hdf5 upload error

[jrapaka1]

I am trying to upload an hdf5 file using napari-itk-io but I am getting the following error message:

I have tried installing the plugin using both pip and conda install, but I still get the "there is no registered plugin named 'napari-itk-io'" error. Is there any other way to troubleshoot this?

[thewtex]

@jrapaka1 @jni are there missing entry points, etc. for the io plugin?

[jni]

As a side note, is itk missing in conda-forge? Or maybe just the macos-arm build?

$ micromamba install napari-itk-io
conda-forge/osx-arm64                               10.3MB @   3.0MB/s  3.4s
conda-forge/noarch                                  15.1MB @   3.8MB/s  3.9s

Pinned packages:
  - python 3.11.*

error    libmamba Could not solve for environment specs
    The following package could not be installed
    └─ napari-itk-io is not installable because it requires
       └─ itk >=5.2.0 , which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs

[jni]

Ok so I was able to:

• create a new environment with micromamba env create -n itk python=3.11 pip napari pyqt
• activate it
• install napari-itk-io with pip install napari-itk-io
• check that napari sees napari itk io:

$ napari --info
napari: 0.4.19.post1
Platform: macOS-14.5-arm64-arm-64bit
System: MacOS 14.5
Python: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ]
Qt: 5.15.8
PyQt5: 5.15.9
NumPy: 1.26.4
SciPy: 1.13.1
Dask: 2024.6.2
VisPy: 0.14.3
magicgui: 0.8.3
superqt: 0.6.7
in-n-out: 0.2.1
app-model: 0.2.7
npe2: 0.7.5

OpenGL:
  - GL version:  2.1 Metal - 88.1
  - MAX_TEXTURE_SIZE: 16384

Screens:
  - screen 1: resolution 1800x1169, scale 2.0

Settings path:
  - /Users/jni/Library/Application Support/napari/itk_381931df36dd163c9f05267134379b2e0734e80c/settings.yaml
Plugins:
  - napari: 0.4.19.post1 (77 contributions)
  - napari-console: 0.0.9 (0 contributions)
  - napari-itk-io: 0.3.0 (6 contributions)
  - napari-svg: 0.1.10 (2 contributions)

and

$ napari --plugin-info
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Name           ┃ Version      ┃ Npe2 ┃ Contributions                         ┃
┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ napari         │ 0.4.19.post1 │ ✅   │ commands (38), readers (1), writers   │
│                │              │      │ (6), sample_data (32)                 │
│ napari-console │ 0.0.9        │ ✅   │                                       │
│ napari-itk-io  │ 0.3.0        │ ✅   │ commands (3), readers (1), writers    │
│                │              │      │ (2)                                   │
│ napari-svg     │ 0.1.10       │ ✅   │ commands (1), writers (1)             │
└────────────────┴──────────────┴──────┴───────────────────────────────────────┘

@jrapaka1 can you share the outputs of napari --info and napari --plugin-info in your case?

(@thewtex so the answer is no, there doesn't seem to be anything wrong here.)

[thewtex]

As a side note, is itk missing in conda-forge?

Yes, pip-only at the moment :-(

[thewtex]

@jni thank you for your expertise and help! :100: :pray: :1st_place_medal: