Test notebooks with CIL v25.0.0

[hrobarts]

Summary
Tried testing the notebooks with https://github.com/TomographicImaging/Build-scripts/blob/demo_script/test_notebooks.py

Found the following issues

• 05_esrf_pipeline.iynb: ValueError: Compression bits not valid. Got 0 expected value in [None, 'uint8', 'uint16']. Fixed with Update default compression for TIFFWriter set_up CIL#2197
• Found some latex rendering errors fixed with Update latex in directional TV, PDHG and SPDHG notebooks #268
• Found some warnings caused by dxchange, fixed with io.ZEISSDataReader: suppress dxchange<=0.2.0 warnings CIL#2207
• Found some warnings caused by unused kwargs, fixed with remove unused kwargs being passed to DataContainer CIL#2206

[hrobarts]

Re test before release. F shows errors or warnings

• demos/1_Introduction/05_usb_limited_angle_fbp_sirt_tmp.ipynb F

data = ZEISSDataReader(file_name=filename).read()
Gives warning:
miniconda3/envs/cil/lib/python3.10/site-packages/dxchange/__init__.py:63: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. import pkg_resources

• demos/1_Introduction/exercises/01_intro_seeds_conebeam_tmp.ipynb F

Unused kwarg 'deep' in TIFF fixed in TomographicImaging/CIL#2206

• demos/1_Introduction/exercises/02_preprocessing_seeds_conebeam_tmp.ipynb F
  Unused kwarg 'deep' in TIFF and 'supress_warning' in image sharpness fixed in remove unused kwargs being passed to DataContainer CIL#2206

• demos/3_Multichannel/03_Hyperspectral_reconstruction_tmp.ipynb F

• demos/2_Iterative/05_Laminography_with_TV_tmp.ipynb F

Unused kwarg 'deep' fixed in TomographicImaging/CIL#2206

• demos/2_Iterative/03_PDHG_tmp.ipynb F
  Same ZeissDataReader warning as above
• demos/2_Iterative/02_tikhonov_block_framework_tmp.ipynb F
• demos/4_Deep_Dives/05_esrf_pipeline_tmp.ipynb F
• demos/4_Deep_Dives/06_directional_TV_tmp.ipynb F

[casperdcl]

pip install git+https://github.com/data-exchange/dxchange.git might be useful whilst we wait for dxchange#121 which will be in the next release (dxchange>0.2.0)

nvm added CIL#2207

[hrobarts]

Callback demo has a runtime user warning
#232

[hrobarts]

Tested notebooks with: https://github.com/TomographicImaging/scripts/blob/demo_script/test_notebooks_sequential.py
Outputs saved here: https://github.com/TomographicImaging/scripts/tree/demo_script/html_outputs

Scratch this - I can't get the script to consistently render our very varied latex to PDF or html.
I am now saving the rendered ipynb files temporarily: https://github.com/TomographicImaging/scripts/tree/demo_script/tmp_notebooks

I will upload them when the tests have run, so far I've checked

• 1_Introduction
• 2_Iterative
• 3_Multichannel
• 4_Deep_Dives
  • Directional TV has a parse error Update latex in directional TV, PDHG and SPDHG notebooks #268

TQDM has an error when I run it inside the script. I see this in a few places and confirm it doesn't happen if you run the notebook directly. If you see this in the rendered notebooks it can be ignored.

Exception in thread Thread-4:
LookupError: <ContextVar name='shell_parent' at 0x7f610859c180>