Code coverage on workspace includes node_modules despite exclusions

[mhuggins]

Describe the bug

I've got a pnpm workspace with packages under apps/* and packages/*. Specifically, one package in each sub-folder has a vitest.config.ts file, containing the following:

import path from "node:path";
import { fileURLToPath } from "node:url";
import {
  coverageConfigDefaults,
  defaultExclude,
  defaultInclude,
  defineConfig,
} from "vitest/config";

const __filename = fileURLToPath(import.meta.url);
const __dirname = path.dirname(__filename);

export default defineConfig({
  test: {
    include: defaultInclude,
    exclude: [...defaultExclude, "**/*.spec.*"],
    coverage: {
      exclude: ["**/node_modules/**", ...coverageConfigDefaults.exclude],
    },
  },
  resolve: {
    alias: {
      "@": path.resolve(__dirname, "./src"),
    },
  },
});

I've tried multiple iterations of defining a vitest.workspace.ts file in my project root.

Most basic approach:

export default ["apps/*", "packages/*"];

Most complex approach:

import { defineWorkspace } from "vitest/config";

const exclude = [
  "**/node_modules/**",
  "**/dist/**",
  "**/cypress/**",
  "**/.{idea,git,cache,output,temp}/**",
  "**/{karma,rollup,webpack,vite,vitest,jest,ava,babel,nyc,cypress,tsup,build,eslint,prettier}.config.*",
  "**/*.spec.*",
];

export default defineWorkspace([
  {
    extends: "./apps/myapp/vitest.config",
    test: {
      include: ["src/**/*.test.{ts,js}"],
      exclude,
    },
  },
  {
    extends: "./packages/mypackage/vitest.config",
    test: {
      include: ["src/**/*.test.{ts,js}"],
      exclude,
    },
  },
]);

When running vitest run --coverage, the correct limited set of tests are being run. However, the code coverage is a very large dump, including coverage of files found in node_modules within each of the individual package folders.

Am I doing something wrong with my configuration? I would not expect node_modules to be included by default or with it being explicitly excluded.

Reproduction

1. Create a pnpm workspace with a pnpm-workspace.yaml file:

   packages:
     - "packages/*"
     - "apps/*"

2. Create a package under each of these folders, and define vitest configs as outlined previously.

3. Run vitest run --coverage.

System Info

System:
    OS: macOS 15.1.1
    CPU: (12) arm64 Apple M3 Pro
    Memory: 2.87 GB / 36.00 GB
    Shell: 5.9 - /bin/zsh
  Binaries:
    Node: 22.7.0 - ~/.nvm/versions/node/v22.7.0/bin/node
    npm: 10.8.2 - ~/.nvm/versions/node/v22.7.0/bin/npm
    pnpm: 9.15.1 - ~/Library/pnpm/pnpm
  Browsers:
    Chrome: 131.0.6778.205
    Safari: 18.1.1
  npmPackages:
    @vitest/coverage-v8: 2.1.3 => 2.1.3 
    vitest: 2.1.3 => 2.1.3 

### Used Package Manager

pnpm

### Validations

- [X] Follow our [Code of Conduct](https://github.com/vitest-dev/vitest/blob/main/CODE_OF_CONDUCT.md)
- [X] Read the [Contributing Guidelines](https://github.com/vitest-dev/vitest/blob/main/CONTRIBUTING.md).
- [X] Read the [docs](https://vitest.dev/guide/).
- [X] Check that there isn't [already an issue](https://github.com/vitest-dev/vitest/issues) that reports the same bug to avoid creating a duplicate.
- [X] Check that this is a concrete bug. For Q&A open a [GitHub Discussion](https://github.com/vitest-dev/vitest/discussions) or join our [Discord Chat Server](https://chat.vitest.dev).
- [X] The provided reproduction is a [minimal reproducible example](https://stackoverflow.com/help/minimal-reproducible-example) of the bug.

[nickm-oua]

The workaround I found was to add this setting to the configuration.

    coverage: {
      excludeAfterRemap: true,
    },

[mhuggins]

excludeAfterRemap: true

@nickm-oua Hmm, I tried this with both v8 & istanbul, but I'm still seeing the same result where files in node_modules are included.

[hi-ogawa]

You probably need a root vitest.config.ts along side vitest.workspace.ts since coverage config cannot be specified for each workspace project individually https://vitest.dev/guide/workspace.html#configuration

Some of the configuration options are not allowed in a project config. Most notably:
coverage: coverage is done for the whole workspace

[github-actions]

Hello @mhuggins. Please provide a minimal reproduction using a GitHub repository or StackBlitz (you can also use examples). Issues marked with needs reproduction will be closed if they have no activity within 3 days.

[mhuggins]

Thanks @hi-ogawa, that helped me to get it working! All I needed to do was:

1. Create a vitest.config.ts in my project root containing the following:

   import { defineConfig } from "vitest/config";
   
   export default defineConfig({
     test: {
       coverage: {
         excludeAfterRemap: true,
       },
     },
   });

2. Revert my vitest.workspace.ts to what I originally had:

   export default ["apps/*", "packages/*"];