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update for pyopenms 3.2.0 #138

Merged
merged 19 commits into from
Oct 4, 2024
Merged

update for pyopenms 3.2.0 #138

merged 19 commits into from
Oct 4, 2024

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jcharkow
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@jcharkow jcharkow commented Oct 1, 2024

Description

  1. rename PeakPickerMRM to PeakPickerChromatogram (pyOpenMS 3.2 update)
  2. Deprecate the requirements.txt, have everything in the .toml file
  3. Add different ways to install to .toml file including separating out the GUI dependencies from the other dependencies.
  4. Update plotting test snapshot (for plotly) to be consistent with new version

Contents (#138)

Other

  • exclude plotly tests on mac
  • fix: another bug
  • test: another bug
  • update peak picker docs

Uncategorised!

  • update for pyopenms==3.2.0
  • temp remove mac tests
  • add mac test back for testing
  • remove all tests from mac
  • fix bug in pytest mark
  • test windows
  • update ci.yml
  • update ci.yml
  • use .toml instead of requirements
  • update pyprject
  • update pyproject
  • remove streamlit dependency transitionPQPDataAccess
  • updates to pyprophet.toml
  • remove streamlit dependency from non gui elements
  • add back all os and python versions

rename PeakPickerMRM to PeakPickerChromatogram
exclude plotly tests on mac and windows due to different results
seems that tests in mac still failing so different from windows
was not skipping on mac
update everything to v5
possibly version dependencies will be better if use .toml
do not use flit
also update snapshots for new plotly
update peak picker docs to fix the broken links
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@singjc singjc left a comment

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I haven't tested, but everything looks good to me.

@@ -43,6 +43,7 @@ def test_plot_3d_vline(featureMap, snapshot_plotly):
fig = plotter.plot(featureMap)
assert snapshot_plotly == fig

@pytest.mark.skipif(sys.platform == 'darwin', reason="Plots slightly different on mac")
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Why/how is it different?

@jcharkow jcharkow merged commit a9a5c8a into dev Oct 4, 2024
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2 participants