Merge pull request #3562 from github/henrymercer/skip-file-coverage-rollout

Prepare for rolling out skipping computing file coverage information on PRs

CHANGELOG.md

@@ -4,6 +4,12 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 
 ## [UNRELEASED]
 
+- Upcoming change: Starting April 2026, the CodeQL Action will skip collecting file coverage information on pull requests to improve analysis performance. File coverage information will still be computed on non-PR analyses. Pull request analyses will log a warning about this upcoming change. [#3562](https://github.com/github/codeql-action/pull/3562)
+
+  To opt out of this change:
+  - **Repositories owned by an organization:** Create a custom repository property with the name `github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to `true` in the repository's settings. For more information, see [Managing custom properties for repositories in your organization](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization). Alternatively, if you are using an advanced setup workflow, you can set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true` in your workflow.
+  - **User-owned repositories using default setup:** Switch to an advanced setup workflow and set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true` in your workflow.
+  - **User-owned repositories using advanced setup:** Set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true` in your workflow.
 - Fixed [a bug](https://github.com/github/codeql-action/issues/3555) which caused the CodeQL Action to fail loading repository properties if a "Multi select" repository property was configured for the repository. [#3557](https://github.com/github/codeql-action/pull/3557)
 - The CodeQL Action now loads [custom repository properties](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization) on GitHub Enterprise Server, enabling the customization of features such as `github-codeql-disable-overlay` that was previously only available on GitHub.com. [#3559](https://github.com/github/codeql-action/pull/3559)
 - Fixed the retry mechanism for database uploads. Previously this would fail with the error "Response body object should not be disturbed or locked". [#3564](https://github.com/github/codeql-action/pull/3564)

lib/analyze-action-post.js

@@ -161731,6 +161731,7 @@ var semver2 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
@@ -162188,11 +162189,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,

lib/autobuild-action.js

@@ -103784,6 +103784,7 @@ var semver2 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
@@ -104237,11 +104238,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,

lib/resolve-environment-action.js

@@ -103783,6 +103783,7 @@ var semver2 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
@@ -104228,11 +104229,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,

lib/start-proxy-action-post.js

@@ -161366,6 +161366,7 @@ var semver2 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
@@ -161594,11 +161595,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,

lib/start-proxy-action.js

@@ -120917,11 +120917,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,
@@ -121353,6 +121350,7 @@ var semver5 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(

lib/upload-sarif-action-post.js

@@ -161516,6 +161516,7 @@ var semver2 = __toESM(require_semver2());
 var RepositoryPropertyName = /* @__PURE__ */ ((RepositoryPropertyName2) => {
   RepositoryPropertyName2["DISABLE_OVERLAY"] = "github-codeql-disable-overlay";
   RepositoryPropertyName2["EXTRA_QUERIES"] = "github-codeql-extra-queries";
+  RepositoryPropertyName2["FILE_COVERAGE_ON_PRS"] = "github-codeql-file-coverage-on-prs";
   return RepositoryPropertyName2;
 })(RepositoryPropertyName || {});
 var KNOWN_REPOSITORY_PROPERTY_NAMES = new Set(
@@ -161756,11 +161757,8 @@ var featureConfig = {
   ["skip_file_coverage_on_prs" /* SkipFileCoverageOnPrs */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
-    minimumVersion: void 0
+    minimumVersion: void 0,
+    toolsFeature: "suppressesMissingFileBaselineWarning" /* SuppressesMissingFileBaselineWarning */
   },
   ["start_proxy_remove_unused_registries" /* StartProxyRemoveUnusedRegistries */]: {
     defaultValue: false,

src/environment.ts

@@ -47,6 +47,15 @@ export enum EnvVar {
   /** Whether the init action has been run. */
   INIT_ACTION_HAS_RUN = "CODEQL_ACTION_INIT_HAS_RUN",
 
