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Add cell builder utility functions #107

Merged
merged 54 commits into from
Aug 31, 2022
Merged

Add cell builder utility functions #107

merged 54 commits into from
Aug 31, 2022

Commits on Jul 26, 2022

  1. feat: add cell builder utilities

    @sanjayankur31
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  2. feat: propagate validation result to writer

    @sanjayankur31
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  3. feat: add cell builder utility

    @sanjayankur31
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  4. feat: add unit tests for cell builder utility

    @sanjayankur31
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  5. feat: add pytest to CI

    @sanjayankur31
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  6. fix: correct type hinting for list of floats

    @sanjayankur31
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  7. fix: use Python 2 compatible type hinting syntax

    @sanjayankur31
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  8. fix: drop f-strings for Python 2 compatibility

    @sanjayankur31
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  9. refactor(ci): move pytest to test scripts

    @sanjayankur31
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  10. feat: add fraction_along to add_segment

    @sanjayankur31
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  11. feat: set default fraction_along in segment parent

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  12. feat: add summary doc string to add_segment

    @sanjayankur31
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  13. chore: remove stray doc string line

    @sanjayankur31
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  14. feat: allow omission of proximal point in add_segment 

    An omitted proximal point means that it is equal to the distal point of
the parent segment
    @sanjayankur31
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  15. fix: make sure p is defined even when prox is None

    @sanjayankur31
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  16. feat: do not repeat includes

    @sanjayankur31
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  17. feat(cellbuilder): define a dict to store neurolex ids

    @sanjayankur31
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  18. feat(cellbuilder): add default segment groups 

    Segments will be added to these by default, for convenience
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  19. feat(cellbuilder): add utilities to easily find segment groups

    @sanjayankur31
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  20. feat(cellbuilder): add newly created segments to default segments

    @sanjayankur31
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  21. fix: correct type annotations 

    https://mypy.readthedocs.io/en/latest/cheat_sheet.html#cheat-sheet-py2
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  22. chore(cellbuilder): add note about order of segment groups in NML files

    @sanjayankur31
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  23. refactor(cellbuilder): migrate segment getters to nml.py in libNeuroML

    @sanjayankur31
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  24. refactor(cellbuilder): use update nml.py methods and make conventiona… 

    …l optional
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  25. feat(cell-builder): use py3 type annotations 

    since we've dropped py2 support
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  26. chore: format with black

    @sanjayankur31
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  27. chore(ci): remove duplicate pytest command

    @sanjayankur31
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  28. feat(deps): set version constraint: libNeuroML>= 0.3.1 

    This is required because the CellBuilder uses methods that were only
added to libNeuroML in version 0.3.1.

Reference: NeuralEnsemble/libNeuroML#105
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  29. docs: add CellBuilder to sphinx docs

    @sanjayankur31
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  30. test(CellBuilder): re-enable skipped tests 

    These were skipped because of issues in the validator, but those have
now been fixed.

References:
- NeuroML/NeuroML2#162
- NeuroML/NeuroML2#165
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  31. chore: correct section heading in docs 

    [skip ci]
    @sanjayankur31
    sanjayankur31 committed Jul 26, 2022
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  32. feat(cell-builder): add missing check 

    (imported from experimental branch)
    @sanjayankur31
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Commits on Jul 27, 2022

  1. feat: handle exception when a segment group does not exist

    @sanjayankur31
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  2. test(cell-builder): add new tests

    @sanjayankur31
    sanjayankur31 committed Jul 27, 2022
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  3. chore: use is for comparison with None instead of ==

    @sanjayankur31
    sanjayankur31 committed Jul 27, 2022
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Commits on Aug 4, 2022

  1. fix(cell-builder): append to resistivities instead of overwriting 

    Different segments can have different resistivity, and we should be able
to set them independently.
    @sanjayankur31
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  2. fix(cell-builder): correct append function call

    @sanjayankur31
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  3. fix(cell-builder): append to list of InitMembPotentials

    @sanjayankur31
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  4. improvement(cell-builder): re-order function args 

    .. to match order in the ConductanceDensity constructor.
    @sanjayankur31
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  5. feat(cell-builder): add generic channel density helper 

    .. allows users to add all types of defined channel densities
    @sanjayankur31
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  6. test(cell-builder): add test for generic conductance density adder

    @sanjayankur31
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  7. feat(cell-builder): add generic method to add membrane properties

    @sanjayankur31
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  8. feat(utils): add general component factory function

    @sanjayankur31
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  9. improvement(utils): make component factory case sensitive 

    If someone uses `iafcell`, we can't get `IafCell` from that without
going through the whole libNeuroML nml module.
    @sanjayankur31
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  10. chore(utils): remove wrong doc noting names are case insensitive

    @sanjayankur31
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  11. test(cell-builder): correct tests 

    ... to verify that channel density objects were added
    @sanjayankur31
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  12. chore: add missing blank line 

    [ci skip]
    @sanjayankur31
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  13. feat(cell-builder): add generic function to add intracellular properties

    @sanjayankur31
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  14. test(cell-builder): test intracellular and membrane property helpers

    @sanjayankur31
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  15. test(utils): add tests for factory helper function

    @sanjayankur31
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  16. feat(utils): add function to check for compulsory parameters

    @sanjayankur31
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Commits on Aug 19, 2022

  1. Merge branch 'development' into feat/cell-builder-methods-105

    @sanjayankur31
    sanjayankur31 committed Aug 19, 2022
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Commits on Aug 22, 2022

  1. fix(component-factory): return created component

    @sanjayankur31
    sanjayankur31 committed Aug 22, 2022
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  2. test(plot): disable interactive

    @sanjayankur31
    sanjayankur31 committed Aug 22, 2022
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