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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
69 stars 25 forks source link

`numpy.distutils` is deprecated #1132

Closed leorrose closed 3 months ago

leorrose commented 3 months ago

Describe the bug Failed building the conda environment after cloning the package and creating conda environment as described in the readme:

Expected behavior Successful installation without errors.

To Reproduce

git clone -b v0.7.0 https://github.com/angelolab/ark-analysis.git
cd ark-analysis
conda env create -f environment.yml

The full error message is too long so i'm attaching the part where the error started:


Channels:
 - conda-forge
 - pytorch
 - nvidia
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/home/leorro/.conda/envs/ark_env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/sise/assafzar-group/assafzar/leor/ark-analysis/condaenv.ps34mpdl.requirements.txt', '--exists-action=b']
Pip subprocess output:
Processing /sise/assafzar-group/assafzar/leor/ark-analysis
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting alpineer==0.1.10 (from ark-analysis==0.7.0)
  Using cached alpineer-0.1.10-py3-none-any.whl.metadata (6.3 kB)
Collecting Cython<1,>=0.29 (from ark-analysis==0.7.0)
  Using cached Cython-0.29.37-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.1 kB)
Collecting datasets<3.0,>=2.6 (from ark-analysis==0.7.0)
  Using cached datasets-2.18.0-py3-none-any.whl.metadata (20 kB)
Collecting dill<0.4,>=0.3.5 (from ark-analysis==0.7.0)
  Using cached dill-0.3.8-py3-none-any.whl.metadata (10 kB)
Collecting feather-format<1,>=0.4.1 (from ark-analysis==0.7.0)
  Using cached feather_format-0.4.1-py3-none-any.whl
Collecting importlib-metadata>=5.0 (from ark-analysis==0.7.0)
  Using cached importlib_metadata-7.1.0-py3-none-any.whl.metadata (4.7 kB)
Collecting ipympl<1.0.0,>=0.9.2 (from ark-analysis==0.7.0)
  Using cached ipympl-0.9.4-py3-none-any.whl.metadata (8.7 kB)
Collecting ipython<9,>=8.4 (from ark-analysis==0.7.0)
  Using cached ipython-8.23.0-py3-none-any.whl.metadata (4.9 kB)
Collecting jupyterlab<4,>=3.4.3 (from ark-analysis==0.7.0)
  Using cached jupyterlab-3.6.7-py3-none-any.whl.metadata (12 kB)
Collecting matplotlib<4,>=3.7 (from ark-analysis==0.7.0)
  Using cached matplotlib-3.8.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting multiprocess>=0.70.13 (from ark-analysis==0.7.0)
  Using cached multiprocess-0.70.16-py311-none-any.whl.metadata (7.2 kB)
Collecting natsort<9,>=8 (from ark-analysis==0.7.0)
  Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy<1.24,>=1.20 (from ark-analysis==0.7.0)
  Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting palettable<4,>=3.3.0 (from ark-analysis==0.7.0)
  Using cached palettable-3.3.3-py2.py3-none-any.whl.metadata (3.3 kB)
Collecting pandas>=2 (from ark-analysis==0.7.0)
  Using cached pandas-2.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting pillow<10,>=9 (from ark-analysis==0.7.0)
  Using cached Pillow-9.5.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB)
Collecting pyFlowSOM>=0.1.15 (from ark-analysis==0.7.0)
  Using cached pyFlowSOM-0.1.16-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (4.0 kB)
Collecting requests<3,>=2.20 (from ark-analysis==0.7.0)
  Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting scikit-image<=0.19.3 (from ark-analysis==0.7.0)
  Using cached scikit-image-0.19.3.tar.gz (22.2 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: still running...
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting scikit-learn<2,>=1.1 (from ark-analysis==0.7.0)
  Using cached scikit_learn-1.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting scipy<2,>=1.7 (from ark-analysis==0.7.0)
  Using cached scipy-1.13.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting seaborn<1,>=0.12 (from ark-analysis==0.7.0)
  Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting spatial-lda<1,>=0.1.3 (from ark-analysis==0.7.0)
  Using cached spatial_lda-0.1.3-py3-none-any.whl.metadata (6.1 kB)
Collecting statsmodels<1,>=0.13.2 (from ark-analysis==0.7.0)
  Using cached statsmodels-0.14.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB)
Collecting tifffile>=2022 (from ark-analysis==0.7.0)
  Using cached tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting tqdm<5,>=4 (from ark-analysis==0.7.0)
  Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting umap-learn<1.0,>=0.5 (from ark-analysis==0.7.0)
  Using cached umap_learn-0.5.6-py3-none-any.whl.metadata (21 kB)
Collecting xarray>=2022 (from ark-analysis==0.7.0)
  Using cached xarray-2024.3.0-py3-none-any.whl.metadata (11 kB)
Collecting xmltodict<1,>=0.13.0 (from ark-analysis==0.7.0)
  Using cached xmltodict-0.13.0-py2.py3-none-any.whl.metadata (7.7 kB)
Collecting zstandard<1,>=0.19.0 (from ark-analysis==0.7.0)
  Using cached zstandard-0.22.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB)
Collecting charset-normalizer<3.0.0,>=2.1.1 (from alpineer==0.1.10->ark-analysis==0.7.0)