+  /** Whether the deprecation warning for file coverage on PRs has been logged. */
+  DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION = "CODEQL_ACTION_DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION",
+
+  /**
+   * Set to `true` to opt out of the upcoming change that skips file coverage
+   * information on pull requests.
+   */
+  FILE_COVERAGE_ON_PRS = "CODEQL_ACTION_FILE_COVERAGE_ON_PRS",
+
   /** Whether the error for a deprecated version of the CodeQL Action was logged. */
   LOG_VERSION_DEPRECATION = "CODEQL_ACTION_DID_LOG_VERSION_DEPRECATION",
 

src/feature-flags.ts

@@ -292,11 +292,8 @@ export const featureConfig = {
   [Feature.SkipFileCoverageOnPrs]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS",
-    // For testing, this is not behind a CLI version check yet. However
-    // before rolling this out externally, we should set a minimum version here
-    // since current versions of the CodeQL CLI will log if baseline information
-    // cannot be found when interpreting results.
     minimumVersion: undefined,
+    toolsFeature: ToolsFeature.SuppressesMissingFileBaselineWarning,
   },
   [Feature.StartProxyRemoveUnusedRegistries]: {
     defaultValue: false,

src/feature-flags/properties.ts

@@ -8,12 +8,14 @@ import { RepositoryNwo } from "../repository";
 export enum RepositoryPropertyName {
   DISABLE_OVERLAY = "github-codeql-disable-overlay",
   EXTRA_QUERIES = "github-codeql-extra-queries",
+  FILE_COVERAGE_ON_PRS = "github-codeql-file-coverage-on-prs",
 }
 
 /** Parsed types of the known repository properties. */
 export type AllRepositoryProperties = {
   [RepositoryPropertyName.DISABLE_OVERLAY]: boolean;
   [RepositoryPropertyName.EXTRA_QUERIES]: string;
+  [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: boolean;
 };
 
 /** Parsed repository properties. */
@@ -23,6 +25,7 @@ export type RepositoryProperties = Partial<AllRepositoryProperties>;
 export type RepositoryPropertyApiType = {
   [RepositoryPropertyName.DISABLE_OVERLAY]: string;
   [RepositoryPropertyName.EXTRA_QUERIES]: string;
+  [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: string;
 };
 
 /** The type of functions which take the `value` from the API and try to convert it to the type we want. */
@@ -69,6 +72,7 @@ const repositoryPropertyParsers: {
 } = {
   [RepositoryPropertyName.DISABLE_OVERLAY]: booleanProperty,
   [RepositoryPropertyName.EXTRA_QUERIES]: stringProperty,
+  [RepositoryPropertyName.FILE_COVERAGE_ON_PRS]: booleanProperty,
 };
 
 /**

src/init-action.ts

@@ -48,6 +48,7 @@ import {
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
   getFileCoverageInformationEnabled,
+  logFileCoverageOnPrsDeprecationWarning,
   initCodeQL,
   initConfig,
   runDatabaseInitCluster,
@@ -343,6 +344,14 @@ async function run(startedAt: Date) {
 
     analysisKinds = await getAnalysisKinds(logger);
     const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
+    const repositoryProperties = repositoryPropertiesResult.orElse({});
+    const fileCoverageResult = await getFileCoverageInformationEnabled(
+      debugMode,
+      codeql,
+      features,
+      repositoryProperties,
+    );
+
     config = await initConfig(features, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
@@ -372,12 +381,8 @@ async function run(startedAt: Date) {
       githubVersion: gitHubVersion,
       apiDetails,
       features,
-      repositoryProperties: repositoryPropertiesResult.orElse({}),
-      enableFileCoverageInformation: await getFileCoverageInformationEnabled(
-        debugMode,
-        repositoryNwo,
-        features,
-      ),
+      repositoryProperties,
+      enableFileCoverageInformation: fileCoverageResult.enabled,
       logger,
     });
 
