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NickAkhmetov/HMP-159 Upgrade vitessce-python dependency #81

Merged
merged 27 commits into from
Aug 14, 2023
Merged

NickAkhmetov/HMP-159 Upgrade vitessce-python dependency #81

merged 27 commits into from
Aug 14, 2023

Commits on Jul 18, 2023

  1. Upgrade vitessce-python dependency

    @NickAkhmetov
    NickAkhmetov committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. replace deprecated view types with new ones

    @NickAkhmetov
    NickAkhmetov committed Jul 19, 2023
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Commits on Aug 3, 2023

  1. update changed names 

    use schema version 1.0.15
use vitessce version 3.0.6
    @NickAkhmetov
    NickAkhmetov committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. CODEX Cytokit + SPRM config works

    @NickAkhmetov
    NickAkhmetov committed Aug 4, 2023
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  2. snATAC-seq config works

    @NickAkhmetov
    NickAkhmetov committed Aug 4, 2023
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  3. snRNA-seq Salmon works

    @NickAkhmetov
    NickAkhmetov committed Aug 4, 2023
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Commits on Aug 7, 2023

  1. MIBI DeepCell+SPRM works

    @NickAkhmetov
    NickAkhmetov committed Aug 7, 2023
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Commits on Aug 8, 2023

  1. snRNA-seq (SNARE-seq2) [Salmon] works

    @NickAkhmetov
    NickAkhmetov committed Aug 8, 2023
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  2. handle coordination values for cases with multiple obsLabels, handle … 

    …old SPRM datasets, troubleshoot tooltip contents
    @NickAkhmetov
    NickAkhmetov committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. autopep8 fixes

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  2. more lint fixes (mostly line length and imports) 

    added vs code ruler to make it easier to spot when lines are too long
    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  3. trailing whitespace fixes

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  4. fix replace_url_in_file test

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  5. update RNASeqViewConfBuilder test conf

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  6. update MultiImageSPRMAnndataViewConfBuilder test

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  7. ATACSeqViewConfBuilder test fixed

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  8. updated StitchedCytokitSPRMViewConfBuilder test

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  9. use obs sets instead of label coordinations to keep tooltips usable, … 

    …update RNASeqAnnDataZarrViewConfBuilder tests
    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  10. update seqfish

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  11. update spatialrnaseqanndatazarrviewconfigbuilder marker gene test case

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  12. update remaining test fixtures

    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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  13. comment out currently unused util function to keep it from affecting … 

    …test coverage
    @NickAkhmetov
    NickAkhmetov committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. Use pending changes from vitessce 3.0.7

    @NickAkhmetov
    NickAkhmetov committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. update fixtures

    @NickAkhmetov
    NickAkhmetov committed Aug 11, 2023
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Commits on Aug 14, 2023

  1. Removed outdated comment

    @NickAkhmetov
    NickAkhmetov authored Aug 14, 2023
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  2. Add _schema_version to base builder with a default of 1.0.15

    @NickAkhmetov
    NickAkhmetov committed Aug 14, 2023
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  3. Add create_coordination_values helper util

    @NickAkhmetov
    NickAkhmetov committed Aug 14, 2023
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