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Add CodeQL workflow #4278

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102 changes: 102 additions & 0 deletions .github/workflows/codeql.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,102 @@
# 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 Advanced"

on:
push:
branches: [ "develop" ]
pull_request:
branches: [ "develop" ]
schedule:
- cron: '22 10 * * 6'

jobs:
analyze:
name: Analyze (${{ matrix.language }})
# Runner size impacts CodeQL analysis time. To learn more, please see:
# - https://gh.io/recommended-hardware-resources-for-running-codeql
# - https://gh.io/supported-runners-and-hardware-resources
# - https://gh.io/using-larger-runners (GitHub.com only)
# Consider using larger runners or machines with greater resources for possible analysis time improvements.
runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
permissions:
# required for all workflows
security-events: write

# required to fetch internal or private CodeQL packs
packages: read

# only required for workflows in private repositories
actions: read
contents: read

strategy:
fail-fast: false
matrix:
include:
- language: java-kotlin
build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
- language: python
build-mode: none
- language: actions
build-mode: none
# CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
# Use `c-cpp` to analyze code written in C, C++ or both
# Use 'java-kotlin' to analyze code written in Java, Kotlin or both
# Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
# To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
# see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
steps:
- name: Checkout repository
uses: actions/checkout@v4

# Add any setup steps before running the `github/codeql-action/init` action.
# This includes steps like installing compilers or runtimes (`actions/setup-node`
# or others). This is typically only required for manual builds.
# - name: Setup runtime (example)
# uses: actions/setup-example@v1

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
build-mode: ${{ matrix.build-mode }}
# 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.

# For more 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

# If the analyze step fails for one of the languages you are analyzing with
# "We were unable to automatically build your code", modify the matrix above
# to set the build mode to "manual" for that language. Then modify this step
# to build your code.
# 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: matrix.build-mode == 'manual'
shell: bash
run: |
echo 'If you are using a "manual" build mode for one or more of the' \
'languages you are analyzing, replace this with the commands to build' \
'your code, for example:'
echo ' make bootstrap'
echo ' make release'
exit 1

- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v3
with:
category: "/language:${{matrix.language}}"
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I think https://github.com/ome/bioformats/pull/4278/checks?check_run_id=37790317684 indicates that the analyze action is being run on the matrix of automatically detected languages, not the matrix defined in lines 44-47.

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@sbesson sbesson Feb 25, 2025

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Added the actions language manually and https://github.com/ome/bioformats/pull/4278/checks?check_run_id=37796169026 looks much better

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Seems kind of weird that's necessary, but the output does look fine now. Probably not a bad idea to run checks against python and actions anyway.