@@ -394,6 +399,21 @@ async function run(startedAt: Date) {
       );
     }
 
+    if (fileCoverageResult.enabledByRepositoryProperty) {
+      addNoLanguageDiagnostic(
+        config,
+        makeTelemetryDiagnostic(
+          "codeql-action/file-coverage-on-prs-enabled-by-repository-property",
+          "File coverage on PRs enabled by repository property",
+          {},
+        ),
+      );
+    }
+
+    if (fileCoverageResult.showDeprecationWarning) {
+      logFileCoverageOnPrsDeprecationWarning(logger);
+    }
+
     await checkInstallPython311(config.languages, codeql);
   } catch (unwrappedError) {
     const error = wrapError(unwrappedError);

src/init.test.ts

@@ -1,6 +1,8 @@
 import * as fs from "fs";
 import path from "path";
 
+import * as core from "@actions/core";
+import * as github from "@actions/github";
 import test, { ExecutionContext } from "ava";
 import * as sinon from "sinon";
 
@@ -11,9 +13,9 @@ import {
   checkPacksForOverlayCompatibility,
   cleanupDatabaseClusterDirectory,
   getFileCoverageInformationEnabled,
+  logFileCoverageOnPrsDeprecationWarning,
 } from "./init";
 import { KnownLanguage } from "./languages";
-import { parseRepositoryNwo } from "./repository";
 import {
   createFeatures,
   LoggedMessage,
@@ -453,13 +455,15 @@ test(
 );
 
 test("file coverage information enabled when debugMode is true", async (t) => {
-  t.true(
-    await getFileCoverageInformationEnabled(
-      true, // debugMode
-      parseRepositoryNwo("github/codeql-action"),
-      createFeatures([Feature.SkipFileCoverageOnPrs]),
-    ),
+  const result = await getFileCoverageInformationEnabled(
+    true, // debugMode
+    createStubCodeQL({}),
+    createFeatures([Feature.SkipFileCoverageOnPrs]),
+    {},
   );
+  t.true(result.enabled);
+  t.false(result.enabledByRepositoryProperty);
+  t.false(result.showDeprecationWarning);
 });
 
 test.serial(
@@ -467,43 +471,69 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(false);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        parseRepositoryNwo("github/codeql-action"),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {},
     );
+    t.true(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
+    t.false(result.showDeprecationWarning);
   },
 );
 
 test.serial(
-  "file coverage information enabled when owner is not 'github'",
+  "file coverage information enabled when feature flag is not enabled, with deprecation warning",
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        parseRepositoryNwo("other-org/some-repo"),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([]),
+      {},
     );
+    t.true(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
+    t.true(result.showDeprecationWarning);
   },
 );
 
 test.serial(
-  "file coverage information enabled when feature flag is not enabled",
+  "file coverage information enabled when repository property is set",
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.true(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        parseRepositoryNwo("github/codeql-action"),
-        createFeatures([]),
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {
+        "github-codeql-file-coverage-on-prs": true,
+      },
     );
+    t.true(result.enabled);
+    t.true(result.enabledByRepositoryProperty);
+    t.false(result.showDeprecationWarning);
+  },
+);
+
+test.serial(
+  "file coverage information enabled when env var opt-out is set",
+  async (t) => {
+    sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
+    process.env["CODEQL_ACTION_FILE_COVERAGE_ON_PRS"] = "true";
+
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {},
+    );
+    t.true(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
+    t.false(result.showDeprecationWarning);
   },
 );
 
@@ -512,12 +542,174 @@ test.serial(
   async (t) => {
     sinon.stub(actionsUtil, "isAnalyzingPullRequest").returns(true);
 
-    t.false(
-      await getFileCoverageInformationEnabled(
-        false, // debugMode
-        parseRepositoryNwo("github/codeql-action"),
-        createFeatures([Feature.SkipFileCoverageOnPrs]),
-      ),
+    const result = await getFileCoverageInformationEnabled(
+      false, // debugMode
+      createStubCodeQL({}),
+      createFeatures([Feature.SkipFileCoverageOnPrs]),
+      {},
     );
+    t.false(result.enabled);
+    t.false(result.enabledByRepositoryProperty);
+    t.false(result.showDeprecationWarning);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for org-owned repo with default setup recommends repo property",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(true);
+    github.context.payload = {
+      repository: {
+        name: "test-repo",
+        owner: { login: "test-org", type: "Organization" },
+      },
+    };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, create a custom repository property " +
+        'with the name `github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to ' +
+        "`true` in the repository's settings.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for org-owned repo with advanced setup recommends env var and repo property",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(false);
+    github.context.payload = {
+      repository: {
+        name: "test-repo",
+        owner: { login: "test-org", type: "Organization" },
+      },
+    };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`. " +
+        "Alternatively, create a custom repository property " +
+        'with the name `github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to ' +
+        "`true` in the repository's settings.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for user-owned repo with default setup recommends advanced setup",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(true);
+    github.context.payload = {
+      repository: {
+        name: "test-repo",
+        owner: { login: "test-user", type: "User" },
+      },
+    };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, switch to an advanced setup workflow and " +
+        "set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for user-owned repo with advanced setup recommends env var",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(false);
+    github.context.payload = {
+      repository: {
+        name: "test-repo",
+        owner: { login: "test-user", type: "User" },
+      },
+    };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for unknown owner type with default setup recommends advanced setup",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(true);
+    github.context.payload = { repository: undefined };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, switch to an advanced setup workflow and " +
+        "set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "file coverage deprecation warning for unknown owner type with advanced setup recommends env var",
+  (t) => {
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    sinon.stub(actionsUtil, "isDefaultSetup").returns(false);
+    github.context.payload = { repository: undefined };
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 1);
+    t.is(messages[0].type, "warning");
+    t.is(
+      messages[0].message,
+      "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+        "to improve analysis performance. File coverage information will still be computed on non-PR analyses.\n\n" +
+        "To opt out of this change, set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.",
+    );
+    t.true(exportVariableStub.calledOnce);
+  },
+);
+
+test.serial(
+  "logFileCoverageOnPrsDeprecationWarning does not log if already logged",
+  (t) => {
+    process.env["CODEQL_ACTION_DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION"] =
+      "true";
+    const exportVariableStub = sinon.stub(core, "exportVariable");
+    const messages: LoggedMessage[] = [];
+    logFileCoverageOnPrsDeprecationWarning(getRecordingLogger(messages));
+    t.is(messages.length, 0);
+    t.true(exportVariableStub.notCalled);
   },
 );

src/init.ts

@@ -1,26 +1,33 @@
 import * as fs from "fs";
 import * as path from "path";
 
+import * as core from "@actions/core";
 import * as toolrunner from "@actions/exec/lib/toolrunner";
+import * as github from "@actions/github";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";
 
 import {
   getOptionalInput,
   isAnalyzingPullRequest,
+  isDefaultSetup,
   isSelfHostedRunner,
 } from "./actions-util";
 import { GitHubApiDetails } from "./api-client";
 import { CodeQL, setupCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
+import { EnvVar } from "./environment";
 import {
   CodeQLDefaultVersionInfo,
   Feature,
   FeatureEnablement,
 } from "./feature-flags";
+import {
+  RepositoryProperties,
+  RepositoryPropertyName,
+} from "./feature-flags/properties";
 import { KnownLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
-import { RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -300,18 +307,112 @@ export function cleanupDatabaseClusterDirectory(
 
