing.