Error occured while installing fabric python API

[Manas Das]

Hello, I am trying to install python API from this tutorial https://learn.fabric-testbed.net/knowledge-base/install-the-python-api/ . While doing it, I encountered the following error.

Building wheel for typed-ast (setup.py) ... error
error: subprocess-exited-with-error

python setup.py bdist_wheel did not run successfully.

 running install
      /users/manasdas/anaconda3/envs/my_env/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-310
      creating build/lib.linux-x86_64-cpython-310/typed_ast
      copying typed_ast/__init__.py -> build/lib.linux-x86_64-cpython-310/typed_ast
      copying typed_ast/ast3.py -> build/lib.linux-x86_64-cpython-310/typed_ast
      copying typed_ast/ast27.py -> build/lib.linux-x86_64-cpython-310/typed_ast
      copying typed_ast/conversions.py -> build/lib.linux-x86_64-cpython-310/typed_ast
      creating build/lib.linux-x86_64-cpython-310/typed_ast/tests
      copying ast3/tests/test_basics.py -> build/lib.linux-x86_64-cpython-310/typed_ast/tests
      running build_ext
      building '_ast27' extension
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/ast27
      creating build/temp.linux-x86_64-cpython-310/ast27/Custom
      creating build/temp.linux-x86_64-cpython-310/ast27/Parser
      creating build/temp.linux-x86_64-cpython-310/ast27/Python
gcc -pthread -B /users/manasdas/anaconda3/envs/my_env/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -fPIC -O2 -isystem /users/manasdas/anaconda3/envs/my_env/include -fPIC -O2 -isystem /users/manasdas/anaconda3/envs/my_env/include -fPIC -Iast27/Include -I/users/manasdas/anaconda3/envs/my_env/include/python3.10 -c ast27/Custom/typed_ast.c -o build/temp.linux-x86_64-cpython-310/ast27/Custom/typed_ast.o
......
.....
error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> typed-ast

I tried both conda environment and virtualenv, I am getting the same error.

Anyone know how to solve it? Please let me know.

Thank you

• This topic was modified 1 year, 7 months ago by Manas Das.

[ADAM GRIFFITH]

If you are looking to interact with Fabric via Python I have had a lot of success with the FABLib API.

Here is our Conda environment.yml file:

# conda env create --file environment.yml
name: uofu-fabrictestbed
channels:
  - defaults
dependencies:
  - pip=21.2.4
  - python=3.9.12
  - pip:
      - fabrictestbed-extensions==1.3.0

[Manas Das]

@Adam Thank you for your reply, I am working with a headless machine so notebooks are of no use to me. So please let me know how to install fabric-testbed on a headless machine. I am trying to install it for many hours now, but still getting the same above mentioned error.

[Manas Das]

@ Adam I will use the configuration file and try to create a slice. If you know how to do it in a headless machine it will be great, Thanks.

• This reply was modified 1 year, 7 months ago by Manas Das.

[ADAM GRIFFITH]

My advice would be to start with copying the FABLib commands documented on the start_here.ipynb --> create_slice.ipynb Jupyter Lab notebook to your local Python script file.

If you would like, feel free to cannibalize my very rough Python code on GitHub.

[Paul Ruth]

@Manas I would strongly encourage you to avoid the native API and, instead, use FABlib.  FABlib does not require Jupyter Notebooks and can be used on its own.

You should be able to install it with pip using the following command:

python3 -m pip install fabrictestbed-extensions

You will need Python 3.9.

Adam’s config for Anaconda likely works too.

• This reply was modified 1 year, 7 months ago by Paul Ruth.

[Manas Das]

@Adam thank you for your help. I will keep in mind your advice.

@Paul, you are correct, I will use fabrictestbed-extensions and hope everything works out.

[Xusheng Ai]

@Adam, I’m also working on build Fablib API on my University Cluster. It doesn’t support a browse, so I have to do it with python scripts. I followed the steps on the github you sent. However, I met an error that AttributeError: module 'cluster' has no attribute 'logger'. I was wondering if it was because of the version of cluster.

[ADAM GRIFFITH]

@Xusheng, the rough Python code is tailored to work with my IntelliJ IDE. However it does contain good examples of what environmental variables FABLib expects, how to call functions in FABLib, etc.. In short, I would write your own Python by grabbing the useful bits from mine.

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