Examples broken after installing docs dependencies with Python 3.11 #689

acse-xm421 · 2023-07-30T20:36:02Z

acse-xm421
Jul 30, 2023

The problem seems to be in the FlorisInterface(). Nothing changed but just run the example1.
Here is the error information.

Answered by rafmudaf

Jul 31, 2023

I generally use Python 3.10, and within NREL we haven't tested Python 3.11 very much in the context of FLORIS. @acse-xm421 I suggest to drop to Python 3.10.

I've created a new conda environment on my side with Python 3.11 and I've noticed a couple of things.

The "docs" dependencies for Python 3.11 are quite a bit longer and heavier than for < 3.11. @acse-xm421 I suggest to not install the "docs" extras with Python 3.11.

The attrs package shows this warning:

/PATH/floris311/lib/python3.11/site-packages/attr/_make.py:918: RuntimeWarning: Running interpreter doesn't sufficiently support code object introspection.  Some features like bare super() or accessing __class__ will not work with slo…

View full answer

Bartdoekemeijer · 2023-07-31T07:36:08Z

Bartdoekemeijer
Jul 31, 2023
Maintainer

The example runs just fine for me with the latest develop branch. How did you install FLORIS?

14 replies

rafmudaf Jul 31, 2023
Maintainer

Can you post your steps and the results? Please copy / paste the terminal outputs or post a screenshot.
As a second sanity check, the examples are run in GitHub Actions for every commit, see here. That's not to say there isn't a problem as it's possible the testing system has an error, but it does suggest that something is incorrect with your environment.

acse-xm421 Jul 31, 2023
Author

Sure!

(base) mm@DESKTOP-xx:~/acse_projects/wind-farm$ git clone -b develop [email protected]:acse-xm421/floris.git
Cloning into 'floris'...
remote: Enumerating objects: 18966, done.
remote: Counting objects: 100% (2439/2439), done.
remote: Compressing objects: 100% (940/940), done.
remote: Total 18966 (delta 2075), reused 1746 (delta 1487), pack-reused 16527
Receiving objects: 100% (18966/18966), 36.59 MiB | 2.43 MiB/s, done.
Resolving deltas: 100% (14089/14089), done.
(base) mm@DESKTOP-xx:~/acse_projects/wind-farm$ cd floris/
(base) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$ conda create --name floris_2
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 22.9.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/mm/miniconda3/envs/floris_2



Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate floris_2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Retrieving notices: ...working... done
(base) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$ conda activate floris_2
(floris_2) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$
conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 22.9.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/mm/miniconda3

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2023.7.22          |   py39h06a4308_0         153 KB    cryptography-41.0.2        |   py39h22a60cf_0         1.9 MB    pip-23.2.1                 |   py39h06a4308_0         2.6 MB    pyopenssl-23.2.0           |   py39h06a4308_0          96 KB    requests-2.31.0            |   py39h06a4308_0          96 KB    setuptools-68.0.0          |   py39h06a4308_0         928 KB    ------------------------------------------------------------                                           Total:         5.7 MB
The following packages will be UPDATED:

  certifi                           2023.5.7-py39h06a4308_0 --> 2023.7.22-py39h06a4308_0 None
  cryptography                        39.0.1-py39h9ce1e76_2 --> 41.0.2-py39h22a60cf_0 None
  pip                                 23.1.2-py39h06a4308_0 --> 23.2.1-py39h06a4308_0 None
  pyopenssl                           23.0.0-py39h06a4308_0 --> 23.2.0-py39h06a4308_0 None
  requests                            2.29.0-py39h06a4308_0 --> 2.31.0-py39h06a4308_0 None
  setuptools                          67.8.0-py39h06a4308_0 --> 68.0.0-py39h06a4308_0 None


Proceed ([y]/n)? y


Downloading and Extracting Packages
pip-23.2.1           | 2.6 MB    | ##################### | 100%
setuptools-68.0.0    | 928 KB    | ##################### | 100%
requests-2.31.0      | 96 KB     | ##################### | 100%
cryptography-41.0.2  | 1.9 MB    | ##################### | 100%
certifi-2023.7.22    | 153 KB    | ##################### | 100%
pyopenssl-23.2.0     | 96 KB     | ##################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Retrieving notices: ...working... done
(floris_2) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$
conda install pip
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 22.9.0
  latest version: 23.7.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/mm/miniconda3/envs/floris_2

