ChipWhisperer installation - error compiling Cython file

[Flybro]

To install the ChipWhisperer software on Linux platform, I followed the instructions at https://chipwhisperer.readthedocs.io/en/latest/linux-install.html. But, when running the command:

python3 -m pip install -e .

Python error occured:

Error compiling Cython file

import numpy as np
  try:
    from libc.math cimport INFINITY
  except:
    from numpy.math cimport INFINITY
    ^
  ------------------------------------------------------------
  
  fastdtw/_fastdtw.pyx:17:2: 'numpy/math.pxd' not found
  
  Error compiling Cython file:
  ------------------------------------------------------------
  import numpy as np
  
  try:
    from libc.math cimport INFINITY
  except:
    from numpy.math cimport INFINITY
    ^
  ------------------------------------------------------------
  
  fastdtw/_fastdtw.pyx:17:2: 'numpy/math/INFINITY.pxd' not found
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 35, in <module>
    File "/tmp/pip-install-kjl_ashk/fastdtw_e332c2520ab24e66a8efd0ceaa7fc522/setup.py", line 53, in <module>
      extensions = cythonize(extensions)
    File "/home/masterchief/.cwvenv/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1145, in cythonize
      cythonize_one(*args)
    File "/home/masterchief/.cwvenv/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1289, in cythonize_one
      raise CompileError(None, pyx_file)
  Cython.Compiler.Errors.CompileError: fastdtw/_fastdtw.pyx
  Compiling fastdtw/_fastdtw.pyx because it changed.
  [1/1] Cythonizing fastdtw/_fastdtw.pyx

[alex-dewar]

Hi,

Thanks for the report on this. It looks like this is an issue with numpy 2 and fastdtw. We do specify a pre version 2 numpy, so it's strange that you're getting this error. Can you post the output of pip freeze?

[Flybro]

Hi,

Sure, but in the meantime the problem has been solved. I'm not entirely sure how, but now everything is OK.
All I did was:

pip install --upgrade pip
pip uninstall wheel

and adding a version for Cython to pyproject.toml:

Cython==3.0.11

There is the output from pip freeze:

anyio==4.9.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
astcheck==0.4.0
asttokens==3.0.0
async-lru==2.0.5
attrs==25.3.0
babel==2.17.0
beautifulsoup4==4.13.4
bleach==6.2.0
bokeh==3.7.3
certifi==2025.4.26
cffi==1.17.1
charset-normalizer==3.4.2
-e git+https://github.com/newaetech/chipwhisperer@eda19612b147f974d6f96b0f1d8663c3cb99ebba#egg=chipwhisperer
colorcet==3.1.0
comm==0.2.2
configobj==5.0.9
contourpy==1.3.2
cycler==0.12.1
Cython==3.0.11
datashader==0.18.1
debugpy==1.8.14
decorator==5.2.1
defusedxml==0.7.1
ECPy==1.2.5
exceptiongroup==1.3.0
executing==2.2.0
fastdtw==0.3.4
fastjsonschema==2.21.1
fonttools==4.58.0
fqdn==1.5.1
h11==0.16.0
holoviews==1.20.2
httpcore==1.0.9
httpx==0.28.1
idna==3.10
importlib_metadata==8.7.0
ipykernel==6.29.5
ipython==8.36.0
ipywidgets==8.1.7
isoduration==20.11.0
jedi==0.19.2
Jinja2==3.1.6
json5==0.12.0
jsonpointer==3.0.0
jsonschema==4.23.0
jsonschema-specifications==2025.4.1
jupyter==1.1.1
jupyter-console==6.6.3
jupyter-events==0.12.0
jupyter-lsp==2.2.5
jupyter_client==8.6.3
jupyter_core==5.7.2
jupyter_server==2.16.0
jupyter_server_terminals==0.5.3
jupyterlab==4.4.2
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.3
jupyterlab_widgets==3.0.15
kiwisolver==1.4.8
libusb==1.0.28.post2
libusb1==3.3.1
linkify-it-py==2.0.3
llvmlite==0.44.0
Markdown==3.8
markdown-it-py==3.0.0
MarkupSafe==3.0.2
matplotlib==3.10.3
matplotlib-inline==0.1.7
mdit-py-plugins==0.4.2
mdurl==0.1.2
mistune==3.1.3
multipledispatch==1.0.0
narwhals==1.40.0
nbclient==0.10.2
nbconvert==7.16.6
nbformat==5.10.4
nbparameterise==0.6.1
nest-asyncio==1.6.0
notebook==7.4.2
notebook_shim==0.2.4
numba==0.61.2
numpy==1.26.4
overrides==7.7.0
packaging==25.0
pandas==2.2.3
pandocfilters==1.5.1
panel==1.7.0
param==2.2.0
parso==0.8.4
pexpect==4.9.0
phoenixAES==0.0.5
pillow==11.2.1
pkg_about==1.3.5
platformdirs==4.3.8
prometheus_client==0.22.0
prompt_toolkit==3.0.51
psutil==7.0.0
ptyprocess==0.7.0
pure_eval==0.2.3
pycparser==2.22
pycryptodome==3.23.0
pyct==0.5.0
Pygments==2.19.1
pyparsing==3.2.3
pyserial==3.5
python-dateutil==2.9.0.post0
python-json-logger==3.3.0
pytz==2025.2
pyviz_comms==3.0.4
PyYAML==6.0.2
pyzmq==26.4.0
referencing==0.36.2
requests==2.32.3
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.25.1
scipy==1.15.3
Send2Trash==1.8.3
six==1.17.0
sniffio==1.3.1
soupsieve==2.7
stack-data==0.6.3
terminado==0.18.1
terminaltables==3.1.10
tinycss2==1.4.0
tomli==2.2.1
toolz==1.0.0
tornado==6.5.1
tqdm==4.67.1
traitlets==5.14.3
types-python-dateutil==2.9.0.20250516
typing_extensions==4.13.2
tzdata==2025.2
uc-micro-py==1.0.3
uri-template==1.3.0
urllib3==2.4.0
wcwidth==0.2.13
webcolors==24.11.1
webencodings==0.5.1
websocket-client==1.8.0
widgetsnbextension==4.0.14
xarray==2025.4.0
xyzservices==2025.4.0
zipp==3.21.0

[masaki42482]

Hi,
I had the same issue, and the previous comment did work perfectly, FYI.

[kaybarkbark]

I got around this issue by doing this:

1. Clone fastdtw to my local machine
2. Apply this patch to fastdtw fix(cython): replace fallback import for INFINITY import in _fastdtw.pyx slaypni/fastdtw#66
3. Activate my chipwhisperer virtualenv
4. Build and install the patched fastdtw

python setup.py build_ext --inplace
python3 -m pip install .

5. Proceed with python3 -m pip install -e . as normal.