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Vectorize impedance matrix calculation for different expansion points #130

Merged
merged 18 commits into from
Jan 25, 2022
Merged

Vectorize impedance matrix calculation for different expansion points #130

merged 18 commits into from
Jan 25, 2022

Commits on Jun 3, 2021

  1. apply normal numpy broadcasting rules to output of ion channel functions

    @WillemWybo
    WillemWybo committed Jun 3, 2021
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  2. adjust ionchannel docstrings

    @WillemWybo
    WillemWybo committed Jun 3, 2021
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  3. expansion point can contain vector of holding potentials in neat.Gree… 

    …nsTree
    @WillemWybo
    WillemWybo committed Jun 3, 2021
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  4. rewrite compartmentfitter.getExpansionPoints to output vectorized exp… 

    …ansion points
    @WillemWybo
    WillemWybo committed Jun 3, 2021
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  5. work in progress on vectorizing impedance matrix calculation for diff… 

    …erent expansion points
    @WillemWybo
    WillemWybo committed Jun 3, 2021
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  6. progress towards vectorization, still a broadcasting error in greenst… 

    …ree when the ion channel is not present at some nodes
    @WillemWybo
    WillemWybo committed Jun 3, 2021
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Commits on Jun 4, 2021

  1. resolve numpy broadcasting bugs in greenstree

    @WillemWybo
    WillemWybo committed Jun 4, 2021
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  2. cleanup compartmentfitter tests

    @WillemWybo
    WillemWybo committed Jun 4, 2021
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  3. remove unused function

    @WillemWybo
    WillemWybo committed Jun 4, 2021
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Commits on Jan 7, 2022

  1. Use format strings 

    Co-authored-by: Jakob Jordan <1562742+jakobj@users.noreply.github.com>
    @WillemWybo @jakobj
    WillemWybo and jakobj committed Jan 7, 2022
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  2. Use format strings 

    Co-authored-by: Jakob Jordan <1562742+jakobj@users.noreply.github.com>
    @WillemWybo @jakobj
    WillemWybo and jakobj committed Jan 7, 2022
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  3. ignore division by zero warning because it yields inf, the intended r… 

    …esult
    @WillemWybo
    WillemWybo committed Jan 7, 2022
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  4. merge remote

    @WillemWybo
    WillemWybo committed Jan 7, 2022
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  5. add comment on possible division by zero

    @WillemWybo
    WillemWybo committed Jan 7, 2022
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  6. added comment on L224 in neat/trees/greenstree

    @WillemWybo
    WillemWybo committed Jan 7, 2022
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  7. activate tests when not using pytest

    @WillemWybo
    WillemWybo committed Jan 7, 2022
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  8. encapsulate activation test in separate function

    @WillemWybo
    WillemWybo committed Jan 7, 2022
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Commits on Jan 25, 2022

  1. change to in-place addition in greenstree line 226

    @WillemWybo
    WillemWybo committed Jan 25, 2022
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