  added / updated specs:
    - pip


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main None
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu None
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 None
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.05.30-h06a4308_0 None
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 None
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 None
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 None
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 None
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 None
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 None
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 None
  openssl            pkgs/main/linux-64::openssl-3.0.9-h7f8727e_0 None
  pip                pkgs/main/linux-64::pip-23.2.1-py311h06a4308_0 None
  python             pkgs/main/linux-64::python-3.11.4-h955ad1f_0 None
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 None
  setuptools         pkgs/main/linux-64::setuptools-68.0.0-py311h06a4308_0 None
  sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 None
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 None
  tzdata             pkgs/main/noarch::tzdata-2023c-h04d1e81_0 None
  wheel              pkgs/main/linux-64::wheel-0.38.4-py311h06a4308_0 None
  xz                 pkgs/main/linux-64::xz-5.4.2-h5eee18b_0 None
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0 None


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Retrieving notices: ...working... done
(floris_2) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$
pip install -e ".[develop, docs]"
Obtaining file:///home/mm/acse_projects/wind-farm/floris
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
Collecting attrs (from FLORIS==3.4)
  Using cached attrs-23.1.0-py3-none-any.whl (61 kB)
......
Successfully installed FLORIS-3.4 GitPython-3.1.32 Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 anyio-3.7.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 arrow-1.2.3 asttokens-2.2.1 async-lru-2.0.4 attrs-21.4.0 babel-2.12.1 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 certifi-2023.7.22 cffi-1.15.1 cfgv-3.3.1 charset-normalizer-3.2.0 click-8.1.6 colorama-0.4.6 coloredlogs-15.0.1 comm-0.1.3 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 distlib-0.3.7 docutils-0.17.1 entrypoints-0.4 executing-1.2.0 fastjsonschema-2.18.0 filelock-3.12.2 fonttools-4.41.1 fqdn-1.5.1 gitdb-4.0.10 greenlet-2.0.2 humanfriendly-10.0 identify-2.5.26 idna-3.4 imagesize-1.4.1 importlib-metadata-6.8.0 iniconfig-2.0.0 ipykernel-6.25.0 ipython-8.14.0 ipython-genutils-0.2.0 ipywidgets-7.8.0 isoduration-20.11.0 isort-5.12.0 jedi-0.19.0 json5-0.9.14 jsonpointer-2.4 jsonschema-4.17.3 jupyter-book-0.13.2 jupyter-cache-0.4.3 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyter-events-0.6.3 jupyter-lsp-2.2.0 jupyter-server-2.7.0 jupyter-server-mathjax-0.2.6 jupyter-server-terminals-0.4.4 jupyter-sphinx-0.3.2 jupyterlab-4.0.3 jupyterlab-pygments-0.2.2 jupyterlab-server-2.24.0 jupyterlab-widgets-1.1.5 kiwisolver-1.4.4 latexcodec-2.0.1 linkify-it-py-2.0.2 lxml-4.9.3 markdown-it-py-1.1.0 matplotlib-3.7.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.2.8 mistune-0.8.4 myst-nb-0.13.2 myst-parser-0.15.2 nbclient-0.5.13 nbconvert-6.5.4 nbdime-3.2.1 nbformat-5.9.2 nest-asyncio-1.5.7 nodeenv-1.8.0 notebook-7.0.0 notebook-shim-0.2.3 numexpr-2.8.4 numpy-1.25.1 overrides-7.3.1 packaging-23.1 pandas-2.0.3 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 pillow-10.0.0 platformdirs-3.10.0 pluggy-1.2.0 pre-commit-3.3.3 prometheus-client-0.17.1 prompt-toolkit-3.0.39 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pybtex-0.24.0 pybtex-docutils-1.0.2 pycparser-2.21 pydata-sphinx-theme-0.8.1 pyparsing-3.0.9 pyrsistent-0.19.3 pytest-7.4.0 python-dateutil-2.8.2 python-json-logger-2.0.7 pytz-2023.3 pyyaml-6.0.1 pyzmq-25.1.0 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 ruamel.yaml-0.16.13 ruff-0.0.280 scipy-1.11.1 send2trash-1.8.2 shapely-2.0.1 six-1.16.0 smmap-5.0.0 sniffio-1.3.0 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-4.5.0 sphinx-autodoc-typehints-1.19.1 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 sphinx_togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-autoyaml-1.1.1 sphinxcontrib-bibtex-2.5.0 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 sphinxcontrib.mermaid-0.9.2 sqlalchemy-1.4.49 stack-data-0.6.2 terminado-0.17.1 tinycss2-1.2.1 tornado-6.3.2 traitlets-5.9.0 tzdata-2023.3 uc-micro-py-1.0.2 uri-template-1.3.0 urllib3-2.0.4 virtualenv-20.24.2 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.1 widgets
(floris_2) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris$ python examples/01_opening_floris_computing_power.py
/home/mm/miniconda3/envs/floris_2/lib/python3.11/site-packages/attr/_make.py:918: RuntimeWarning: Running interpreter doesn't sufficiently support code object introspection.  Some features like bare super() or accessing __class__ will not work with slotted classes.
  set_closure_cell(cell, cls)
FlorisInterface...(This is the line added to test the change source code)
Traceback (most recent call last):
  File "/home/mm/acse_projects/wind-farm/floris/examples/01_opening_floris_computing_power.py", line 33, in <module>
    fi = FlorisInterface("examples/inputs/gch.yaml")
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mm/acse_projects/wind-farm/floris/floris/tools/floris_interface.py", line 58, in __init__
    self.floris = Floris.from_file(self.configuration)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mm/acse_projects/wind-farm/floris/floris/simulation/floris.py", line 338, in from_file
    return Floris.from_dict(input_dict)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mm/acse_projects/wind-farm/floris/floris/type_dec.py", line 160, in from_dict
    return cls(**kwargs)
           ^^^^^^^^^^^^^
  File "<attrs generated init floris.simulation.floris.Floris>", line 11, in __init__
  File "/home/mm/acse_projects/wind-farm/floris/floris/simulation/floris.py", line 104, in __attrs_post_init__
    self.grid = TurbineGrid(
                ^^^^^^^^^^^^
  File "<attrs generated init floris.simulation.grid.TurbineGrid>", line 15, in __init__
  File "/home/mm/acse_projects/wind-farm/floris/floris/simulation/grid.py", line 161, in __attrs_post_init__
    super().__attrs_post_init__()
    ^^^^^^^
TypeError: super(type, obj): obj must be an instance or subtype of type

