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(BREAKING) Rewrite Julia interface with PyJulia -> JuliaCall; other changes #535

Merged
merged 115 commits into from
Feb 12, 2024
Merged

(BREAKING) Rewrite Julia interface with PyJulia -> JuliaCall; other changes #535

merged 115 commits into from
Feb 12, 2024

Commits on Jan 21, 2024

  1. Start third attempt at porting to PythonCall

    @MilesCranmer
    MilesCranmer committed Jan 21, 2024
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Commits on Jan 26, 2024

  1. Force conversion to Vector

    @MilesCranmer
    MilesCranmer committed Jan 26, 2024
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  2. Disable PythonCall GC during equation search

    @MilesCranmer
    MilesCranmer committed Jan 26, 2024
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  3. Fix environ assertion

    @MilesCranmer
    MilesCranmer committed Jan 26, 2024
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  4. Disable unused install command

    @MilesCranmer
    MilesCranmer committed Jan 26, 2024
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  5. Run in Main

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    MilesCranmer committed Jan 26, 2024
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  6. Set num threads before juliacall init

    @MilesCranmer
    MilesCranmer committed Jan 26, 2024
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  7. Automatically check if juliacall was already imported

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    MilesCranmer committed Jan 26, 2024
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Commits on Jan 27, 2024

  1. Avoid disabling GC by simply copying inside Julia

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  2. Save raw bytes so can warm-restart in new python session

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  3. Fix hanging with GC disabled

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  4. Remove unneeded copying

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  5. Better docs

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  6. Remove unused function

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  7. Fix missing pickle warning

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  8. Fix symbolic regression version exactly

    @MilesCranmer
    MilesCranmer committed Jan 27, 2024
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  9. Fix PythonCall issue of not converting np.str_ to String

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    MilesCranmer committed Jan 27, 2024
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Commits on Feb 4, 2024

  1. Check if user already set JULIA_NUM_THREADS

    @MilesCranmer
    MilesCranmer committed Feb 4, 2024
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  2. Clean up default params

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    MilesCranmer committed Feb 4, 2024
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  3. WIP move python -m pysr.test call to click interface

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    MilesCranmer committed Feb 4, 2024
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Commits on Feb 7, 2024

  1. Use git version of SymbolicRegression.jl to avoid Pkg server issues

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    MilesCranmer committed Feb 7, 2024
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  2. Add Serialization.jl to juliapkg.json

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    MilesCranmer committed Feb 7, 2024
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  3. Remove Python 3.12 warning

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  4. Fix click API usage

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  5. Update all workflows to use python -m pysr test syntax

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  6. Switch to using pyproject.toml for build options

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  7. Use setuptools_scm for version management

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  8. Remove generated version.py file

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  9. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Feb 7, 2024
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  10. Update conda env

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    MilesCranmer committed Feb 7, 2024
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  11. Remove unused juliapkg

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    MilesCranmer committed Feb 7, 2024
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  12. Update installation guide

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    MilesCranmer committed Feb 7, 2024
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  13. Add missing pyproject.toml file

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    MilesCranmer committed Feb 7, 2024
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  14. Permit versioning without git repo

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    MilesCranmer committed Feb 7, 2024
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  15. Use relative import for CMD line interface

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  16. Add missing juliapkg.json to dockerfile

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    MilesCranmer committed Feb 7, 2024
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  17. Ignore lack of type hints in JuliaCall

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    MilesCranmer committed Feb 7, 2024
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  18. Move juliapkg into source

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  19. Remove Feynman problems and dataset

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  20. Ensure that juliapkg.json is installed

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  21. Fix incremental install tests

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  22. Remove incremental install altogether

    @MilesCranmer
    MilesCranmer committed Feb 7, 2024
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  23. Remove custom environment tests

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    MilesCranmer committed Feb 7, 2024
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  24. Remove use of custom env tests

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    MilesCranmer committed Feb 7, 2024
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  25. Ensure julia is loaded as soon as possible

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Commits on Feb 8, 2024

  1. Add install function back with deprecation warning

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    MilesCranmer committed Feb 8, 2024
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  2. Include asserts for Julia version found by PythonCall

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  3. Merge branch 'master' into pythoncall-try-3

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    MilesCranmer authored Feb 8, 2024
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  4. Fix version assertion for earlier Julia

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    MilesCranmer committed Feb 8, 2024
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  5. Update docs to use seval

