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Speed upgrade - Refactor generate network #152

Merged
merged 99 commits into from Jun 22, 2022
Merged

Speed upgrade - Refactor generate network #152

merged 99 commits into from Jun 22, 2022

Commits on Jun 6, 2022

  1. clean up verbosity steps

    @zktuong
    zktuong committed Jun 6, 2022
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  2. Update _core.py 

    fix issue with querier
    @zktuong
    zktuong committed Jun 6, 2022
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Commits on Jun 7, 2022

  1. add deprecation

    @zktuong
    zktuong committed Jun 7, 2022
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  2. deprecate distance

    @zktuong
    zktuong committed Jun 7, 2022
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  3. Update _tools.py 

    deprecate distance
    @zktuong
    zktuong committed Jun 7, 2022
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  4. speed up generate network and transfer

    @zktuong
    zktuong committed Jun 7, 2022
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  5. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  6. oops

    @zktuong
    zktuong committed Jun 7, 2022
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  7. Update _network.py 

    make generate network more verbose
    @zktuong
    zktuong committed Jun 7, 2022
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  8. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  9. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  10. small bug

    @zktuong
    zktuong committed Jun 7, 2022
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  11. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  12. Update _network.py 

    try and free up memory
    @zktuong
    zktuong committed Jun 7, 2022
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  13. update documentations

    @zktuong
    zktuong committed Jun 7, 2022
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  14. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  15. Update _network.py

    @zktuong
    zktuong committed Jun 7, 2022
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  16. update tests

    @zktuong
    zktuong committed Jun 7, 2022
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  17. Update test_plotting.py

    @zktuong
    zktuong committed Jun 7, 2022
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  18. Update test_tools_light.py

    @zktuong
    zktuong committed Jun 7, 2022
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Commits on Jun 9, 2022

  1. Update _io.py

    @zktuong
    zktuong committed Jun 9, 2022
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  2. update note books

    @zktuong
    zktuong committed Jun 9, 2022
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  3. add check for transfer = True

    @zktuong
    zktuong committed Jun 9, 2022
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Commits on Jun 10, 2022

  1. fix #154

    @zktuong
    zktuong committed Jun 10, 2022
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  2. Update test_io.py

    @zktuong
    zktuong committed Jun 10, 2022
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  3. Update _network.py

    @zktuong
    zktuong committed Jun 10, 2022
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  4. Update _tools.py

    @zktuong
    zktuong committed Jun 10, 2022
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  5. update notebooks

    @zktuong
    zktuong committed Jun 10, 2022
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Commits on Jun 11, 2022

  1. Update _network.py

    @zktuong
    zktuong committed Jun 11, 2022
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  2. reduce plot size

    @zktuong
    zktuong committed Jun 11, 2022
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Commits on Jun 13, 2022

  1. Update _preprocessing.py 

    speed update
    @zktuong
    zktuong committed Jun 13, 2022
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  2. slight update to notebooks

    @zktuong
    zktuong committed Jun 13, 2022
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  3. Update _preprocessing.py 

    test speed upgrade
    @zktuong
    zktuong committed Jun 13, 2022
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  4. Update _preprocessing.py

    @zktuong
    zktuong committed Jun 13, 2022
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  5. speed increase in io?

    @zktuong
    zktuong committed Jun 13, 2022
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  6. speed up dandelion initialisation

    @zktuong
    zktuong committed Jun 13, 2022
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  7. Update _utilities.py 

    add a sort function
    @zktuong
    zktuong committed Jun 13, 2022
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  8. oops

    @zktuong
    zktuong committed Jun 13, 2022
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  9. Update _io.py 

    silence deprecation warning
    @zktuong
    zktuong committed Jun 13, 2022
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  10. refactor Dandelion initialisation

    @zktuong
    zktuong committed Jun 13, 2022
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  11. Update test_io.py

    @zktuong
    zktuong committed Jun 13, 2022
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  12. Update _core.py 

    rename to be clearer
    @zktuong
    zktuong committed Jun 13, 2022
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  13. Update test_tools.py

    @zktuong
    zktuong committed Jun 13, 2022
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  14. Update _core.py 

    oops
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    zktuong committed Jun 13, 2022
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Commits on Jun 14, 2022

  1. Update _io.py

    @zktuong
    zktuong committed Jun 14, 2022
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  2. update notebooks

    @zktuong
    zktuong committed Jun 14, 2022
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  3. Update test_tools.py

    @zktuong
    zktuong committed Jun 14, 2022
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  4. Update _tools.py

    @zktuong
    zktuong committed Jun 14, 2022
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  5. remove d_call_VJ column from final output.

