structured_2d issue from call: gamma_x = vario_estimate_structured(herten_trans_skip, direction='x')

[ChristopherFowler]

When running the example Estimating the Variogram in Specific Directions I get the following error:

Estimating structured variograms
Traceback (most recent call last):
File "real.py", line 111, in
gamma_x = vario_estimate_structured(herten_trans_skip, direction='x')
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/gstools/variogram/variogram.py", line 170, in vario_estimate_structured
gamma = structured_2d(field)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/gstools/variogram/py_estimator.py", line 100, in structured_2d
raise NotImplementedError(__EXCEPT_MSG)
NotImplementedError: A pure Python version is not yet implemented. Only a Cython version is available.

It is true that when I run the script: usr$ python3 real.py
Warning: No Cython functions imported

shows up. I'm not sure how to resolve this issue. Have you guys run into this issue with the examples that use the structured_2d function?

I'm on a Mac but I'm hoping that this issue isn't OS dependent.

Chris

[MuellerSeb]

Hey Chris, thanks for your feedback.
It seems, that your package wasn't installed by a wheel so it was build locally. In this case it is checked if cython is installed and if not, the python implementations of the variogram routines are used. These routines don't contain an estimator for structured fields yet, thats why the error:

NotImplementedError: A pure Python version is not yet implemented. Only a Cython version is available.

From your error-log I see, that you are using python3.7.. and there is the problem, since we don't provide wheels for python3.7 on mac yet.
What you can try is the following:

pip install cython
pip install -I gstools

If you have installed it via pip (or with pip3 maybe).
Then cython should be installed and gstools should be reinstalled with cython support. If the error from above comes again (or even cython fails to install), you maybe don't have a c-compiler installed. In this case follow the instructions from here: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
to install Apple’s XCode and to get gcc.
Then run the following command again:

pip install -I gstools

Maybe you also have to reinstall cython. I don't know how cython reacts to a missing compiler.
I hope this is helping you! Good luck!

Sebastian

[ChristopherFowler]

Hi Sebastian, Thanks for the quick reply. All that was needed was the -I flag! I encourage you to add this to your documentation for Mac users. I had already installed cython before. The command that I used was: usr$ python3 -m pip install -I gstools The working screenshot is attached. Best, Chris Fowler

…

On Tue, Apr 30, 2019 at 2:09 PM Sebastian Müller ***@***.***> wrote: Hey Chris, thanks for your feedback. It seems, that your package wasn't installed by a wheel so it was build locally. In this case it is checked if cython is installed and if not, the python implementations of the variogram routines are used. These routines don't contain an estimator for structured fields yet, thats why the error: NotImplementedError: A pure Python version is not yet implemented. Only a Cython version is available. From your error-log I see, that you are using python3.7.. and there is the problem, since we don't provide wheels for python3.7 on mac yet. What you can try is the following: pip install cython pip install -I gstools If you have installed it via pip (or with pip3 maybe). Then cython should be installed and gstools should be reinstalled with cython support. If the error from above comes again (or even cython fails to install), you maybe don't have a c-compiler installed. In this case follow the instructions from here: https://cython.readthedocs.io/en/latest/src/quickstart/install.html to install Apple’s XCode and to get gcc. Then run the following command again: pip install -I gstools Maybe you also have to reinstall cython. I don't know how cython reacts to a missing compiler. I hope this is helping you! Good luck! Sebastian — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABIRBTGY7HZQTTFS6IMQCFDPTCDMHANCNFSM4HJOQECA> .

[MuellerSeb]

Nice to hear it worked!
The -I flag just forces a reinstall and this is in my opinion a pip related problem and not at all Mac specific. I think there was a previous installed version of gstools in your Python package list which was lacking the cython routines and it was not updated by pip since it was the latest version.. So I think putting this in the documentation would be a bit misleading since it's a workaround for a pip related problem.
Hope you understand that! But thanks for using and the feedback!
Sebastian

[ChristopherFowler]

Ah I see. If our group finds the tool to be what we think it is then we will be citing you in our manuscript. Thanks for the great code!

…

On Tue, Apr 30, 2019 at 6:52 PM Sebastian Müller ***@***.***> wrote: Nice to hear it it worked! The -I flag just forces a reinstall and this is in my opinion a pip related problem and not at all Mac specific. I think there was a previous installed version of gstools in your Python package list which was lacking the cython routines and it was not updated by pip since it was the latest version.. So I think putting this in the documentation would be a bit misleading since it's a workaround for a pip related problem. Hope you understand that! But thanks for using and the feedback! Sebastian — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABIRBTEWCJZ3SHUQFHMLJZ3PTDEUJANCNFSM4HJOQECA> .

[MuellerSeb]

If you have any recommendations on tools, methods, models that would fit into the package, don't hesitate to write an issue! We are happy for feedback!
We are working on a publication for citing. At the moment you can cite the code from Zenodo!

[ChristopherFowler]

Thus far I am quite happy with the code. If we continue to use it through to publication we will definitely cite you. Thanks! Chris

…

On Thu, May 2, 2019 at 6:18 AM Sebastian Müller ***@***.***> wrote: If you have any recommendations on tools, methods, models that would fit into the package, don't hesitate to write an issue! We are happy for feedback! We are working on a publication for citing. At the moment you can cite the code from Zenodo! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABIRBTAQA2CDBEBSUUQZWHTPTK5XZANCNFSM4HJOQECA> .

[MuellerSeb]

I now put a little hint in the README about the -I flag, if something is going wrong during installation.