jest: Coverage broken, reports everything undefined

Do you want to request a feature or report a bug? Reporting a Bug

What is the current behavior? After upgrading from Jest 15 to 16 (I also upgraded node from 4 to 6) and getting everything running again (no changes were required to make Jest tests run again) I noticed coverage reports undefined.

----------|----------|----------|----------|----------|----------------|
File      |  % Stmts | % Branch |  % Funcs |  % Lines |Uncovered Lines |
----------|----------|----------|----------|----------|----------------|
All files |  Unknown |  Unknown |  Unknown |  Unknown |                |
----------|----------|----------|----------|----------|----------------|

If the current behavior is a bug, please provide the steps to reproduce and if possible a minimal repository on GitHub that we can npm install and npm test.

What is the expected behavior? Coverage gets reported like normal:

------------|----------|----------|----------|----------|----------------|
File        |  % Stmts | % Branch |  % Funcs |  % Lines |Uncovered Lines |
------------|----------|----------|----------|----------|----------------|
All files   |    88.37 |    82.26 |     96.3 |    90.98 |                |
 core       |     90.2 |    81.82 |      100 |    97.73 |                |
  env.js    |    90.91 |    78.57 |      100 |      100 |                |
  logger.js |    88.89 |     87.5 |      100 |    94.12 |             22 |
 tv/events  |    87.18 |     82.5 |    92.86 |    87.18 |                |
  events.js |    87.18 |     82.5 |    92.86 |    87.18 |... ,92,103,136 |
------------|----------|----------|----------|----------|----------------|

Run Jest again with --debug and provide the full configuration it prints. Please mention your node and npm version and operating system.

I did a bunch of debugging since no one else has reported this issue. (note, this still occurs when using jest installed globally and ran globally) Here is my command:
npm run test

cd …/node_modules/.bin/ && jest --no-cache --config “…/…/frameworks/jest.json”

I have sub packages inside a parent package, with the parent package having everything installed, hence the directory difference. I did try switching to global jest, updated all my paths, same issue. It seems to be a bug thats exposed with windows and node 6 possibly.

I tracked down the source of the issue to babel-plugin-istanbul but I do not believe the bug is on their side (maybe it is) as it was working previously.

Issue is here:

babel-plugin-istanbul/index.js

    exclude = testExclude(Object.keys(opts).length > 0 ? opts : {
      cwd: process.env.NYC_CWD || getRealpath(process.cwd()),
      configKey: 'nyc',
      configPath: (0, _path.dirname)(findUp.sync('package.json'))
    });

cwd NEVER aligns with the file path, and ALWAYS reports as node_modules/.bin as the path. Even when ran globally.

Heres some examples outputs of filename compared to cwd:

C:\Users\[NAME]\Documents\nodejs\projects\wichita\frameworks\base\sdk\tv\events\events.js 
C:\Users\[NAME]\Documents\nodejs\projects\wichita\node_modules\.bin

C:\Users\[NAME]\Documents\nodejs\projects\wichita\frameworks\base\sdk\core\logger.js 
C:\Users\[NAME]\Documents\nodejs\projects\wichita\node_modules\.bin

C:\Users\[NAME]\Documents\nodejs\projects\wichita\frameworks\base\sdk\core\env.js 
C:\Users\[NAME]\Documents\nodejs\projects\wichita\node_modules\.bin

Test exclude flags everything as exclude due to this rule:

  // Don't instrument files that are outside of the current working directory.
  if (/^\.\./.test(path.relative(this.cwd, filename))) return false

I dont see how this could work, or did work before for me honestly.

If its determined not to be Jest, I have no issues reporting this to the proper project.

Edit: It is NOT windows specific, and also occurs on node 5.