rafmudaf Jul 31, 2023
Maintainer

Thanks @acse-xm421. Can you try with Python 3.10? Uninstall Python (conda uninstall python) and then pin the version (conda install python==3.10). You'll have to reinstall floris after that (pip install -e ...).

As an aside, I wonder why conda raised the same error about your base environment being out of date immediately after you updated it.

rafmudaf Jul 31, 2023
Maintainer

I generally use Python 3.10, and within NREL we haven't tested Python 3.11 very much in the context of FLORIS. @acse-xm421 I suggest to drop to Python 3.10.

I've created a new conda environment on my side with Python 3.11 and I've noticed a couple of things.

The "docs" dependencies for Python 3.11 are quite a bit longer and heavier than for < 3.11. @acse-xm421 I suggest to not install the "docs" extras with Python 3.11.

The attrs package shows this warning:

/PATH/floris311/lib/python3.11/site-packages/attr/_make.py:918: RuntimeWarning: Running interpreter doesn't sufficiently support code object introspection.  Some features like bare super() or accessing __class__ will not work with slotted classes.

After a quick web search, I found Add support for Python 3.11 python-attrs/attrs#969 that fixes this issue. This should be resolved but FLORIS must use attrs > 22.1.0.

The "docs" extras installs attrs==21.4 while the develop extras uses the latest attrs==23.1.0

The issue reported here is actually a dependency problem. Somewhere, the docs dependencies are requiring an older version of attrs, in addition to a ton more packages, for Python 3.11.

@acse-xm421 can you confirm these details?

Answer selected by rafmudaf

acse-xm421 Jul 31, 2023
Author

Thank you @rafmudaf . I have changed to python 3.10. Example 01_opening_floris_computing_power works pretty well, but
02_visualization doesn't. It takes much longer time than expected, and it comes out with this.

