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Extending and testing the AMR-based modeling API #239

Merged
merged 37 commits into from
Sep 10, 2023
Merged

Extending and testing the AMR-based modeling API #239

merged 37 commits into from
Sep 10, 2023

Commits on Aug 24, 2023

  1. Implement replacing state ID

    @bgyori
    bgyori committed Aug 24, 2023
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  2. Implement first batch of AMR ops

    @bgyori
    bgyori committed Aug 24, 2023
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  3. Implement more modeling operations

    @bgyori
    bgyori committed Aug 24, 2023
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  4. Comment out function that doesn't work yet

    @bgyori
    bgyori committed Aug 24, 2023
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  5. Added two unit tests for modeling_api

    @nanglo123 @bgyori
    nanglo123 authored and bgyori committed Aug 24, 2023
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  6. Added pass statement to unfinished test in test_ops.py and removed ir… 

    …relevant comment in ops.py
    @nanglo123 @bgyori
    nanglo123 authored and bgyori committed Aug 24, 2023
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  7. Expose operations from template model module

    @bgyori
    bgyori committed Aug 24, 2023
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  8. Fix return values

    @bgyori
    bgyori committed Aug 24, 2023
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  9. Fix initials generation in Model

    @bgyori
    bgyori committed Aug 24, 2023
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  10. Separate AMR-based operations

    @bgyori
    bgyori committed Aug 24, 2023
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  11. Added a unit test for replacing observable id and fixed bug concernin… 

    …g picking dict item objects in repplace observable id method
    @nanglo123 @bgyori
    nanglo123 authored and bgyori committed Aug 24, 2023
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Commits on Aug 28, 2023

  1. Added unit test for replace_parameter_id and changed test_replace_sta… 

    …te_id unit test to not check for length equality between old and new amr expressions asstates do not have to be a single letter
    @nanglo123 @bgyori
    nanglo123 authored and bgyori committed Aug 28, 2023
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  2. Fix implementation of initial id replacement

    @bgyori
    bgyori committed Aug 28, 2023
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Commits on Aug 29, 2023

  1. Added minimal unit tests for 4 interface methods and unit test for re… 

    …move_state
    @nanglo123
    nanglo123 committed Aug 29, 2023
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  2. Made minor bug fixes in ops.py and init.py and added test that doesnt… 

    … currently pass for replace_initial_id
    @nanglo123
    nanglo123 committed Aug 29, 2023
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  3. Changed two assertion statements in test_remove_state and added unit … 

    …tests for remove_transition and replace_rate_law_sympy
    @nanglo123
    nanglo123 committed Aug 29, 2023
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Commits on Aug 30, 2023

  1. Change asserts to address deprecation warning

    @bgyori
    bgyori committed Aug 30, 2023
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  2. Added replace_rate_law_mathml and unit tests and modified unit_test f… 

    …or test_replace_rate_law_sympy to test both output amr expression and expression_mathml
    @nanglo123
    nanglo123 committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. Added return tm line for replace_initial_id

    @nanglo123
    nanglo123 committed Aug 31, 2023
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  2. Further changed unit test test_replace_law_sympy to pass in mathml_to… 

    …_expression(xml_str) rather than sympy.repr(str) to method
    @nanglo123
    nanglo123 committed Aug 31, 2023
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Commits on Sep 1, 2023

  1. Further changed unit tests to be more informative and make point of f… 

    …ailure more apparent and fixed bug where changed parameter ids not showing in parameter list of new_amr
    @nanglo123
    nanglo123 committed Sep 1, 2023
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Commits on Sep 5, 2023

  1. Changed name field for observable to show a separate value for displa… 

    …y_name
    @nanglo123
    nanglo123 committed Sep 5, 2023
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Commits on Sep 6, 2023

  1. Added add_parameter method and unit test, updated method header for r… 

    …eplacing observable id to accept a display name argument
    @nanglo123
    nanglo123 committed Sep 6, 2023
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  2. Added remove_X where X is an observable or parameter method and its a… 

    …ccompanying unit test
    @nanglo123
    nanglo123 committed Sep 6, 2023
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  3. Changed amr->template model method such that template model observabl… 

    …e objects have a non None value for their display name attribute
    @nanglo123
    nanglo123 committed Sep 6, 2023
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Commits on Sep 7, 2023

  1. Added add_observable and replace_expression and their respective unit… 

    … tests
    @nanglo123
    nanglo123 committed Sep 7, 2023
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  2. Implemented add_transition (unfinished as currently newly added state… 

    …s and parameters are not showing in the output amr) and its accompanying unit test
    @nanglo123
    nanglo123 committed Sep 7, 2023
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  3. Removed some comments

    @nanglo123
    nanglo123 committed Sep 7, 2023
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  4. Limit anyio version

    @bgyori
    bgyori committed Sep 7, 2023
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Commits on Sep 8, 2023

  1. Added comments in ops.py showing next possible steps for test_transit… 

    …ion and added decorator to all unit tests that require sbmlmath
    @nanglo123
    nanglo123 committed Sep 8, 2023
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  2. Updated unit test for add_transition, add pytest mark for unit tests … 

    …that require sbmlmath, forced pydantic<2.0 dependency for purpose of testing due to conflict with TestModelAPi
    @nanglo123
    nanglo123 committed Sep 8, 2023
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  3. Fixed typo in tox.ini file where marks were not separated by commas i… 

    …n list of markers
    @nanglo123
    nanglo123 committed Sep 8, 2023
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  4. Changed slight typo in description of sbmlmath marker and limited any… 

    …io version
    @nanglo123
    nanglo123 committed Sep 8, 2023
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  5. Remove anyio constraint from tests.yml

    @bgyori
    bgyori committed Sep 8, 2023
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  6. Various improvements in the code

    @bgyori
    bgyori committed Sep 8, 2023
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  7. Review and update operations

    @bgyori
    bgyori committed Sep 8, 2023
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  8. Changed some askenet op methods and respective unit tests to reflect … 

    …changed mira operations
    @nanglo123
    nanglo123 committed Sep 8, 2023
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