    @zktuong
    zktuong committed Jun 14, 2022
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  6. update docs

    @zktuong
    zktuong committed Jun 14, 2022
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  7. update swap to 'None'

    @zktuong
    zktuong committed Jun 14, 2022
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  8. clean up code

    @zktuong
    zktuong committed Jun 14, 2022
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  9. Update _tools.py

    @zktuong
    zktuong committed Jun 14, 2022
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  10. further speed upgrade for filter_contigs

    @zktuong
    zktuong committed Jun 14, 2022
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Commits on Jun 15, 2022

  1. typo

    @zktuong
    zktuong committed Jun 15, 2022
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  2. Update _network.py 

    add graph-tool
    @zktuong
    zktuong committed Jun 15, 2022
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  3. Update test_tools.py 

    test graph-tool
    @zktuong
    zktuong committed Jun 15, 2022
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  4. update dependencies

    @zktuong
    zktuong committed Jun 15, 2022
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  5. typo

    @zktuong
    zktuong committed Jun 15, 2022
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  6. can't pip install graph-tool

    @zktuong
    zktuong committed Jun 15, 2022
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  7. Update _network.py

    @zktuong
    zktuong committed Jun 15, 2022
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  8. Update _network.py 

    order of nodes are not the same
    @zktuong
    zktuong committed Jun 15, 2022
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  9. Update _network.py 

    don't force install of graph_tool.

also fix bug where min_size wasn't respected.
    @zktuong
    zktuong committed Jun 15, 2022
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  10. Update _network.py

    @zktuong
    zktuong committed Jun 15, 2022
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  11. Update _network.py 

    typo
    @zktuong
    zktuong committed Jun 15, 2022
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  12. rescue docs

    @zktuong
    zktuong committed Jun 15, 2022
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  13. Update test_mouse3.py

    @zktuong
    zktuong committed Jun 15, 2022
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  14. Update test_mouse.py

    @zktuong
    zktuong committed Jun 15, 2022
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  15. bump version

    @zktuong
    zktuong committed Jun 15, 2022
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  16. bump versions

    @zktuong
    zktuong committed Jun 15, 2022
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  17. typo in read mes

    @zktuong
    zktuong committed Jun 15, 2022
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Commits on Jun 16, 2022

  1. Update environment.yml

    @zktuong
    zktuong committed Jun 16, 2022
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Commits on Jun 17, 2022

  1. Update requirements.txt 

    does this work?
    @zktuong
    zktuong committed Jun 17, 2022
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  2. Update requirements.txt

    @zktuong
    zktuong committed Jun 17, 2022
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  3. Update _plotting.py

    @zktuong
    zktuong committed Jun 17, 2022
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Commits on Jun 18, 2022

  1. Update _tools.py

    @zktuong
    zktuong committed Jun 18, 2022
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  2. Update _plotting.py

    @zktuong
    zktuong committed Jun 18, 2022
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  3. Update test_mouse_plotting.py

    @zktuong
    zktuong committed Jun 18, 2022
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  4. Update _tools.py 

    formatting
    @zktuong
    zktuong committed Jun 18, 2022
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  5. Update _preprocessing.py

    @zktuong
    zktuong committed Jun 18, 2022
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  6. move fixtures

    @zktuong
    zktuong committed Jun 18, 2022
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  7. Update fixtures.py 

    formatting
    @zktuong
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  8. let's see if this works

    @zktuong
    zktuong committed Jun 18, 2022
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  9. black code style check

    @zktuong
    zktuong committed Jun 18, 2022
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  10. fix doctstring and typos

    @zktuong
    zktuong committed Jun 18, 2022
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  11. Update test_rpy2.py

    @zktuong
    zktuong committed Jun 18, 2022
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  12. Update _plotting.py 

    fix typo
    @zktuong
    zktuong committed Jun 18, 2022
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  13. check doc strings again

    @zktuong
    zktuong committed Jun 18, 2022
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  14. fix docstrings

    @zktuong
    zktuong committed Jun 18, 2022
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  15. Update test_filter.py

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  16. Update test_preprocessing.py

    @zktuong
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  17. Update test_zz_mouse3.py

    @zktuong
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  18. Update test_zz_mouse3.py

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Commits on Jun 20, 2022

  1. Update _diversity.py

    @zktuong
    zktuong committed Jun 20, 2022
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  2. Update _network.py 

    faster way to build the matrix
    @zktuong
    zktuong committed Jun 20, 2022
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Commits on Jun 21, 2022

  1. Update _network.py 

    simplify the membership construction
    @zktuong
    zktuong committed Jun 21, 2022
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  2. small bug with the recent speed upgrade

    @zktuong
    zktuong committed Jun 21, 2022
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  3. Update _utilities.py

    @zktuong
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Commits on Jun 22, 2022

  1. Create test_load_data.py

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