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This version of GitHub Enterprise was discontinued on 2023-01-18. No patch releases will be made, even for critical security issues. For better performance, improved security, and new features, upgrade to the latest version of GitHub Enterprise. For help with the upgrade, contact GitHub Enterprise support.

Configuring code scanning for a repository

In this article

You can configure code scanning for a repository to find security vulnerabilities in your code.

Who can use this feature

If you have write permissions to a repository, you can configure code scanning for that repository.

Code scanning is available for organization-owned repositories in GitHub Enterprise Server. This feature requires a license for GitHub Advanced Security. For more information, see "About GitHub Advanced Security."

Note: Your site administrator must enable code scanning for your GitHub Enterprise Server instance before you can use this feature. If you want to use GitHub Actions to scan your code, the site administrator must also enable GitHub Actions and set up the infrastructure required. For more information, see "Configuring code scanning for your appliance."

Options for configuring code scanning

You decide how to generate code scanning alerts, and which tools to use, at a repository level. GitHub Enterprise Server provides fully integrated support for CodeQL analysis, and also supports analysis using third-party tools. For more information, see the following bullets and "About code scanning."

Note: If you want to use the CodeQL analysis, note that this article describes the features available with the version of the CodeQL action and associated CodeQL CLI bundle included in the initial release of this version of GitHub Enterprise Server. If your enterprise uses a more recent version of the CodeQL action, see the GitHub Enterprise Cloud article for information on the latest features. For information on using the latest version, see "Configuring code scanning for your appliance."

Configuring code scanning manually

  1. On your GitHub Enterprise Server instance, navigate to the main page of the repository.

  2. Under the repository name, click Security. Security tab

  3. To the right of "Code scanning alerts", click Set up code scanning. If code scanning is missing, you need to ask an organization owner or repository administrator to enable GitHub Advanced Security. For more information, see "Managing security and analysis settings for your organization" or "Managing security and analysis settings for your repository." "Set up code scanning" button to the right of "Code scanning" in the Security Overview

  4. Under "Get started with code scanning", click Set up this workflow on the CodeQL analysis workflow or on a third-party workflow. "Set up this workflow" button under "Get started with code scanning" headingWorkflows are only displayed if they are relevant for the programming languages detected in the repository. The CodeQL analysis workflow is always displayed, but the "Set up this workflow" button is only enabled if CodeQL analysis supports the languages present in the repository.

  5. To customize how code scanning scans your code, edit the workflow.

    Generally, you can commit the CodeQL analysis workflow without making any changes to it. However, many of the third-party workflows require additional configuration, so read the comments in the workflow before committing.

    For more information, see "Customizing code scanning."

  6. Use the Start commit drop-down, and type a commit message. Start commit

  7. Choose whether you'd like to commit directly to the default branch, or create a new branch and start a pull request. Choose where to commit

  8. Click Commit new file or Propose new file.

In the suggested CodeQL analysis workflow, code scanning is configured to analyze your code each time you either push a change to the default branch or any protected branches, or raise a pull request against the default branch. As a result, code scanning will now commence.

The on:pull_request and on:push triggers for code scanning are each useful for different purposes. For more information, see "Customizing code scanning."

Bulk configuration of code scanning

You can configure code scanning in many repositories at once using a script. If you'd like to use a script to raise pull requests that add a GitHub Actions workflow to multiple repositories, see the jhutchings1/Create-ActionsPRs repository for an example using PowerShell, or nickliffen/ghas-enablement for teams who do not have PowerShell and instead would like to use NodeJS.

Viewing the logging output from code scanning

After configuring code scanning for your repository, you can watch the output of the actions as they run.

  1. Under your repository name, click Actions. Actions tab in the main repository navigation

    You'll see a list that includes an entry for running the code scanning workflow. The text of the entry is the title you gave your commit message.

    Actions list showing code scanning workflow

  2. Click the entry for the code scanning workflow.

  3. Click the job name on the left. For example, Analyze (LANGUAGE).

    Log output from the code scanning workflow

  4. Review the logging output from the actions in this workflow as they run.

  5. Once all jobs are complete, you can view the details of any code scanning alerts that were identified. For more information, see "Managing code scanning alerts for your repository."

Note: If you raised a pull request to add the code scanning workflow to the repository, alerts from that pull request aren't displayed directly on the Code scanning page until the pull request is merged. If any alerts were found you can view these, before the pull request is merged, by clicking the NUMBER alerts found link in the banner on the Code scanning page.

Click the "n alerts found" link

Understanding the pull request checks

Each code scanning workflow you set to run on pull requests always has at least two entries listed in the checks section of a pull request. There is one entry for each of the analysis jobs in the workflow, and a final one for the results of the analysis.

The names of the code scanning analysis checks take the form: "TOOL NAME / JOB NAME (TRIGGER)." For example, for CodeQL, analysis of C++ code has the entry "CodeQL / Analyze (cpp) (pull_request)." You can click Details on a code scanning analysis entry to see logging data. This allows you to debug a problem if the analysis job failed. For example, for code scanning analysis of compiled languages, this can happen if the action can't build the code.

code scanning pull request checks

When the code scanning jobs complete, GitHub works out whether any alerts were added by the pull request and adds the "Code scanning results / TOOL NAME" entry to the list of checks. After code scanning has been performed at least once, you can click Details to view the results of the analysis.

If you used a pull request to add code scanning to the repository, you will initially see an "Analysis not found" message when you click Details on the "Code scanning results / TOOL NAME" check.

Analysis not found for commit message

The table lists one or more categories. Each category relates to specific analyses, for the same tool and commit, performed on a different language or a different part of the code. For each category, the table shows the two analyses that code scanning attempted to compare to determine which alerts were introduced or fixed in the pull request.

For example, in the screenshot above, code scanning found an analysis for the merge commit of the pull request, but no analysis for the head of the main branch.

Reasons for the "Analysis not found" message

After code scanning has analyzed the code in a pull request, it needs to compare the analysis of the topic branch (the branch you used to create the pull request) with the analysis of the base branch (the branch into which you want to merge the pull request). This allows code scanning to compute which alerts are newly introduced by the pull request, which alerts were already present in the base branch, and whether any existing alerts are fixed by the changes in the pull request. Initially, if you use a pull request to add code scanning to a repository, the base branch has not yet been analyzed, so it's not possible to compute these details. In this case, when you click through from the results check on the pull request you will see the "Analysis not found" message.

There are other situations where there may be no analysis for the latest commit to the base branch for a pull request. These include:

  • The pull request has been raised against a branch other than the default branch, and this branch hasn't been analyzed.

    To check whether a branch has been scanned, go to the Code scanning page, click the Branch drop-down and select the relevant branch.

    Choose a branch from the Branch drop-down menu

    The solution in this situation is to add the name of the base branch to the on:push and on:pull_request specification in the code scanning workflow on that branch and then make a change that updates the open pull request that you want to scan.

  • The latest commit on the base branch for the pull request is currently being analyzed and analysis is not yet available.

    Wait a few minutes and then push a change to the pull request to retrigger code scanning.

  • An error occurred while analyzing the latest commit on the base branch and analysis for that commit isn't available.

    Merge a trivial change into the base branch to trigger code scanning on this latest commit, then push a change to the pull request to retrigger code scanning.

Next steps

After configuring code scanning, and allowing its actions to complete, you can: