Cvapipe_analysis, cannot run test case (shape analysis on 300 cells)

Software & Code
1

Description

A clear description of the bug

Successfully installed cvapipe_analysis, although I had to use Python 3.9 instead of Python 3.8 as recommended. I tried running cvapipe_analysis loaddata run --test, but the the command was not found.

-bash: cvapipe_analysis: command not found

Also, the config.yaml file does not appear in the cvapipe_analysis directory after this installation.

Reproduction

A minimal example that exhibits the behavior.

I ran these commands in order:

Lucass-MacBook-Pro:~ lucasphilipp$ conda create --name cvapipe python=3.8
Error while loading conda entry point: conda-libmamba-solver (dlopen(/Users/lucasphilipp/anaconda3/lib/python3.10/site-packages/libmambapy/bindings.cpython-310-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.13.dylib
  Referenced from: <076ECB5C-F72E-3262-85B7-5A6BCF91985A> /Users/lucasphilipp/anaconda3/lib/libmamba.2.0.0.dylib
  Reason: tried: '/Users/lucasphilipp/anaconda3/lib/libarchive.13.dylib' (no such file), '/Users/lucasphilipp/anaconda3/lib/python3.10/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/lucasphilipp/anaconda3/lib/python3.10/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/lucasphilipp/anaconda3/bin/../lib/libarchive.13.dylib' (no such file), '/Users/lucasphilipp/anaconda3/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file, not in dyld cache))
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.9.0
  latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

     conda install conda=25.1.1



## Package Plan ##

  environment location: /Users/lucasphilipp/anaconda3/envs/cvapipe

  added / updated specs:
    - python=3.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libsqlite-3.49.1           |       hdb6dae5_2         955 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         955 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7 
  ca-certificates    conda-forge/osx-64::ca-certificates-2025.1.31-h8857fd0_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_0 
  liblzma            conda-forge/osx-64::liblzma-5.6.4-hd471939_0 
  liblzma-devel      conda-forge/osx-64::liblzma-devel-5.6.4-hd471939_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.4.1-hc426f3f_0 
  pip                conda-forge/noarch::pip-22.1.2-pyhd8ed1ab_0 
  python             conda-forge/osx-64::python-3.8.20-h4f978b9_2_cpython 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  setuptools         conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0 
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 
  xz                 conda-forge/osx-64::xz-5.6.4-h357f2ed_0 
  xz-gpl-tools       conda-forge/osx-64::xz-gpl-tools-5.6.4-h357f2ed_0 
  xz-tools           conda-forge/osx-64::xz-tools-5.6.4-hd471939_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:
                                                                                
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cvapipe
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Lucass-MacBook-Pro:~ lucasphilipp$ conda activate cvapipe
(cvapipe) Lucass-MacBook-Pro:~ lucasphilipp$ git clone https://github.com/AllenCell/cvapipe_analysis.git
Cloning into 'cvapipe_analysis'...
remote: Enumerating objects: 3750, done.
remote: Counting objects: 100% (219/219), done.
remote: Compressing objects: 100% (169/169), done.
remote: Total 3750 (delta 68), reused 51 (delta 50), pack-reused 3531 (from 4)
Receiving objects: 100% (3750/3750), 190.15 MiB | 5.09 MiB/s, done.
Resolving deltas: 100% (2568/2568), done.
(cvapipe) Lucass-MacBook-Pro:~ lucasphilipp$ cd cvapipe_analysis
(cvapipe) Lucass-MacBook-Pro:cvapipe_analysis lucasphilipp$ pip install -e .
Obtaining file:///Users/lucasphilipp/cvapipe_analysis
  Preparing metadata (setup.py) ... done
Collecting jupyter
  Using cached jupyter-1.1.1-py2.py3-none-any.whl (2.7 kB)
Collecting aicsshparam
  Using cached aicsshparam-0.1.7-py2.py3-none-any.whl (13 kB)
Collecting aicscytoparam
  Using cached aicscytoparam-0.1.12-py2.py3-none-any.whl (15 kB)
ERROR: Package 'cvapipe-analysis' requires a different Python: 3.8.20 not in '>=3.9'
(cvapipe) Lucass-MacBook-Pro:cvapipe_analysis lucasphilipp$ python -V
Python 3.8.20
(cvapipe) Lucass-MacBook-Pro:cvapipe_analysis lucasphilipp$ conda install python=3.9
(cvapipe) Lucass-MacBook-Pro:cvapipe_analysis lucasphilipp$ cvapipe_analysis loaddata run --test
-bash: cvapipe_analysis: command not found
(cvapipe) Lucass-MacBook-Pro:cvapipe_analysis lucasphilipp$ cvapipe_analysis loaddata run --test
2

Hi @lucas.philipp1! Thanks for the detailed example. It looks like the editable install (pip install -e .) failed before the cvapipe installation completed due to the python version. Now that you’ve upgraded the python version, I’m curious if running that line again will help. Let me know what you find!

Best,
Benji