Merge pull request #6 from AFM-SPM/ns-rse/5-pre-commit

.markdownlint-cli2.yaml

@@ -0,0 +1,17 @@
+# Configuration
+config:
+  # MD013 - line-length
+  line_length:
+    line_length: 120
+    code_blocks: false
+    tables: false
+  html:
+    allowed_elements:
+      - div
+
+# Globs
+globs:
+  - "**/*.md"
+
+# Fix any fixable errors
+fix: true

.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the ref you want to point at
+    hooks:
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+        types: [python]
+      - id: fix-byte-order-marker
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+        types: [python, yaml, markdown]
+
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.10.0
+    hooks:
+      - id: markdownlint-cli2
+        args: []
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.4
+    hooks:
+      - id: ruff
+        args: [ --fix, --exit-non-zero-on-fix ]
+
+  - repo: https://github.com/psf/black
+    rev: 23.10.1
+    hooks:
+      - id: black
+        types: [python]
+        additional_dependencies: ['click==8.0.4']
+        args: ["--extend-exclude", "topostats/plotting.py"]
+      - id: black-jupyter
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+
+  - repo: local
+    hooks:
+      - id: pylint
+        args: ["--rcfile=.pylintrc"]
+        name: Pylint
+        entry: python -m pylint
+        language: system
+        files: \.py$
+
+ci:
+  autofix_prs: true
+  autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit'
+  autoupdate_schedule: weekly
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit-autoupdate'
+  skip: [pylint] # Optionally list ids of hooks to skip on CI