Refactor/pyopenms viz no streamlit

[jcharkow]

Description

Integrates pyopenms_viz plotting with the python plot_chromatogram function. Relevant tests should be in pyopenms_viz

Please delete options that are not relevant.

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• [ ] Test A
• [ ] Test B

Test Configuration:

• Firmware version:
• Hardware:

Checklist:

• [ ] My code follows the style guidelines of this project
• [ ] I have performed a self-review of my code
• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] I have made corresponding changes to the documentation
• [ ] My changes generate no new warnings
• [ ] I have added tests that prove my fix is effective or that my feature works
• [ ] New and existing unit tests pass locally with my changes
• [ ] Any dependent changes have been merged and published in downstream modules

  Contents (#151)

Other

• add warning message to 1D plotting docs
• auto labelling by software
• typing for python 3.9
• add runNames parameter for loadTransitionGroupFeatures
• add tests for loadTransitionGroupFeatures
• temp workaround fix for bokeh 3.0 and streamlit
• update plotting snapshots for new bokeh
• fix plotting for bokeh 3.6.0
• add back deleted snapshots
• fix: rendering of figures in docs

Uncategorised!

• initial implementation of pyopenms_viz
• update pyproject .toml
• Merge branch 'refactor/resultsPlotting' into refactor/pyopenms_viz_no_streamlit
• Merge branch 'refactor/resultsPlotting' into refactor/pyopenms_viz_no_streamlit
• add guassian smoothing
• Merge branch 'dev' into refactor/pyopenms_viz_no_streamlit
• remove support for python 3.9
• update 3d plot snapshots

[jcharkow]

Note: This updates bokeh to 3.0 which has breaking changes with bokeh 2.4.3. Thus currently old plotting does not work with this PR.

[singjc]

Note: This updates bokeh to 3.0 which has breaking changes with bokeh 2.4.3. Thus currently old plotting does not work with this PR.

I added a workaround to get bokeh 3.x working with the current version of streamlit to this PR, tested the example sqMass and raw data workflow in GUI and it works fine with rendering the plots. Everything else looks good.

If you're fine with including the bokeh 3.x fix in this PR, you can go ahead and merge.