scipy does not install

[vaimaro]

Hello,

it is a great project!

However scipy does not install. I get this log:

Collecting scipy

  Downloading scipy-0.19.0.zip (15.3MB)

Installing collected packages: scipy

  Running setup.py install for scipy: started

    Running setup.py install for scipy: finished with status 'error'

    Complete output from command C:\Users\Namai\.thonny\BundledPython36\Scripts\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Namai\\AppData\\Local\\Temp\\pip-build-vcphr4w6\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Namai\AppData\Local\Temp\pip-fjl7az0o-record\install-record.txt --single-version-externally-managed --compile --install-headers C:\Users\Namai\.thonny\BundledPython36\include\site\python3.6\scipy:

    

    Note: if you need reliable uninstall behavior, then install

    with pip instead of using `setup.py install`:

    

      - `pip install .`       (from a git repo or downloaded source

                               release)

      - `pip install scipy`   (last SciPy release on PyPI)

    

    

    lapack_opt_info:

    lapack_mkl_info:

      libraries mkl_rt not found in ['C:\\Users\\Namai\\.thonny\\BundledPython36\\lib', 'C:\\']

      NOT AVAILABLE

    

    openblas_lapack_info:

      libraries openblas not found in ['C:\\Users\\Namai\\.thonny\\BundledPython36\\lib', 'C:\\']

      NOT AVAILABLE

    

    atlas_3_10_threads_info:

    Setting PTATLAS=ATLAS

    C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\system_info.py:1051: UserWarning: Specified path C:\projects\numpy-wheels\windows-wheel-builder\atlas-builds\atlas-3.10.1-sse2-32\lib is invalid.

      pre_dirs = system_info.get_paths(self, section, key)

    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>

      NOT AVAILABLE

    

    atlas_3_10_info:

    <class 'numpy.distutils.system_info.atlas_3_10_info'>

      NOT AVAILABLE

    

    atlas_threads_info:

    Setting PTATLAS=ATLAS

    <class 'numpy.distutils.system_info.atlas_threads_info'>

      NOT AVAILABLE

    

    atlas_info:

    <class 'numpy.distutils.system_info.atlas_info'>

      NOT AVAILABLE

    

    C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:

        Atlas (http://math-atlas.sourceforge.net/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [atlas]) or by setting

        the ATLAS environment variable.

      self.calc_info()

    lapack_info:

      libraries lapack not found in ['C:\\Users\\Namai\\.thonny\\BundledPython36\\lib', 'C:\\']

      NOT AVAILABLE

    

    C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:

        Lapack (http://www.netlib.org/lapack/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [lapack]) or by setting

        the LAPACK environment variable.

      self.calc_info()

    lapack_src_info:

      NOT AVAILABLE

    

    C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:

        Lapack (http://www.netlib.org/lapack/) sources not found.

        Directories to search for the sources can be specified in the

        numpy/distutils/site.cfg file (section [lapack_src]) or by setting

        the LAPACK_SRC environment variable.

      self.calc_info()

      NOT AVAILABLE

    

    Running from scipy source directory.

    non-existing path in 'scipy\\integrate': 'quadpack.h'

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

      File "C:\Users\Namai\AppData\Local\Temp\pip-build-vcphr4w6\scipy\setup.py", line 416, in <module>

        setup_package()

      File "C:\Users\Namai\AppData\Local\Temp\pip-build-vcphr4w6\scipy\setup.py", line 412, in setup_package

        setup(**metadata)

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\core.py", line 135, in setup

        config = configuration()

      File "C:\Users\Namai\AppData\Local\Temp\pip-build-vcphr4w6\scipy\setup.py", line 336, in configuration

        config.add_subpackage('scipy')

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage

        caller_level = 2)

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage

        caller_level = caller_level + 1)

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 907, in _get_configuration_from_setup_py

        config = setup_module.configuration(*args)

      File "scipy\setup.py", line 15, in configuration

        config.add_subpackage('linalg')

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage

        caller_level = 2)

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage

        caller_level = caller_level + 1)

      File "C:\Users\Namai\.thonny\BundledPython36\lib\site-packages\numpy\distutils\misc_util.py", line 907, in _get_configuration_from_setup_py

        config = setup_module.configuration(*args)

