Windows pip install fail: UnicodeDecodeError: 'charmap' codec can't decode byte

[niemasd]

I'm running Windows 11 with Python 3.13.9 and pip 26.2.1, and I tried installing empress via pip install empress, but I got this error message:

Defaulting to user installation because normal site-packages is not writeable
Collecting empress
  Using cached empress-1.2.0.tar.gz (302 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [26 lines of output]
      Traceback (most recent call last):
        File "C:\Users\nmoshiri\AppData\Roaming\Python\Python313\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "C:\Users\nmoshiri\AppData\Roaming\Python\Python313\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\nmoshiri\AppData\Roaming\Python\Python313\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
        File "C:\Users\nmoshiri\AppData\Local\Temp\pip-build-env-0bbwprkq\overlay\Lib\site-packages\setuptools\build_meta.py", line 333, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\nmoshiri\AppData\Local\Temp\pip-build-env-0bbwprkq\overlay\Lib\site-packages\setuptools\build_meta.py", line 301, in _get_build_requires
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "C:\Users\nmoshiri\AppData\Local\Temp\pip-build-env-0bbwprkq\overlay\Lib\site-packages\setuptools\build_meta.py", line 520, in run_setup
          super().run_setup(setup_script=setup_script)
          ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "C:\Users\nmoshiri\AppData\Local\Temp\pip-build-env-0bbwprkq\overlay\Lib\site-packages\setuptools\build_meta.py", line 317, in run_setup
          exec(code, locals())  # noqa: S102 # exec is intentional here
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 35, in <module>
        File "C:\Program Files\Python313\Lib\encodings\cp1252.py", line 23, in decode
          return codecs.charmap_decode(input,self.errors,decoding_table)[0]
                 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 13340: character maps to <undefined>
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed to build 'empress' when getting requirements to build wheel

Perhaps it's some special character somewhere in the source code or other files that get read by the setup code?

[fedarko]

Hi Niema! Wow, that is a foul-looking error.

I tried to replicate the issue on my (Ubuntu) system by setting up a basic conda environment with Python 3.13.9 and pip 26.2.1, but running pip install empress didn't give me this particular error -- although running Empress in the resulting environment failed anyway due to the reason given in #571 (pkg_resources has been removed in setuptools >= 82).

Setting aside the Empress side of things, it looks like one of Empress' dependencies does not support Python 3.13 and up yet (biocore/improved-octo-waddle#63). So, I am not sure how feasible it will be to run Empress in this particular environment :(

---

That being said! It is still possible to install Empress in older versions of Python. After fighting with numpy versions for a while (PyProphet/pyprophet#124, biocore/improved-octo-waddle#59, #562, ...), it looks like the following configuration works consistently on my system:

mamba create -n empress-notbusted "setuptools < 82" "python < 3.10"
pip install "cython < 3" "numpy < 2"
pip install empress

It is also possible to get this to work with Python 3.10 (instead of Python 3.9), but you start needing to fight with the dependencies more...

Anyway, hope this is helpful!