  Using cached charset_normalizer-2.1.1-py3-none-any.whl.metadata (11 kB)
Collecting networkx>=2.2 (from scikit-image<=0.19.3->ark-analysis==0.7.0)
  Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB)
Collecting imageio>=2.4.1 (from scikit-image<=0.19.3->ark-analysis==0.7.0)
  Using cached imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting PyWavelets>=1.1.1 (from scikit-image<=0.19.3->ark-analysis==0.7.0)
  Using cached pywavelets-1.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.0 kB)
Collecting packaging>=20.0 (from scikit-image<=0.19.3->ark-analysis==0.7.0)
  Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
Collecting cmasher (from ark-analysis==0.7.0)
  Using cached cmasher-1.8.0-py3-none-any.whl.metadata (8.2 kB)
Collecting cmocean (from ark-analysis==0.7.0)
  Using cached cmocean-4.0.3-py3-none-any.whl.metadata (4.2 kB)
Collecting colorcet (from ark-analysis==0.7.0)
  Using cached colorcet-3.1.0-py3-none-any.whl.metadata (6.3 kB)
Collecting scienceplots (from ark-analysis==0.7.0)
  Using cached SciencePlots-2.1.1-py3-none-any.whl.metadata (11 kB)
Collecting jupyterlab-lsp (from ark-analysis==0.7.0)
  Using cached jupyterlab_lsp-5.1.0-py3-none-any.whl.metadata (12 kB)
Collecting python-lsp-server[all] (from ark-analysis==0.7.0)
  Using cached python_lsp_server-1.11.0-py3-none-any.whl.metadata (10 kB)
Collecting jupyterlab-git (from ark-analysis==0.7.0)
  Using cached jupyterlab_git-0.50.0-py3-none-any.whl.metadata (31 kB)
Collecting jupyterlab-execute-time (from ark-analysis==0.7.0)
  Using cached jupyterlab_execute_time-3.1.2-py3-none-any.whl.metadata (6.0 kB)
Collecting jupyterlab-skip-traceback (from ark-analysis==0.7.0)
  Using cached jupyterlab_skip_traceback-5.1.0-py3-none-any.whl.metadata (7.4 kB)
Collecting lckr-jupyterlab-variableinspector (from ark-analysis==0.7.0)
  Using cached lckr_jupyterlab_variableinspector-3.2.1-py3-none-any.whl.metadata (7.8 kB)
Collecting filelock (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached filelock-3.13.4-py3-none-any.whl.metadata (2.8 kB)
Collecting pyarrow>=12.0.0 (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached pyarrow-15.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting pyarrow-hotfix (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached pyarrow_hotfix-0.6-py3-none-any.whl.metadata (3.6 kB)
Collecting xxhash (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached xxhash-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting fsspec<=2024.2.0,>=2023.1.0 (from fsspec[http]<=2024.2.0,>=2023.1.0->datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting aiohttp (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached aiohttp-3.9.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.5 kB)
Collecting huggingface-hub>=0.19.4 (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached huggingface_hub-0.22.2-py3-none-any.whl.metadata (12 kB)
Collecting pyyaml>=5.1 (from datasets<3.0,>=2.6->ark-analysis==0.7.0)
  Using cached PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting zipp>=0.5 (from importlib-metadata>=5.0->ark-analysis==0.7.0)
  Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
Collecting ipython-genutils (from ipympl<1.0.0,>=0.9.2->ark-analysis==0.7.0)
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl.metadata (755 bytes)
Collecting ipywidgets<9,>=7.6.0 (from ipympl<1.0.0,>=0.9.2->ark-analysis==0.7.0)
  Using cached ipywidgets-8.1.2-py3-none-any.whl.metadata (2.4 kB)
Collecting traitlets<6 (from ipympl<1.0.0,>=0.9.2->ark-analysis==0.7.0)
  Using cached traitlets-5.14.2-py3-none-any.whl.metadata (10 kB)
Collecting decorator (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached prompt_toolkit-3.0.43-py3-none-any.whl.metadata (6.5 kB)
Collecting pygments>=2.4.0 (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting stack-data (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting typing-extensions (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached typing_extensions-4.11.0-py3-none-any.whl.metadata (3.0 kB)
Collecting pexpect>4.3 (from ipython<9,>=8.4->ark-analysis==0.7.0)
  Using cached pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting tornado>=6.1.0 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting jupyter-core (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting jupyterlab-server~=2.19 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached jupyterlab_server-2.26.0-py3-none-any.whl.metadata (5.9 kB)
Collecting jupyter-server<3,>=1.16.0 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached jupyter_server-2.14.0-py3-none-any.whl.metadata (8.4 kB)
Collecting jupyter-ydoc~=0.2.4 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached jupyter_ydoc-0.2.5-py3-none-any.whl.metadata (2.2 kB)
Collecting jupyter-server-ydoc~=0.8.0 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached jupyter_server_ydoc-0.8.0-py3-none-any.whl.metadata (5.3 kB)
