Merge pull request duartegroup#190 from duartegroup/v1.3.2

v1.3.2

.github/workflows/lint.yml

@@ -0,0 +1,35 @@
+name: "Lint"
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  CodeQL:
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          version: "~= 22.0"
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: python, cpp
+
+      - name: Install build requirements
+        run: pip3 install cython
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2

.github/workflows/pytest.yml

@@ -6,6 +6,10 @@ on:
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Env (${{ matrix.python-version }}, ${{ matrix.os }})

.github/workflows/pytest_cov.yml

@@ -6,6 +6,10 @@ on:
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Env (${{ matrix.python-version }}, ${{ matrix.os }})

.gitignore

@@ -1,6 +1,7 @@
 \build/
 \dist/
 \.idea/
+.eggs/
 **__MACOSX/
 autode/ext/*.cpp
 **cmake-build-debug/
@@ -18,4 +19,4 @@ tests/*.xyz
 *.so
 *.inp
 *.pyc
-**.autode_calculations
+.autode_calculations

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+        language_version: python3.9
+

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://github.com/duartegroup/autodE/actions/workflows/pytest.yml/badge.svg)](https://github.com/duartegroup/autodE/actions) [![codecov](https://codecov.io/gh/duartegroup/autodE/branch/master/graph/badge.svg)](https://codecov.io/gh/duartegroup/autodE/branch/master) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/duartegroup/autodE.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/duartegroup/autodE/context:python) [![Language grade: C/C++](https://img.shields.io/lgtm/grade/cpp/g/duartegroup/autodE.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/duartegroup/autodE/context:cpp) [![Conda Recipe](https://img.shields.io/badge/recipe-autode-green.svg)](https://anaconda.org/conda-forge/autode) [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/autode.svg)](https://anaconda.org/conda-forge/autode)
+[![Build Status](https://github.com/duartegroup/autodE/actions/workflows/pytest.yml/badge.svg)](https://github.com/duartegroup/autodE/actions) [![codecov](https://codecov.io/gh/duartegroup/autodE/branch/master/graph/badge.svg)](https://codecov.io/gh/duartegroup/autodE/branch/master) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![GitHub CodeQL](https://github.com/duartegroup/autodE/actions/workflows/codeql.yml/badge.svg)](https://github.com/duartegroup/autodE/actions/workflows/codeql.yml) [![Conda Recipe](https://img.shields.io/badge/recipe-autode-green.svg)](https://anaconda.org/conda-forge/autode) [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/autode.svg)](https://anaconda.org/conda-forge/autode)
 
 ![alt text](autode/common/llogo.png)
 ***

autode/__init__.py

@@ -8,13 +8,19 @@
 from autode.reactions.reaction import Reaction
 from autode.reactions.multistep import MultiStepReaction
 from autode.atoms import Atom
-from autode.species.molecule import (Reactant,  Product, Molecule, Species)
+from autode.species.molecule import Reactant, Product, Molecule, Species
 from autode.species.complex import NCIComplex
 from autode.config import Config
 from autode.calculations import Calculation
-from autode.wrappers.keywords import (KeywordsSet, OptKeywords,
-                                      HessianKeywords, SinglePointKeywords,
-                                      Keywords, GradientKeywords)
+from autode.wrappers.keywords import (
+    KeywordsSet,
+    OptKeywords,
+    HessianKeywords,
+    SinglePointKeywords,
+    Keywords,
+    GradientKeywords,
+)
+
 """
 Bumping the version number requires following the release proceedure:
 
@@ -32,31 +38,31 @@
   - Merge when tests pass
 """
 
-__version__ = '1.3.1'
+__version__ = "1.3.2"
 
 
 __all__ = [
-    'KeywordsSet',
-    'Keywords',
-    'OptKeywords',
-    'HessianKeywords',
-    'SinglePointKeywords',
-    'GradientKeywords',
-    'Reaction',
-    'MultiStepReaction',
-    'Atom',
-    'Species',
-    'Reactant',
-    'Product',
-    'Molecule',
-    'NCIComplex',
-    'Config',
-    'Calculation',
-    'pes',
-    'neb',
-    'geom',
-    'methods',
-    'mol_graphs',
-    'utils',
-    'hessians'
+    "KeywordsSet",
+    "Keywords",
+    "OptKeywords",
+    "HessianKeywords",
+    "SinglePointKeywords",
+    "GradientKeywords",
+    "Reaction",
+    "MultiStepReaction",
+    "Atom",
+    "Species",
+    "Reactant",
+    "Product",
+    "Molecule",
+    "NCIComplex",
+    "Config",
+    "Calculation",
+    "pes",
+    "neb",
+    "geom",
+    "methods",
+    "mol_graphs",
+    "utils",
+    "hessians",
 ]