From 704dfcc5f9e605d3dd1abe80d60d4fb18f59bec9 Mon Sep 17 00:00:00 2001
From: Gavin Huttley <Gavin.Huttley@anu.edu.au>
Date: Mon, 26 Aug 2024 07:15:11 +1000
Subject: [PATCH 1/2] DEV: add codeql workflow

---
 .github/workflows/codeql.yml | 75 ++++++++++++++++++++++++++++++++++++
 1 file changed, 75 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 0000000..8cca1ba
--- /dev/null
+++ b/.github/workflows/codeql.yml
@@ -0,0 +1,75 @@
+# 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-ignore:
+      - master
+  pull_request:
+    branches-ignore:
+      - master
+  schedule:
+    - cron: '39 20 * * 6'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+        
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

From 380e802430b72c61230475e08dc3d548dbe89ee6 Mon Sep 17 00:00:00 2001
From: Gavin Huttley <Gavin.Huttley@anu.edu.au>
Date: Mon, 26 Aug 2024 07:25:10 +1000
Subject: [PATCH 2/2] TST: make merge test more robust

---
 tests/test_records.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/test_records.py b/tests/test_records.py
index 9e5360e..7d4587a 100644
--- a/tests/test_records.py
+++ b/tests/test_records.py
@@ -152,11 +152,9 @@ def test_merge_summed_records(DATA_DIR, brca1_coll):
     sr2 = app(names[10:20])
     rnames1 = sr1.record_names
     rnames2 = sr2.record_names
+    assert set(rnames1) != set(rnames2)
     got = dvgt_records.dvgt_final_nmost()([sr1, sr2])
-    final_selected = got.record_names
-    assert len(final_selected) == 5
-    assert set(final_selected) != set(rnames1)
-    assert set(final_selected) != set(rnames2)
+    assert len(got.record_names) == 5
 
 
 def test_dvgt_select_max(brca1_coll):