Merge pull request #511 from avcopan/dev

New: Formatting, linting, type-checking

.github/workflows/test.yaml

@@ -1,23 +1,25 @@
 name: test
 
-on: [push, pull_request]
+on: 
+  push:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
+  # Run tests
   test:
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
 
-    name: test
-    runs-on: ubuntu-latest
-
     steps:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      - name: Download central config files
+      - name: Download environment files
         run: |
-          wget https://raw.githubusercontent.com/avcopan/amech-dev/main/pixi.toml
-          wget https://raw.githubusercontent.com/avcopan/amech-dev/main/pixi.lock
+          wget https://raw.githubusercontent.com/Auto-Mech/amech-dev/main/pixi.toml
+          wget https://raw.githubusercontent.com/Auto-Mech/amech-dev/main/pixi.lock
 
       - name: Set up Pixi
         uses: prefix-dev/[email protected]
@@ -26,13 +28,17 @@ jobs:
         run: |
           pixi run pip install . --no-deps
 
-      - name: Run linter
+      - name: Lint (new)
+        run: |
+          pixi run ./lint.sh
+
+      - name: Lint (old)
         run: |
           pixi run pylint --rcfile=.pylintrc automol
           pixi run pylint --rcfile=.pylintrc phydat
           pixi run pylint --rcfile=.pylintrc autoreact
 
-      - name: Run pytests
+      - name: Test
         run: |
           pixi run pytest -v automol -v automol --ignore=automol/tests/test_convert.py
           pixi run pytest -v autoreact

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+        exclude: docs/
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.291
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+        exclude: docs/
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        exclude: docs/

automol/error.py

@@ -1,10 +1,9 @@
-""" Library of automol errors.
-"""
+"""Library of automol errors."""
 
 
 class FailedGeometryGenerationError(RuntimeError):
-    """ exception for when we fail to generate a correct geometry """
+    """exception for when we fail to generate a correct geometry."""
 
 
 class FailedInchiGenerationError(RuntimeError):
-    """ exception for when we fail to generate a correct inchi """
+    """exception for when we fail to generate a correct inchi."""

automol/inchi_key.py

@@ -1,5 +1,4 @@
-""" ChIKeys
-"""
+"""ChIKeys."""
 
 import pyparsing as pp
 
@@ -20,7 +19,7 @@
 
 
 def to_dict(chk: str) -> dict:
-    """Split the ChI key into a dictionary of parsed elements
+    """Split the ChI key into a dictionary of parsed elements.
 
     :param chk: The ChI key
     :type chk: str