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With yarn, I am forcing ^4.1 version using resolution in package.json

"resolutions": {
  "microbundle/typescript": "^4.1"
},

However, it throws an error when using react-jsx option.

rpt2: options error TS5089: Option 'jsxFactory' cannot be specified when option 'jsx' is 'react-jsx'.

Here is where jsxFactory set by minibundle: https://github.com/developit/microbundle/blob/master/src/index.js#L498-L503

The workaround is to set jsxFactory inside of tsconfig.json; however, maybe microbundle should try to detect settings from tsconfig.json and don't try to set jsxFactory if jsx is set to react-jsx?

Here is where jsxFactory set by minibundle: https://github.com/developit/microbundle/blob/master/src/index.js#L498-L503

The workaround is to set jsxFactory inside of tsconfig.json; however, maybe microbundle should try to detect settings from tsconfig.json and don't try to set jsxFactory if jsx is set to react-jsx?

Not quite.

Microbundle passes a set of defaults to rollup-plugin-typescript2, but the user's tsconfig overrides with a deep merge (with the small exception of module and target -- those Microbundle does enforce).

rpt2 has not been updated for TS 4.1, so until it does, you can't user newer features.

Edit: This was a bad quick assumption on my part. rpt2 was doing just fine.

I think this may be superceded by #741.