Error 127 in Building the documentation

[Clarkszw]

Hi :)
I have tried to
make clean
make html
in my docs folder to generate build folder in my windows 11. However it ends up with the following message:

html
Running Sphinx v6.1.3
fetching https://api.github.com/repos/fury-gl/fury/tags
fetching https://api.github.com/repos/fury-gl/fury
fetching https://api.github.com/repos/fury-gl/fury/stats/contributors
Initializing GitHub plugin
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/docs/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://dipy.org/documentation/latest/objects.inv/...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
intersphinx inventory has moved: https://dipy.org/documentation/latest/objects.inv/ -> https://dipy.org/documentation/1.6.0./objects.inv/
generating gallery...
Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files.
WARNING: C:\Users\Clark\Desktop\coder\GSoC\FURY\docs\examples\viz_roi_contour.py failed to execute correctly: Traceback (most recent call last):
  File "C:\Users\Clark\Desktop\coder\GSoC\FURY\docs\examples\viz_roi_contour.py", line 36, in <module>
    data = hardi_img.get_data()
           ^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Clark\AppData\Local\Programs\Python\Python311\Lib\site-packages\nibabel\deprecator.py", line 185, in deprecated_func
    raise error_class(message)
nibabel.deprecator.ExpiredDeprecationError: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0

make: *** [Makefile:43: html] Error 127 [ 64%] viz_tesseract.py

Could someone help me with this?
Thanks in advance.

[skoudoro]

Yes, We recently have an issue with the docs generation. A segfault appears randomly, and you need to run the generation 3-5 times in row to get the final results. This is on our todo list to understand and fix this issue.

Also, what is the result of a pip freeze ? I am surprised that you have an old version of Nibabel package. You might need to update the docs.txt

[Clarkszw]

Hi @skoudoro, thanks for your answer:)
Here is the result of pip freeze

$ pip freeze
ablog==0.10.33.post1
accessible-pygments==0.0.3
aiohttp==3.8.4
aiosignal==1.3.1
alabaster==0.7.13
asgiref==3.6.0
asttokens==2.2.1
async-timeout==4.0.2
attrs==22.2.0
autopep8==2.0.1
Babel==2.12.1
backcall==0.2.0
beautifulsoup4==4.11.2
certifi==2022.12.7
charset-normalizer==3.1.0
click==8.1.3
codecov==2.1.12
colorama==0.4.6
contourpy==1.0.7
coverage==7.2.1
cycler==0.11.0
Cython==0.29.33
dataclasses-json==0.5.7
decorator==5.1.1
Deprecated==1.2.13
dipy==1.6.0
Django==4.1.6
docutils==0.19
et-xmlfile==1.1.0
executing==1.2.0
feedgen==0.9.0
flake8==6.0.0
fonttools==4.38.0
frozenlist==1.3.3
-e git+https://github.com/Clarkszw/fury.git@db2398a0cb1550c2c3bf2a286c7c1608f365cd88#egg=fury
h5py==3.8.0
idna==3.4
imagesize==1.4.1
iniconfig==2.0.0
invoke==2.0.0
ipython==8.11.0
jedi==0.18.2
Jinja2==3.1.2
joblib==1.2.0
kiwisolver==1.4.4
lxml==4.9.2
MarkupSafe==2.1.2
marshmallow==3.19.0
marshmallow-enum==1.5.1
matplotlib==3.7.1
matplotlib-inline==0.1.6
mccabe==0.7.0
multidict==6.0.4
mypy-extensions==1.0.0
networkx==3.0
nibabel==5.0.1
nltk==3.8.1
numpy==1.24.2
opencv-python==4.7.0.72
openpyxl==3.1.0
packaging==23.0
parso==0.8.3
pickleshare==0.7.5
Pillow==9.4.0
pluggy==1.0.0
prompt-toolkit==3.0.38
pure-eval==0.2.2
pybullet==3.2.5
pycodestyle==2.10.0
pydata-sphinx-theme==0.13.0
pyflakes==3.0.1
pygltflib==1.15.5
Pygments==2.14.0
pyparsing==3.0.9
pytest==7.2.2
python-dateutil==2.8.2
regex==2022.10.31
requests==2.28.2
ruby==0.0.2
scipy==1.10.1
six==1.16.0
snowballstemmer==2.2.0
soupsieve==2.4
Sphinx==6.1.3
sphinx-copybutton==0.5.1
sphinx-gallery==0.11.1
sphinxcontrib-applehelp==1.0.4
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
sqlparse==0.4.3
stack-data==0.6.2
tqdm==4.64.1
traitlets==5.9.0
typing-inspect==0.8.0
typing_extensions==4.5.0
tzdata==2022.7
urllib3==1.26.14
vtk==9.2.6
watchdog==2.3.1
wcwidth==0.2.6
wrapt==1.15.0
yarl==1.8.2

I forked the fury github repo today and installed it from source in my windows 11. I assume the docs.txt is the same as published.

[skoudoro]

thanks, Can you create a PR to update viz_roi_contour.py? Just follow the warning above that you got and replace the deprecated function by the new one.

Thanks!

ps: doc generation will still fail and need many iteration, but this is one less warning :-)

[Clarkszw]

Hi @skoudoro, I have created a PR for this update.
I have not gone through the test as the guideline (as I am too new to understand it all..) I assume it is ok for this kind of simple fix.

now there is only error 127 left in the end of the output:

$ make html
html
Running Sphinx v6.1.3
fetching https://api.github.com/repos/fury-gl/fury/tags
fetching https://api.github.com/repos/fury-gl/fury
fetching https://api.github.com/repos/fury-gl/fury/stats/contributors
Initializing GitHub plugin
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/docs/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://dipy.org/documentation/latest/objects.inv/...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
intersphinx inventory has moved: https://dipy.org/documentation/latest/objects.inv/ -> https://dipy.org/documentation/1.6.0./objects.inv/
generating gallery...
Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files.
make: *** [Makefile:43: html] Error 127 [ 64%] viz_tesseract.py