Collecting nbclassic (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached nbclassic-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting notebook<7 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached notebook-6.5.6-py3-none-any.whl.metadata (2.5 kB)
Collecting jinja2>=2.1 (from jupyterlab<4,>=3.4.3->ark-analysis==0.7.0)
  Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting contourpy>=1.0.1 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached contourpy-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached fonttools-4.51.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
Collecting pyparsing>=2.3.1 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Collecting python-dateutil>=2.7 (from matplotlib<4,>=3.7->ark-analysis==0.7.0)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas>=2->ark-analysis==0.7.0)
  Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas>=2->ark-analysis==0.7.0)
  Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
INFO: pip is looking at multiple versions of pyflowsom to determine which version is compatible with other requirements. This could take a while.
Collecting pyFlowSOM>=0.1.15 (from ark-analysis==0.7.0)
  Using cached pyFlowSOM-0.1.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (4.0 kB)
Collecting idna<4,>=2.5 (from requests<3,>=2.20->ark-analysis==0.7.0)
  Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests<3,>=2.20->ark-analysis==0.7.0)
  Using cached urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests<3,>=2.20->ark-analysis==0.7.0)
  Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting joblib>=1.2.0 (from scikit-learn<2,>=1.1->ark-analysis==0.7.0)
  Using cached joblib-1.4.0-py3-none-any.whl.metadata (5.4 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn<2,>=1.1->ark-analysis==0.7.0)
  Using cached threadpoolctl-3.4.0-py3-none-any.whl.metadata (13 kB)
Collecting patsy>=0.5.4 (from statsmodels<1,>=0.13.2->ark-analysis==0.7.0)
  Using cached patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting numba>=0.51.2 (from umap-learn<1.0,>=0.5->ark-analysis==0.7.0)
  Using cached numba-0.59.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting pynndescent>=0.5 (from umap-learn<1.0,>=0.5->ark-analysis==0.7.0)
  Using cached pynndescent-0.5.12-py3-none-any.whl.metadata (6.8 kB)
Collecting colorspacious>=1.1.0 (from cmasher->ark-analysis==0.7.0)
  Using cached colorspacious-1.1.2-py2.py3-none-any.whl.metadata (3.6 kB)
INFO: pip is looking at multiple versions of jupyterlab-execute-time to determine which version is compatible with other requirements. This could take a while.
Collecting jupyterlab-execute-time (from ark-analysis==0.7.0)
  Using cached jupyterlab_execute_time-3.1.1-py3-none-any.whl.metadata (6.0 kB)
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  Using cached jupyterlab_execute_time-2.3.1-py3-none-any.whl.metadata (5.7 kB)
Collecting nbdime~=4.0.1 (from jupyterlab-git->ark-analysis==0.7.0)
  Using cached nbdime-4.0.1-py3-none-any.whl.metadata (9.5 kB)
Collecting nbformat (from jupyterlab-git->ark-analysis==0.7.0)
  Using cached nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting jupyter-lsp>=2.0.0 (from jupyterlab-lsp->ark-analysis==0.7.0)
  Using cached jupyter_lsp-2.2.5-py3-none-any.whl.metadata (1.8 kB)
INFO: pip is looking at multiple versions of jupyterlab-lsp to determine which version is compatible with other requirements. This could take a while.
Collecting jupyterlab-lsp (from ark-analysis==0.7.0)
  Using cached jupyterlab_lsp-5.0.3-py3-none-any.whl.metadata (12 kB)
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  Using cached jupyterlab_lsp-4.3.0-py3-none-any.whl.metadata (12 kB)
Collecting docstring-to-markdown (from python-lsp-server[all]; extra == "lab_ext"->ark-analysis==0.7.0)
  Using cached docstring_to_markdown-0.15-py3-none-any.whl.metadata (2.0 kB)
Collecting pluggy>=1.0.0 (from python-lsp-server[all]; extra == "lab_ext"->ark-analysis==0.7.0)
  Using cached pluggy-1.4.0-py3-none-any.whl.metadata (4.3 kB)
Collecting python-lsp-jsonrpc<2.0.0,>=1.1.0 (from python-lsp-server[all]; extra == "lab_ext"->ark-analysis==0.7.0)
  Using cached python_lsp_jsonrpc-1.1.2-py3-none-any.whl.metadata (1.5 kB)
Collecting ujson>=3.0.0 (from python-lsp-server[all]; extra == "lab_ext"->ark-analysis==0.7.0)
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Building wheels for collected packages: ark-analysis, scikit-image
  Building wheel for ark-analysis (pyproject.toml): started
  Building wheel for ark-analysis (pyproject.toml): finished with status 'done'
  Created wheel for ark-analysis: filename=ark_analysis-0.7.0-cp311-cp311-linux_x86_64.whl size=360830 sha256=006c65794c8b732f6cc341bc966f1a620646d028a0dac947ec0cbfa5435a7758
  Stored in directory: /sise/home/leorro/.cache/pip/wheels/ea/fe/53/97de35b91ba26fca51d184d68646ac4544b8cd348bc1f62278
  Building wheel for scikit-image (pyproject.toml): started
  Building wheel for scikit-image (pyproject.toml): finished with status 'error'
Successfully built ark-analysis
Failed to build scikit-image

