Installation

[will-moore]

Hi, this looks like a handy tool, so I wanted to give it a try but I'm having trouble installing...

I created a new python 3.10 conda environment, then...

$ conda install -c euro-bioimaging -c conda-forge eubi-bridge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - 

But it's been stuck at this point for about half an hour now and doesn't feel like it's ever going to complete (I'll update if it does)...

I'm using a MacOS 15.5 with:

$ which conda
/Users/wmoore/opt/anaconda3/condabin/conda
$ conda -V
conda 22.9.0
$ python
Python 3.10.18 (main, Jun  5 2025, 08:13:51) [Clang 14.0.6 ] on darwin

Any ideas what's up or if there's anything I can try?

[bugraoezdemir]

Hi @will-moore ,

First of all, thank you for giving EuBI-Bridge a try!

Regarding the installation issue, I haven’t encountered this behavior myself yet. But it might be related to the conda version or macOS. I’ll try to reproduce the issue on a similar setup and get back to you with any findings.

In the meantime, with the release of version 0.0.7 last week, EuBI-Bridge is now hosted on PyPI, and the recommended installation method has changed. You can try the following steps:

# Create a conda environment with the required dependencies. Python 3.11 or 3.12 is required.
conda create -n eubizarr openjdk=8.* maven python=3.12 
# Then activate the environment and install EuBI-Bridge via pip
conda activate eubizarr
pip install --no-cache-dir eubi-bridge==0.0.7b3

Could you give this a try and let me know if it works for you?

Thanks again for the report!

[will-moore]

Thanks @bugraoezdemir, I tried...

$ conda create -n eubizarr openjdk=8.* maven python=3.12 
$ conda activate eubizarr
$ pip install --no-cache-dir eubi-bridge==0.0.7b3
Collecting eubi-bridge==0.0.7b3
  Downloading eubi_bridge-0.0.7b3-py3-none-any.whl.metadata (2.1 kB)
Collecting aicspylibczi>=0.0.0 (from eubi-bridge==0.0.7b3)
  Downloading aicspylibczi-3.3.1-cp312-cp312-macosx_10_13_x86_64.whl.metadata (10 kB)
...

  Building wheel for pylibczirw (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [182 lines of output]
...
        File "/Users/wmoore/opt/anaconda3/envs/eubizarr/lib/python3.12/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/private/var/folders/l7/fy41yg5n67q_4ck550wbkrfh0000gn/T/pip-install-692etmlf/pylibczirw_9d66f4213bda41f4a3125f0b6e719a5c', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/private/var/folders/l7/fy41yg5n67q_4ck550wbkrfh0000gn/T/pip-install-692etmlf/pylibczirw_9d66f4213bda41f4a3125f0b6e719a5c/build/lib.macosx-10.15-x86_64-cpython-312', '-DPYTHON_EXECUTABLE=/Users/wmoore/opt/anaconda3/envs/eubizarr/bin/python3.12', '-DLIBCZI_BUILD_DYNLIB=OFF', '-DLIBCZI_BUILD_UNITTESTS=OFF', '-DLIBCZI_BUILD_CURL_BASED_STREAM=ON', '-DPYLIBCZIRW_VERSION=5.0.0', '-DLIBCZI_BUILD_PREFER_EXTERNALPACKAGE_LIBCURL=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pylibczirw
  Running setup.py clean for pylibczirw
Successfully built asciitree fire
Failed to build pylibczirw
ERROR: Failed to build installable wheels for some pyproject.toml based projects (pylibczirw)

I get the same error if I simply try $ pip install pylibczirw.

https://pypi.org/project/pylibCZIrw/ says:

"In case there is no wheel available for your system configuration, you can:

• try to install from the provided source distribution
• reach out to the maintainers of this project to add more wheels

I don't see any mention of Mac on https://github.com/zeiss/pylibczirw so looks like it's not supported?

[bugraoezdemir]

Hi @will-moore,

Thanks a lot for your feedback! I had not noticed that there isn’t a prebuilt wheel for pylibczirw for macOS. I’ll reach out to the maintainers to request one.

In the meantime, could you try this?

# Updated for the latest version of eubi-bridge
conda create -n eubizarr python=3.12 openjdk=11.* maven cmake zlib boost
conda activate eubizarr
pip install --no-cache-dir eubi-bridge==0.0.7b4

Hopefully, adding cmake, zlib, and boost should enable building pylibczirw from source. Please let me know if that works.

[will-moore]

That worked! Thanks 👍

The thread above might be useful to others for installing, so hopefully you can include this in the install docs?

Also, just wondering if pylibczirw is needed for all usage of the library, or if it could be made optional for just the users who need it?

OK, now I have other questions, but I'll save that for a new issue...

[bugraoezdemir]

@will-moore,

Great to hear that it worked and thanks again for the helpful report!

I agree that this thread could be useful for others troubleshooting similar installation issues. I’ll update the documentation accordingly.

Regarding pylibczirw, it is a specific requirement for reading .czi files. Making certain readers optional is indeed a good idea. I will look into supporting that in a future release.