Update dependencies in poetry.lock and improve GHAs

[tcompa]

Updated dependencies:

Updating dependencies
Resolving dependencies...

Package operations: 0 installs, 14 updates, 0 removals

  - Updating typing-extensions (4.14.1 -> 4.15.0)
  - Updating platformdirs (4.3.8 -> 4.4.0)
  - Updating tornado (6.5.1 -> 6.5.2)
  - Updating certifi (2025.7.14 -> 2025.8.3)
  - Updating charset-normalizer (3.4.2 -> 3.4.3)
  - Updating requests (2.32.4 -> 2.32.5)
  - Updating wrapt (1.17.2 -> 1.17.3)
  - Updating pandas (2.3.1 -> 2.3.2)
  - Updating fasteners (0.19 -> 0.20)
  - Updating multidict (6.6.3 -> 6.6.4)
  - Updating ome-zarr-models (0.1.9 -> 0.1.10)
  - Updating polars (1.31.0 -> 1.33.0)
  - Updating xarray (2025.7.1 -> 2025.8.0)
  - Updating ngio (0.2.10 -> 0.2.12)

Writing lock file

Outdated dependencies before PR:

anndata                                            0.10.9             
anyio                                          (!) 4.9.0              
argon2-cffi-bindings                           (!) 21.2.0             
astropy-iers-data                              (!) 0.2025.7.28.0.41.50
asttokens                                      (!) 2.4.1              
beautifulsoup4                                 (!) 4.13.4             
build                                          (!) 1.2.2.post1        
cellpose                                       (!) 2.2.3              
certifi                                            2025.7.14          
charset-normalizer                                 3.4.2              
debugpy                                        (!) 1.8.15             
docstring-parser                                   0.16               
docutils                                       (!) 0.21.2             
eval-type-backport                                 0.1.3              
executing                                      (!) 0.10.0             
fasteners                                          0.19               
fastjsonschema                                 (!) 2.21.1             
fastremap                                      (!) 1.17.2             
filelock                                           3.13.4             
fonttools                                      (!) 4.59.0             
fractal-task-tools                                 0.0.12             
imagecodecs                                    (!) 2025.3.30          
imageio-ffmpeg                                 (!) 0.4.9              
ipycanvas                                      (!) 0.13.3             
ipykernel                                      (!) 6.30.0             
ipython                                        (!) 9.4.0              
json5                                          (!) 0.12.0             
jsonschema                                     (!) 4.25.0             
jupyter-lsp                                    (!) 2.2.6              
jupyter-server                                 (!) 2.16.0             
jupyterlab                                     (!) 4.4.5              
jupytext                                       (!) 1.17.2             
kiwisolver                                     (!) 1.4.8              
lxml                                               5.4.0              
markdown-it-py                                 (!) 3.0.0              
matplotlib                                     (!) 3.10.3             
mdit-py-plugins                                (!) 0.4.2              
mistune                                        (!) 3.1.3              
multidict                                          6.6.3              
napari                                         (!) 0.6.2              
napari-segment-blobs-and-things-with-membranes (!) 0.3.8              
napari-skimage-regionprops                     (!) 0.8.2              
ngio                                               0.2.10             
notebook                                       (!) 7.4.4              
numcodecs                                          0.15.1             
numpy                                              2.1.0              
nvidia-cublas-cu12                             (!) 12.6.4.1           
nvidia-cuda-cupti-cu12                         (!) 12.6.80            
nvidia-cuda-nvrtc-cu12                         (!) 12.6.77            
nvidia-cuda-runtime-cu12                       (!) 12.6.77            
nvidia-cudnn-cu12                              (!) 9.5.1.17           
nvidia-cufft-cu12                              (!) 11.3.0.4           
nvidia-cufile-cu12                             (!) 1.11.1.6           
nvidia-curand-cu12                             (!) 10.3.7.77          
nvidia-cusolver-cu12                           (!) 11.7.1.2           
nvidia-cusparse-cu12                           (!) 12.5.4.2           
nvidia-cusparselt-cu12                         (!) 0.6.3              
nvidia-nccl-cu12                               (!) 2.26.2             
nvidia-nvjitlink-cu12                          (!) 12.6.85            
nvidia-nvtx-cu12                               (!) 12.6.77            
ome-zarr-models                                    0.1.9              
pandas                                             2.3.1              
parso                                          (!) 0.8.4              
pint                                           (!) 0.24.4             
platformdirs                                       4.3.8              
polars                                             1.31.0             
pooch                                              1.8.0              
prompt-toolkit                                 (!) 3.0.51             
psygnal                                        (!) 0.14.0             
pydantic                                           2.8.2              
pydantic-core                                      2.20.1             
pydantic-zarr                                      0.7.0              
pyopengl                                       (!) 3.1.9              
pytest                                         (!) 7.4.4              
pyzmq                                          (!) 27.0.0             
requests                                           2.32.4             
rpds-py                                        (!) 0.26.0             
soupsieve                                      (!) 2.7                
stack-data                                     (!) 0.5.1              
stackview                                      (!) 0.8.2              
superqt                                        (!) 0.7.5              
tifffile                                       (!) 2025.6.11          
torch                                          (!) 2.7.1              
tornado                                            6.5.1              
triton                                         (!) 3.3.1              
typer                                          (!) 0.16.0             
types-python-dateutil                          (!) 2.9.0.20250708     
typing-extensions                                  4.14.1             
wrapt                                              1.17.2             
xarray                                             2025.7.1           
zarr                                               2.18.7             

