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Mathml -> sympy conversion #188

Merged
merged 56 commits into from
Aug 14, 2023
Merged

Mathml -> sympy conversion #188

merged 56 commits into from
Aug 14, 2023

Commits on Aug 14, 2023

  1. Add mathml -> sympy parser using sbmlmath package

    @kkaris
    kkaris committed Aug 14, 2023
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  2. Ensure sbmlmath is installed for tests

    @kkaris
    kkaris committed Aug 14, 2023
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  3. Add sbmlmath in setup.cfg

    @kkaris
    kkaris committed Aug 14, 2023
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  4. Add function to __all__

    @kkaris
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  5. Add closing </math> in template

    @kkaris
    kkaris committed Aug 14, 2023
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  6. Write test for some expressions in scenario1a json

    @kkaris
    kkaris committed Aug 14, 2023
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  7. Handle mathml -> sympy in state_to_concept

    @kkaris
    kkaris committed Aug 14, 2023
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  8. Handle sympy -> mathml for initials

    @kkaris
    kkaris committed Aug 14, 2023
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  9. More clear logic for state_to_concept mathml handling

    @kkaris
    kkaris committed Aug 14, 2023
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  10. Clearer logic for mathml handling for initals

    @kkaris
    kkaris committed Aug 14, 2023
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  11. Add mathml support for observables

    @kkaris
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  12. Handle mathml for time units

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  13. Handle mathml for rates

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  14. DRY implementation of sympy and mathml parsing

    @kkaris
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  15. Clean up mathml->sympy tests

    @kkaris
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  16. Add test for sympy -> mathml

    @kkaris
    kkaris committed Aug 14, 2023
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  17. Fix bug

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    kkaris committed Aug 14, 2023
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  18. Test askenet petrinet sir example

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  19. Fix(?) sbmlmath install

    @kkaris
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  20. Check for None in _get_sympy

    @kkaris
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  21. Simplify logic

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  22. Move sorted_json_str to tests.__init__.py

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  23. Add test for recovering expressions from mathml

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  24. Move helpers to tests/__init__.py

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  25. Move tests

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  26. Delete unused file

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  27. Add method and inplace args in _remove_all_sympy

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  28. Add docstring to helpers

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  29. Rename helpers

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  30. Remove inplace option

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  31. Add option to 'null' values in sympy deleter

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  32. Add test for no sympy in model api tests

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  33. Use safe_parse_expr in sympy helper

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  34. Clean up after rebase conflicts

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  35. Rename _get_sympy -> get_sympy, add docstring

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  36. Use askenet.petrinet's get_sympy

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  37. Clean up import

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  38. Initial try to install sbmlmath for tests

    @kkaris
    kkaris committed Aug 14, 2023
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  39. Force install despite wrong python version

    @kkaris
    kkaris committed Aug 14, 2023
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  40. Revert --ignore-requires-python, test bump lower python version

    @kkaris
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  41. Import sbmlmath locally to avoid missing package

    @kkaris
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  42. Skip tests that use sbmlmath

    @kkaris
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  43. Put sbmlmath under its own extra

    @kkaris
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  44. Revert to python 3.8, skip sbmlmath install

    @kkaris
    kkaris committed Aug 14, 2023
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  45. Update skip message

    @kkaris
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  46. Use sir model with expressions filled out

    @kkaris
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  47. Add functionality to test a docker running locally

    @kkaris
    kkaris committed Aug 14, 2023
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  48. Add comment on how to install sbmlmath locally

    @kkaris
    kkaris committed Aug 14, 2023
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  49. Update dkg docker file

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  50. Fix grammar

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    kkaris committed Aug 14, 2023
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  51. Try disabling codecov

    @kkaris
    kkaris committed Aug 14, 2023
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  52. Skip another sbmlmath dependent test

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    kkaris committed Aug 14, 2023
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  53. Mark sbmlmath tests and skip them on github

    @kkaris
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  54. Import SympyExprStr

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  55. Restore docker build branch

    @kkaris
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  56. pip install sbmlmath

    @kkaris
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