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    MilesCranmer committed Feb 8, 2024
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Commits on Feb 9, 2024

  1. Avoid git version to fix windows issues

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  2. Override seval to allow multiple expressions

    @MilesCranmer
    MilesCranmer committed Feb 9, 2024
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  3. Update colab notebook

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    MilesCranmer committed Feb 9, 2024
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  4. Automatically load ipython extension

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    MilesCranmer committed Feb 9, 2024
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  5. Simplify IPython detection

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    MilesCranmer committed Feb 9, 2024
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Commits on Feb 10, 2024

  1. Use julia_state_ instead

    @MilesCranmer
    MilesCranmer authored Feb 10, 2024
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  2. Remove use of julia_kwargs

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    MilesCranmer committed Feb 10, 2024
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  3. Only show warnings if juliacall not yet imported

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  4. Automatically load ipython extension

    @MilesCranmer
    MilesCranmer committed Feb 10, 2024
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  5. Allow user to disable juliacall extension

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    MilesCranmer committed Feb 10, 2024
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  6. Don't install editable version of docker file

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    MilesCranmer committed Feb 10, 2024
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  7. Fix julia_state_ typo

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    MilesCranmer committed Feb 10, 2024
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  8. Only overwrite seval on recent Julia versions

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  9. Add Python 3.12 to test suite

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    MilesCranmer committed Feb 10, 2024
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  10. Export SymbolicRegression.jl module

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  11. Save options to PySRRegressor

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    MilesCranmer committed Feb 10, 2024
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  12. Overload operators at import rather than fit

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  13. Update julia_helpers.py

    @MilesCranmer
    MilesCranmer authored Feb 10, 2024
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  14. Clean up torch tests

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    MilesCranmer committed Feb 10, 2024
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  15. Rename all instances of PyJulia to juliacall in docs

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  16. Update documentation on backend modifications

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    MilesCranmer committed Feb 10, 2024
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  17. Mention new backend page

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    MilesCranmer committed Feb 10, 2024
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  18. Fix juliacall version as we are using non-public API

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  19. Add warm_start test

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    MilesCranmer committed Feb 10, 2024
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  20. Update test suite to test warm starts

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  21. Update CLI tests

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    MilesCranmer committed Feb 10, 2024
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  22. Clean up testing caller

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    MilesCranmer committed Feb 10, 2024
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  23. Deprecate ncyclesperiteration -> ncycles_per_iteration

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  24. Remove unused TODO file

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    MilesCranmer committed Feb 10, 2024
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  25. Rename loss => elementwise_loss and full_objective => loss_function

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  26. Do tests of deprecated functions

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  27. Unused imports

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  28. Fix SymbolicRegression version

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  29. Ensure equation state is reset for warm start test

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  30. Test additional branches of code

    @MilesCranmer
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  31. Extend startup tests to other warning messages

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  32. Fix CLI tests

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  33. Fix CLI tests

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  34. Weaken complex test

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  35. Try to get coverage working in subprocesses

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  36. Use correct python for subprocess

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  37. Remove COVERAGE_PROCESS_START

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  38. Try to get subprocess coverage working again

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  39. Standard names for JuliaCall env variables

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  40. Include test of multi-line seval

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Commits on Feb 11, 2024

  1. Test that we can use development version of backend

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  2. Test jupyter notebook in test suite

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  3. Sanitize nb output for testing

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  4. Try to fix nb sanitizer

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  5. Try to fix nb sanitizer

    @MilesCranmer
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  6. Fix CLI test

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  7. Always try to set jl.seval

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  8. Skip param groupings test if doesnt exist

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  9. Fix tests on Julia 1.7 due to module assignment

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Commits on Feb 12, 2024

  1. Add Zygote.jl to PySR env

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  2. Fail job if unittest unsuccessful

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    MilesCranmer committed Feb 12, 2024
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  3. Always overwrite with Meta.parseall version

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    MilesCranmer committed Feb 12, 2024
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  4. Turn back up complex test

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  5. Needs longer for complex search

    @MilesCranmer
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  6. Fix jl.test_state issue

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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  7. Only load Julia extension on recent julia

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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  8. Skip notebook test on older Julia

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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  9. Skip notebook test on Windows

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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  10. Skip warm start test on Windows

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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  11. Show off %%julia magic in notebook example

    @MilesCranmer
    MilesCranmer committed Feb 12, 2024
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