 export async function getFileCoverageInformationEnabled(
   debugMode: boolean,
-  repositoryNwo: RepositoryNwo,
+  codeql: CodeQL,
   features: FeatureEnablement,
-): Promise<boolean> {
-  return (
-    // Always enable file coverage information in debug mode
-    debugMode ||
-    // We're most interested in speeding up PRs, and we want to keep
-    // submitting file coverage information for the default branch since
-    // it is used to populate the status page.
-    !isAnalyzingPullRequest() ||
-    // For now, restrict this feature to the GitHub org
-    repositoryNwo.owner !== "github" ||
-    !(await features.getValue(Feature.SkipFileCoverageOnPrs))
-  );
+  repositoryProperties: RepositoryProperties,
+): Promise<{
+  enabled: boolean;
+  enabledByRepositoryProperty: boolean;
+  showDeprecationWarning: boolean;
+}> {
+  // Always enable file coverage information in debug mode
+  if (debugMode) {
+    return {
+      enabled: true,
+      enabledByRepositoryProperty: false,
+      showDeprecationWarning: false,
+    };
+  }
+  // We're most interested in speeding up PRs, and we want to keep
+  // submitting file coverage information for the default branch since
+  // it is used to populate the status page.
+  if (!isAnalyzingPullRequest()) {
+    return {
+      enabled: true,
+      enabledByRepositoryProperty: false,
+      showDeprecationWarning: false,
+    };
+  }
+  // If the user has explicitly opted out via an environment variable, don't
+  // show the deprecation warning.
+  if (
+    (process.env[EnvVar.FILE_COVERAGE_ON_PRS] || "").toLocaleLowerCase() ===
+    "true"
+  ) {
+    return {
+      enabled: true,
+      enabledByRepositoryProperty: false,
+      showDeprecationWarning: false,
+    };
+  }
+  // Allow repositories to opt in to file coverage information on PRs
+  // using a repository property. In this case, don't show the deprecation
+  // warning since the repository has explicitly opted in.
+  if (
+    repositoryProperties[RepositoryPropertyName.FILE_COVERAGE_ON_PRS] === true
+  ) {
+    return {
+      enabled: true,
+      enabledByRepositoryProperty: true,
+      showDeprecationWarning: false,
+    };
+  }
+  // If the feature is disabled, then maintain the previous behavior of
+  // unconditionally computing file coverage information, but warn that
+  // file coverage on PRs will be disabled in a future release.
+  if (!(await features.getValue(Feature.SkipFileCoverageOnPrs, codeql))) {
+    return {
+      enabled: true,
+      enabledByRepositoryProperty: false,
+      showDeprecationWarning: true,
+    };
+  }
+  // Otherwise, disable file coverage information on PRs to speed up analysis.
+  return {
+    enabled: false,
+    enabledByRepositoryProperty: false,
+    showDeprecationWarning: false,
+  };
+}
+
+/**
+ * Log a warning about the deprecation of file coverage information on PRs, including how to opt
+ * back in via an environment variable or repository property.
+ */
+export function logFileCoverageOnPrsDeprecationWarning(logger: Logger): void {
+  if (process.env[EnvVar.DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION]) {
+    return;
+  }
+
+  const repositoryOwnerType: string | undefined =
+    github.context.payload.repository?.owner.type;
+
+  let message =
+    "Starting April 2026, the CodeQL Action will skip computing file coverage information on pull requests " +
+    "to improve analysis performance. File coverage information will still be computed on non-PR analyses.";
+  const envVarOptOut =
+    "set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true`.";
+  const repoPropertyOptOut =
+    "create a custom repository property with the name " +
+    '`github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to ' +
+    "`true` in the repository's settings.";
+
+  if (repositoryOwnerType === "Organization") {
+    // Org-owned repo: can use the repository property
+    if (isDefaultSetup()) {
+      message += `\n\nTo opt out of this change, ${repoPropertyOptOut}`;
+    } else {
+      message += `\n\nTo opt out of this change, ${envVarOptOut} Alternatively, ${repoPropertyOptOut}`;
+    }
+  } else if (isDefaultSetup()) {
+    // User-owned repo on default setup: no repo property available and
+    // no way to set env vars, so need to switch to advanced setup.
+    message += `\n\nTo opt out of this change, switch to an advanced setup workflow and ${envVarOptOut}`;
+  } else {
+    // User-owned repo on advanced setup: can set the env var
+    message += `\n\nTo opt out of this change, ${envVarOptOut}`;
+  }
+
+  logger.warning(message);
+  core.exportVariable(EnvVar.DID_LOG_FILE_COVERAGE_ON_PRS_DEPRECATION, "true");
 }

src/tools-features.ts

@@ -10,6 +10,7 @@ export enum ToolsFeature {
   ForceOverwrite = "forceOverwrite",
   IndirectTracingSupportsStaticBinaries = "indirectTracingSupportsStaticBinaries",
   PythonDefaultIsToNotExtractStdlib = "pythonDefaultIsToNotExtractStdlib",
+  SuppressesMissingFileBaselineWarning = "suppressesMissingFileBaselineWarning",
 }
 
 /**