From 4e063fed0fb32ff385b514518849258126a2e618 Mon Sep 17 00:00:00 2001
From: Ezra Peisach <ezra.peisach@rcsb.org>
Date: Sat, 11 Jul 2020 23:23:08 -0400
Subject: [PATCH 1/2] Add codeql

---
 .github/workflows/codeql-analysis.yml | 63 +++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 .github/workflows/codeql-analysis.yml

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
new file mode 100644
index 0000000..b3b8cd6
--- /dev/null
+++ b/.github/workflows/codeql-analysis.yml
@@ -0,0 +1,63 @@
+name: "Code scanning - action"
+
+on:
+  push:
+    branches: [master, development]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [master, development]
+  schedule:
+    - cron: '0 15 * * 6'
+
+jobs:
+  CodeQL-Build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+        submodules: true
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    - name: Install dependencies
+      run: |
+           sudo apt-get clean
+           sudo apt-get install flex bison
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      # Override language selection by uncommenting this and choosing your languages
+      # with:
+      #   languages: go, javascript, csharp, python, cpp, java
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    #- name: Autobuild
+    #  uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+    - name: configure
+      run: mkdir build && cd build && cmake ..
+    - name: build
+      run: cmake --build build
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

From 94f776fd2b817ce307c0f4186109cdb45e7456d5 Mon Sep 17 00:00:00 2001
From: Ezra Peisach <ezra.peisach@rcsb.org>
Date: Sat, 11 Jul 2020 23:30:38 -0400
Subject: [PATCH 2/2] Declare C++

---
 .github/workflows/codeql-analysis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index b3b8cd6..c6cb33c 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -36,8 +36,8 @@ jobs:
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v1
       # Override language selection by uncommenting this and choosing your languages
-      # with:
-      #   languages: go, javascript, csharp, python, cpp, java
+      with:
+        languages: cpp
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)