Github Actions - file not found when build cython module

I created a GitHub action as follow to build the module, the setup file and the source code of my Cython module are placed in a sub-folder ./deps/cystdf/.

jobs:
  build:
    runs-on: macos-latest
    steps:
      - uses: actions/checkout@v2
      - name: Setup Python
        uses: actions/setup-python@v2.2.2
        with:
          python-version: 3.9
          architecture: x64

      - name: Install dependencies
        run: |
          python -m pip install cython
          python -m pip install numpy
        
      - name: Compile cystdf module
        working-directory: ./deps/cystdf
        run: python cystdf_amalgamation_setup.py build_ext --inplace

I’ve set the working-directory to the sub-folder. However, Cython still complains files are missing:

Error compiling Cython file:

cystdf_amalgamation.pyx:38:0: 'includes/pthread.pxd' not found
cystdf_amalgamation.pyx:39:0: 'hashmap_src/hashmap_libc.pxd' not found
cystdf_amalgamation.pyx:40:0: 'sqlite3_src/sqlite3_libc.pxd' not found
...

I am pretty sure those files exist, what I am missing here?

Here is the Link to my setup file and cython module.

use the latest version of cython fix the problem:

python -m pip install cython==3.0a6