Switch LGTM to CodeQL

.github/workflows/codeql.yml

@@ -0,0 +1,29 @@
+name: "GitHub CodeQL"
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  CodeQL:
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - 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

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) [![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)
 ***

doc/install.rst

@@ -53,7 +53,7 @@ then, install the appropriate dependencies (you may want to create a new `virtua
 environment <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_) and install::
 
     $ conda install --file requirements.txt --channel conda-forge
-    $ pip install . --no-deps
+    $ pip install .
 
 
 .. note::

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "cython"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -1,22 +1,19 @@
 from setuptools import setup
-from Cython.Build import cythonize
 from setuptools.extension import Extension
+from Cython.Build import cythonize
 
 extensions = [Extension('cconf_gen', ['autode/conformers/cconf_gen.pyx']),
               Extension('ade_dihedrals',
                         sources=['autode/ext/ade_dihedrals.pyx'],
                         include_dirs=['autode/ext/include'],
                         language='c++',
-                        extra_compile_args=["-std=c++11",
-                                            "-Wno-missing-braces", "-O3"],
+                        extra_compile_args=["-std=c++11", "-Wno-missing-braces", "-O3"],
                         extra_link_args=["-std=c++11"]),
-
               Extension('ade_rb_opt',
                         sources=['autode/ext/ade_rb_opt.pyx'],
                         include_dirs=['autode/ext/include'],
                         language='c++',
-                        extra_compile_args=["-std=c++11",
-                                            "-Wno-missing-braces", "-O3"],
+                        extra_compile_args=["-std=c++11", "-Wno-missing-braces", "-O3"],
                         extra_link_args=["-std=c++11"])]
 
 setup(name='autode',