      File "scipy\linalg\setup.py", line 20, in configuration

        raise NotFoundError('no lapack/blas resources found')

    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    

    ----------------------------------------

Command "C:\Users\Namai\.thonny\BundledPython36\Scripts\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Namai\\AppData\\Local\\Temp\\pip-build-vcphr4w6\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Namai\AppData\Local\Temp\pip-fjl7az0o-record\install-record.txt --single-version-externally-managed --compile --install-headers C:\Users\Namai\.thonny\BundledPython36\include\site\python3.6\scipy" failed with error code 1 in C:\Users\Namai\AppData\Local\Temp\pip-build-vcphr4w6\scipy\

Return code: 

Thanks

Vaidotas

[Aivar Annamaa]

Hi Vaidotas!

SciPy is a quite complex package with many dependencies. Looks like it misses some dependencies that can't be installed automatically.

I would recommend installing a separate scientific Python distribution and make Thonny use this as a backend.  More info here: https://bitbucket.org/plas/thonny/wiki/InstallingPackages

best regards,
Aivar

[Mr Mills]

I was scratching my head with this as well! I'd installed Python 3.5, numpy, scipy, PyQt4 and matplotlib before I installed thonnyapp (with pip) but Thonny couldn't see any of the packages because it's using it's own built in interpreter. Just change Thonny's interpreter to your standard Python installation from 'Tools > Options > Interpreter'. I haven't tried installing any other packages with Thonny yet, but I might play it safe and install them with 'pip' at the command line to force 'pip' to run from my Python 3.5 installation.

Mark

[eric marchand]

Hi Aivar

I try to install libraries for my students, but I can not do it with Thonny. I do not have access to: https://bitbucket.org/plas/thonny/wiki/InstallingPackages
but I have a bitbucket account?
Thank you

Eric

[Aivar Annamaa]

Hi Eric,

I try to install libraries for my students, but I can not do it with Thonny. I do not have access to: https://bitbucket.org/plas/thonny/wiki/InstallingPackages

but I have a bitbucket account

 

Oops, looks like I have closed Bitbucket wiki too soon. The new location for this page is here: https://github.com/thonny/thonny/wiki/InstallingPackages

Best regards,
Aivar

[eric marchand]

Hi Aivar

Thank you for the answer and for the speed!
I can install libraries for thonny from Tools / Manages packages or with pip.
But my goal is to install these libraries on esp32. For information, it is the pygame library that I want to install. I can also make programs and run them on esp32.
Best regards,
Eric

[Aivar Annamaa]

Hi Eric,

I'm pretty sure neither NumPy nor PyGame work on esp32.

Best regards,
Aivar

[eric marchand]

Hi Aivar,

Argghh ... a pity.
What is surprising is that some libraries are already installed by default, for example "time". I can not "see" where they are installed. % lsdevice only sends me the files I dropped on the ESP32. I know we can drop a simple library like a my_lib.py file but not a folder?
So it is impossible to add libraries "classic" on an ESP32?
Thanks again.
Eric

[Aivar Annamaa]

I believe esp32 MicroPython also support custom packages (folders), but you need to use some other tool to create and upload them (eg. ampy). Next Thonny version will allow to create directories in MicroPython devices.

With NumPy and PyGame the problem is not their being packages instead of single files. The problem is that they are big libraries with OS and architecture dependent features. I'm not even sure if PyGame + NumPy would fit into average esp32 flash.

There has been discussions about creating a game library in CircuitPython community: https://github.com/adafruit/circuitpython/issues/899, https://github.com/python-ugame/circuitpython-stage

Aivar

[eric marchand]

Hi Aivar,

Thanks for the links. I installed ampy. But I have the impression that it is made to run under linux, and not for windows commands because I can not do any basic command ... example: I installed ampy under cmd.exe windows

python -m pip install adafruit-ampy
But if I want to run it directly:
ampy --help
'ampy' is not recognized as a command or executable. And if I make it work via python:
Python -m ampy
'ampy' is a package and can not be executed directly.
I would have liked to try this tool, to understand a little better the structure of my esp32.

Have a good day

Eric

[Aivar Annamaa]

Check into your Python's "Scripts" directory. But I think we should stop this thread, at least in the forum, because it's not really specific to Thonny.

Best regards,
Aivar

[eric marchand]

Thanks