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Add CvodeBlock and CvodeVisitor #1467

Merged
merged 55 commits into from
Oct 28, 2024
Merged

Add CvodeBlock and CvodeVisitor #1467

merged 55 commits into from
Oct 28, 2024

Commits on Sep 24, 2024

  1. Add DerivativeOriginalFunctionBlock and DerivativeVisitor

    @JCGoran
    JCGoran committed Sep 24, 2024
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  2. Remove unused functions

    @JCGoran
    JCGoran committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Add test for DerivativeOriginalVisitor

    @JCGoran
    JCGoran committed Sep 25, 2024
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  2. Fmt

    @JCGoran
    JCGoran committed Sep 25, 2024
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  3. Fix leak

    @JCGoran
    JCGoran committed Sep 25, 2024
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  4. Remove unused stuff 

    `DERIVATIVE` blocks can't have array variables in NOCMODL by default, so
let's go with that.
    @JCGoran
    JCGoran committed Sep 25, 2024
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  5. Update block description

    @JCGoran
    JCGoran committed Sep 25, 2024
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Commits on Sep 27, 2024

  1. Rename DERIVATIVE_ORIGINAL to CVODE

    @JCGoran
    JCGoran committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. Finish renaming

    @JCGoran
    JCGoran committed Sep 30, 2024
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  2. Add item with Jacobian

    @JCGoran
    JCGoran committed Sep 30, 2024
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  3. Merge branch 'master' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Sep 30, 2024
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  4. Do not use an int but an enum-wrapped int

    @JCGoran
    JCGoran committed Sep 30, 2024
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  5. Add support for diffing expressions with indexed vars

    @JCGoran
    JCGoran committed Sep 30, 2024
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  6. Allow diffing implicit functions in differentiate2c 

    Uses finite differences
    @JCGoran
    JCGoran committed Sep 30, 2024
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  7. Simplify condition

    @JCGoran
    JCGoran committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Better testing

    @JCGoran
    JCGoran committed Oct 1, 2024
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  2. Add suggestions from code review

    @JCGoran
    JCGoran committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Add stepsize param to differentiate2c

    @JCGoran
    JCGoran committed Oct 2, 2024
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  2. Merge remote-tracking branch 'origin/master' into jelic/diff_implicit

    @JCGoran
    JCGoran committed Oct 2, 2024
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  3. Try Python 3.9 maybe?

    @JCGoran
    JCGoran committed Oct 2, 2024
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  4. Merge branch 'jelic/diff_indexed' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 2, 2024
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  5. Merge branch 'jelic/diff_implicit' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 2, 2024
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Commits on Oct 7, 2024

  1. Merge remote-tracking branch 'origin/master' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 7, 2024
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  2. Put back Python 3.8 for now

    @JCGoran
    JCGoran committed Oct 7, 2024
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  3. Remove remaining occurrences of DerivativeOriginalVisitor

    @JCGoran
    JCGoran committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. WIP on CONSERVE

    @JCGoran
    JCGoran committed Oct 8, 2024
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Commits on Oct 9, 2024

  1. Ignore CONSERVE equations 

    They are just hints to the NMODL compiler, but they are not at all
necessary to use when solving the ODEs.
    @JCGoran
    JCGoran committed Oct 9, 2024
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Commits on Oct 10, 2024

  1. Add documentation

    @JCGoran
    JCGoran committed Oct 10, 2024
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  2. Really delete CONSERVE statements this time

    @JCGoran
    JCGoran committed Oct 10, 2024
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  3. Add test for CONSERVE statement

    @JCGoran
    JCGoran committed Oct 10, 2024
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  4. Fix variable naming

    @JCGoran
    JCGoran committed Oct 10, 2024
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  5. Update docstring

    @JCGoran
    JCGoran committed Oct 10, 2024
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  6. Fix typo

    @JCGoran
    JCGoran committed Oct 10, 2024
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  7. Update docstring

    @JCGoran
    JCGoran committed Oct 10, 2024
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Commits on Oct 14, 2024

  1. Merge branch 'master' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 14, 2024
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  2. Add option for diffing IndexedName

    @JCGoran
    JCGoran committed Oct 14, 2024
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  3. Refactor

    @JCGoran
    JCGoran committed Oct 14, 2024
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  4. Merge branch 'master' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 14, 2024
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  5. Enable sympy if NEURON codegen

    @JCGoran
    JCGoran committed Oct 14, 2024
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  6. Mark constructors as explicit

    @JCGoran
    JCGoran committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. Merge branch 'master' into jelic/cvode_visitors

    @JCGoran
    JCGoran committed Oct 15, 2024
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  2. Update tests

    @JCGoran
    JCGoran committed Oct 15, 2024
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  3. Remove code duplication

    @JCGoran
    JCGoran committed Oct 15, 2024
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  4. Remove unused class field

    @JCGoran
    JCGoran committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. Only enable sympy if DERIVATIVE block exists

    @JCGoran
    JCGoran committed Oct 16, 2024
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  2. Rename CVODE subblocks with more apt names

    @JCGoran
    JCGoran committed Oct 16, 2024
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  3. nonstiff -> non_stiff

    @JCGoran
    JCGoran committed Oct 16, 2024
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Commits on Oct 21, 2024

  1. Get # of ODEs to solve

    @JCGoran
    JCGoran committed Oct 21, 2024
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  2. der_block(s) -> derivative_block(s)

    @JCGoran
    JCGoran committed Oct 21, 2024
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  3. get_name_map -> get_indexed_variables 

    Also use a set since we don't care about the actual index for the RHS
    @JCGoran
    JCGoran committed Oct 21, 2024
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  4. Add check for multiple DERIVATIVE blocks

    @JCGoran
    JCGoran committed Oct 21, 2024
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  5. Update tests for CVODE

    @JCGoran
    JCGoran committed Oct 21, 2024
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  6. Update docs

    @JCGoran
    JCGoran committed Oct 21, 2024
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Commits on Oct 24, 2024

  1. Address comments from review

    @JCGoran
    JCGoran committed Oct 24, 2024
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  2. Fix variable name

    @JCGoran
    JCGoran committed Oct 24, 2024
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