(floris_2) mm@DESKTOP-xx:~/acse_projects/wind-farm/floris_0$ /home/mm/miniconda3/envs/floris_2/bin/python /home/mm/acse_projects/wind-farm/floris_0/examples/02_visualizations.py
FlorisInterface
Traceback (most recent call last):
 File "/home/mm/acse_projects/wind-farm/floris_0/examples/02_visualizations.py", line 82, in <module>
   fig, ax_list = plt.subplots(3, 1, figsize=(10, 8))
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1501, in subplots
   fig = figure(**fig_kw)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/_api/deprecation.py", line 454, in wrapper
   return func(*args, **kwargs)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/pyplot.py", line 840, in figure
   manager = new_figure_manager(
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/pyplot.py", line 384, in new_figure_manager
   return _get_backend_mod().new_figure_manager(*args, **kwargs)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 3574, in new_figure_manager
   return cls.new_figure_manager_given_figure(num, fig)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 3579, in new_figure_manager_given_figure
   return cls.FigureCanvas.new_manager(figure, num)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 1742, in new_manager
   return cls.manager_class.create_with_canvas(cls, figure, num)
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/site-packages/matplotlib/backends/_backend_tk.py", line 483, in create_with_canvas
   window = tk.Tk(className="matplotlib")
 File "/home/mm/miniconda3/envs/floris_2/lib/python3.10/tkinter/__init__.py", line 2299, in __init__
   self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: couldn't connect to display "192.168.112.1:0.0"

And I will check dependency problem now.

rafmudaf Jul 31, 2023
Maintainer

Yea, the WSL is "headless" so it won't be able to display a plot from matplotlib without further configuration. I've not done this myself, but I'm sure there are instructions on the internet. Essentially, you have to configure matplotlib to use your host system's (Windows) display rather than the WSL.

@bayc since you use WSL, have you tried anything similar?

Bartdoekemeijer Jul 31, 2023
Maintainer

_tkinter.TclError: couldn't connect to display "192.168.112.1:0.0"

is a WSL problem indeed. You can find your solution here: https://stackoverflow.com/questions/61110603/how-to-set-up-working-x11-forwarding-on-wsl2. Note that the solution differs depending on whether you are running WSL1 or WSL2. For WSL1, you need to install VcXsrv on Windows, start an XServer in Windows, and redirect your figures to that server inside WSL by adding a couple commands in the Terminal. Your best bet is to use a very simplistic tool like xeyes to test out whether the WSL graphics work, before heading on to more complicated stuff like Python.

Cheers,
Bart

acse-xm421 Jul 31, 2023
Author

Hi @rafmudaf ,I tried python 3.11.

The detail 1 is right. The "docs" extras takes longer.

For detail 2, if I only install develop pip install -e ".[develop]", the example works well. But if installing both develop and docs, it doesn't work anymore. And the error is the same as you showed before.

For detail 3, I tried to uninstall attr and reinstall attrs==23.1.0, the error still happens. I guess there are some other dependency problems in "docs" extra?

acse-xm421 · 2023-08-01T14:57:45Z

acse-xm421
Aug 1, 2023
Author

The "docs" dependencies for Python 3.11 are quite a bit longer and heavier than for < 3.11. @acse-xm421 I suggest to not install the "docs" extras with Python 3.11.
The attrs package shows this warning:
/PATH/floris311/lib/python3.11/site-packages/attr/_make.py:918: RuntimeWarning: Running interpreter doesn't sufficiently support code object introspection.  Some features like bare super() or accessing __class__ will not work with slotted classes.
After a quick web search, I found Add support for Python 3.11 python-attrs/attrs#969 that fixes this issue. This should be resolved but FLORIS must use attrs > 22.1.0.
The "docs" extras installs attrs==21.4 while the develop extras uses the latest attrs==23.1.0
The issue reported here is actually a dependency problem. Somewhere, the docs dependencies are requiring an older version of attrs, in addition to a ton more packages, for Python 3.11.

2 replies

rafmudaf Aug 1, 2023
Maintainer

@acse-xm421 is this the message you intended?

acse-xm421 Aug 1, 2023
Author

Yes.

Provide feedback

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Examples broken after installing docs dependencies with Python 3.11 #689

acse-xm421 Jul 30, 2023

Replies: 2 comments · 16 replies

Bartdoekemeijer Jul 31, 2023 Maintainer

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acse-xm421
Jul 30, 2023

Replies: 2 comments 16 replies

Bartdoekemeijer
Jul 31, 2023
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rafmudaf Jul 31, 2023
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acse-xm421 Jul 31, 2023
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rafmudaf Jul 31, 2023
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rafmudaf Jul 31, 2023
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acse-xm421 Jul 31, 2023
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rafmudaf Jul 31, 2023
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Bartdoekemeijer Jul 31, 2023
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acse-xm421 Jul 31, 2023
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acse-xm421
Aug 1, 2023
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rafmudaf Aug 1, 2023
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acse-xm421 Aug 1, 2023
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