Pip subprocess error:
  error: subprocess-exited-with-error

  × Building wheel for scikit-image (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [1805 lines of output]
      setup.py:9: DeprecationWarning:

        `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
        of the deprecation of `distutils` itself. It will be removed for
        Python >= 3.12. For older Python versions it will remain present.
        It is recommended to use `setuptools < 60.0` for those Python versions.
        For more details, see:
          https://numpy.org/devdocs/reference/distutils_status_migration.html

        from numpy.distutils.command.build_ext import build_ext as npy_build_ext
      Partial import of skimage during the build process.
      Compiling /tmp/pip-install-sof65snf/scikit-image_8c83aa1b617f40a6b5b8d00264ed4fef/skimage/morphology/_skeletonize_3d_cy.pyx because it changed.
      [1/1] Cythonizing /tmp/pip-install-sof65snf/scikit-image_8c83aa1b617f40a6b5b8d00264ed4fef/skimage/morphology/_skeletonize_3d_cy.pyx
      running bdist_wheel
      running build
      running config_cc
      INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
      running config_fc
      INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
      running build_src
      INFO: build_src
      INFO: building extension "skimage._shared.geometry" sources
      INFO: building extension "skimage._shared.transform" sources
      INFO: building extension "skimage._shared.interpolation" sources
      INFO: building extension "skimage._shared.fast_exp" sources
      INFO: building extension "skimage.draw._draw" sources
      INFO: building extension "skimage.feature._cascade" sources
      INFO: building extension "skimage.feature.corner_cy" sources
      INFO: building extension "skimage.feature.censure_cy" sources
      INFO: building extension "skimage.feature.orb_cy" sources
      INFO: building extension "skimage.feature._texture" sources
      INFO: building extension "skimage.feature._hoghistogram" sources
      INFO: building extension "skimage.feature._haar" sources
      INFO: building extension "skimage.feature._sift" sources
leorrose commented 3 months ago

Downgrading python to 3.10 in the environment.yml file seems to solve the problem.

srivarra commented 3 months ago

@leorrose Thanks for reporting this, I'll get a quick fix in.