From 42c27f34824e20f709433a0122ae3026ef0e457c Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Mon, 16 Jan 2023 08:52:52 -0500
Subject: [PATCH] Add CodeQL scanning build to check for quality and security

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 .github/workflows/codeql.yml | 113 +++++++++++++++++++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 .github/workflows/codeql.yml

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
new file mode 100644
index 0000000000..6a2d54dcc8
--- /dev/null
+++ b/.github/workflows/codeql.yml
@@ -0,0 +1,113 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "master" ]
+  schedule:
+    - cron: '42 6 * * 6'
+
+env:
+  QT_VERSION: 5.15.2
+  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout openchemistry
+      uses: actions/checkout@v3
+      with:
+        repository: openchemistry/openchemistry
+        submodules: recursive
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v3
+      with:
+        repository: openchemistry/avogadroapp
+        path: avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v3
+      with:
+        path: avogadrolibs
+
+    - name: Install Dependencies (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev 
+        sudo apt-get -qq install qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools libqt5x11extras5-dev libqt5svg5-dev
+
+    - name: Cache Qt
+      id: cache-qt
+      uses: actions/cache@v3
+      with:
+        path: ../Qt
+        key: ${{ runner.os }}-QtCache
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v3
+      with:
+        cached: ${{ steps.cache-qt.outputs.cache-hit }}
+        version: ${{ env.QT_VERSION }}
+
+    - name: Grab cache files
+      uses: actions/cache@v3
+      with:
+        path: |
+          ${{ runner.workspace }}/build/thirdparty
+          ${{ runner.workspace }}/build/Downloads
+        key: ${{ matrix.config.name }}-thirdparty
+
+    - name: Configure
+      run: |
+        cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=RelWithDebInfo ${{matrix.config.cmake_flags}}
+      shell: bash
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        source-root: ${{ github.workspace }}/avogadrolibs
+        # queries: security-extended,security-and-quality
+
+    - name: Build
+      run: |
+        cmake --build . -j 4 --config RelWithDebInfo
+      shell: bash
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
+        checkout_path: ${{ github.workspace }}/avogadrolibs