Compile Cython Extensions Error - Pycharm IDE [duplicate]

Question

Non-zero exit code (1): _pydevd_bundle/pydevd_cython.c:13:20: fatal error: Python.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Please help me resolve this error of trying to install Cython in PyCharm.

Undersexed

Does this answer your question? fatal error: Python.h: No such file or directory – Addi

Answer 1

JetBrains has provided an answer:

https://www.jetbrains.com/help/pycharm/2017.3/cython-speedups.html

If you're on Ubuntu, run:

For Python 2.7: sudo apt-get install python-dev

For Python 3.5: sudo apt-get install python3-dev

For Python 3.6: sudo apt-get install python3.6-dev

For Python 3.7: sudo apt-get install python3.7-dev

Uninstructed

If using a virtualenv you might have to do the above after activating the env. – Renaldo

For RHEL / CentOS it's named "-devel", e.g. sudo yum install python36-devel – Vivisection

In my case sudo apt-get install python3.7-dev solved the issue – Edee

For Python 3.8, I had to run sudo apt-get install python3.8-dev – Bladderwort

Thanks! Currently for python2.7 on Ubuntu use python2-dev – Swagerty

Answer 2

For python 3.7 sudo apt install libpython3.7-dev solved my problem

Hortense

It does not work for me, "Couldn't locate package libpython3.7-dev" – Glamour

Answer 3

Every time PyCharm makes an IDE update, I spend endless hours searching for how to do it again in Linux.

I'd like to register my answer here for my own self next time.

1. You have to use the system python.
2. Before anything, you have to have sudo apt-get install python<your_bin_version>-dev Obs. Use which python at usr/bin to find out.
3. However, the system python does not recognize conda setuptools.
4. Thus, you also need sudo apt-get install python3-setuptools

After that, if you run, the updated place of PyCharm help, as such:

sudo /usr/bin/python3 /<your_pycharm_installation_dir>/pycharm-2021.1/plugins/python/helpers/pydev/setup_cython.py build_ext --inplace

Then, and only then, it works ... (but only for the base python).

Next, I found the recently constructed directory /_pydevd_bundle and manually (yeah) copied it into

/<your conda environmenbt>/.conda/envs/py39web/compiler_compat

Except for jupyter notebooks, though.

Traumatize

Answer 4

Works also for Python 3.9

sudo apt-get install python3.9-dev

Winepress

We don't need to add an answer for every minor version of Python. One would expect this syntax to continue to work going forward unless something changes. If it's really necessary, though, you can propose an edit to the accepted answer so include this. – Moraine