Add pre commit

.github/dependabot.yml

@@ -9,4 +9,4 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    open-pull-requests-limit: 10
+    open-pull-requests-limit: 10

.github/workflows/envs/environment.yml

@@ -4,4 +4,4 @@ channels:
 
 dependencies:
   - pip:
-    - -r ../../../requirements/requirements-test.txt
+    - -r ../../../requirements/requirements-test.txt

.github/workflows/publish-to-pypi.yml

@@ -20,12 +20,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build 
+        pip install build
     - name: Build package
       run: python -m build
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@master
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
-

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+ci:
+  autoupdate_schedule: quarterly
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.5.0'
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-builtin-literals
+      - id: check-executables-have-shebangs
+      - id: check-yaml
+      - id: debug-statements
+      - id: requirements-txt-fixer
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.2.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

.ruff.toml

@@ -0,0 +1,66 @@
+target-version = "py38"
+
+[lint]
+select = [
+    "A",
+    "B",
+    "D",
+    "E501",
+    "EM",
+    "E",
+    "F",
+    "I",
+    "ICN",
+    "ISC",
+    "N",
+    "NPY",
+    "PL",
+    "PT",
+    "RET",
+    "RUF",
+    "UP",
+    "W",
+]
+
+ignore = [
+  "D107", # Do not document __init__ separately from the class.
+  "D105",
+  "D103",
+  "D100",
+  "N806",
+  "N802",
+  "N813",
+  "PLR0913",
+  "PLR0912",
+  "PLR0915",
+  "PLR2004",
+  "ISC001",
+  "N803",
+  "D200",
+  "N999",
+]
+
+[lint.per-file-ignores]
+
+"*/__init__.py" = ["F401", # __init__.py import submodules for use by the package importer.
+"D104",
+"N999",
+"D205",
+"D415",
+"E501"
+]
+
+"tests/*.py" = ["PLR2004", # unit test value comparisons are not magic values
+                "N999",
+                "D104"
+]
+
+"docs/source/conf.py" = ["A001", # Allow copyright variable name
+                 "D", # conf.py does not need documentation
+    ]
+
+[lint.pydocstyle]
+convention = "google"
+
+[format]
+quote-style = "double"

ConservedWaterSearch/__init__.py

@@ -1,4 +1,3 @@
-"""
-ConservedWaterSearch
+"""ConservedWaterSearch
 Module for identification of conserved waters from MD trajetory
 """