Outdated dependencies after PR:

anndata                                            0.10.9    0.12.2    
asttokens                                      (!) 2.4.1     3.0.0     
cellpose                                       (!) 2.2.3     4.0.6     
docstring-parser                                   0.16      0.17.0    
docutils                                       (!) 0.21.2    0.22      
eval-type-backport                                 0.1.3     0.2.2     
executing                                      (!) 0.10.0    2.2.1     
filelock                                           3.13.4    3.19.1    
fractal-task-tools                                 0.0.12    0.0.13    
imageio-ffmpeg                                 (!) 0.4.9     0.6.0     
lxml                                               5.4.0     6.0.1     
napari-segment-blobs-and-things-with-membranes (!) 0.3.8     0.3.12    
napari-skimage-regionprops                     (!) 0.8.2     0.10.1    
ngio                                               0.2.12    0.3.5     
numcodecs                                          0.15.1    0.16.2    
numpy                                              2.1.0     2.3.2     
nvidia-cublas-cu12                             (!) 12.8.4.1  12.9.1.4  
nvidia-cuda-cupti-cu12                         (!) 12.8.90   12.9.79   
nvidia-cuda-nvrtc-cu12                         (!) 12.8.93   12.9.86   
nvidia-cuda-runtime-cu12                       (!) 12.8.90   12.9.79   
nvidia-cudnn-cu12                              (!) 9.10.2.21 9.12.0.46 
nvidia-cufft-cu12                              (!) 11.3.3.83 11.4.1.4  
nvidia-cufile-cu12                             (!) 1.13.1.3  1.14.1.1  
nvidia-curand-cu12                             (!) 10.3.9.90 10.3.10.19
nvidia-cusolver-cu12                           (!) 11.7.3.90 11.7.5.82 
nvidia-cusparse-cu12                           (!) 12.5.8.93 12.5.10.65
nvidia-cusparselt-cu12                         (!) 0.7.1     0.8.0     
nvidia-nccl-cu12                               (!) 2.27.3    2.27.7    
nvidia-nvjitlink-cu12                          (!) 12.8.93   12.9.86   
nvidia-nvtx-cu12                               (!) 12.8.90   12.9.79   
ome-zarr-models                                    0.1.10    1.0.0     
pooch                                              1.8.0     1.8.2     
pydantic                                           2.8.2     2.11.7    
pydantic-core                                      2.20.1    2.39.0    
pydantic-zarr                                      0.7.0     0.8.3     
pytest                                         (!) 7.4.4     8.4.1     
stack-data                                     (!) 0.5.1     0.6.3     
stackview                                      (!) 0.8.2     0.18.0    
zarr                                               2.18.7    3.1.2     

Note: there may be dependencies in the table above which were not updated as part of this PR.
The reason is they require manual updating due to the way they are pinned.

[github-actions]

Coverage report

This PR does not seem to contain any modification to coverable code.

[tcompa]

At least part of the CI issues were related to the GHA caching of the poetry environment. For the moment I simply disabled it.