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Documentation and type checking #11

Merged
merged 43 commits into from
Oct 11, 2024
Merged

Documentation and type checking #11

merged 43 commits into from
Oct 11, 2024

Commits on Sep 26, 2024

  1. first attempt at docs

    @jat255
    jat255 committed Sep 26, 2024
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  2. add ruff cache to gitignore

    @jat255
    jat255 committed Sep 26, 2024
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  3. fix isort on conf.py

    @jat255
    jat255 committed Sep 26, 2024
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  4. conda GH actions test

    @jat255
    jat255 committed Sep 26, 2024
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  5. put environment file in conda setup action

    @jat255
    jat255 committed Sep 26, 2024
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  6. try adding CUDA to actions matrix

    @jat255
    jat255 committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. remove CUDA (can't use on standard GH action runners)

    @jat255
    jat255 committed Sep 27, 2024
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  2. Test doc build in GH action

    @jat255
    jat255 committed Sep 27, 2024
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  3. upload built docs artifact

    @jat255
    jat255 committed Sep 27, 2024
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  4. try check links

    @jat255
    jat255 committed Sep 27, 2024
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  5. try installing CUDA so astra-toolbox can be installed using poetry

    @jat255
    jat255 committed Sep 27, 2024
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  6. try setting up re-usable installation workflow

    @jat255
    jat255 committed Sep 27, 2024
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  7. add poetry to reusable actions

    @jat255
    jat255 committed Sep 27, 2024
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  8. add dependencies and poetry pytest runs

    @jat255
    jat255 committed Sep 27, 2024
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  9. fix ruff issues that only sometimes appeared?

    @jat255
    jat255 committed Sep 27, 2024
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  10. test switching branch

    @jat255
    jat255 committed Sep 27, 2024
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  11. try committing docs to nist-pages using action

    @jat255
    jat255 committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. Get doc navigation working better

    @jat255
    jat255 committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. add type hints to align module, add intersphinx, fix some docstrings, 

    formalize alignment methods into a reusable Enum
    @jat255
    jat255 committed Oct 1, 2024
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  2. add explicit groups for methods and classes

    @jat255
    jat255 committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Improve base.py docstrings

    @jat255
    jat255 committed Oct 2, 2024
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  2. Fix align.py type issues and datasets.py docstrings

    @jat255
    jat255 committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Improve io, recon, simulation, and utils.py docstrings (add type hints) 

    Switch to Literal types for strings that have explicit options.
Fix inconsistent optionality of dart_iterations in TomoStack.reconstruct.
    @jat255
    jat255 committed Oct 3, 2024
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  2. fix remaining lint issues and get tests passing again 

    re-enable 3.12 tests since pystackreg is on pypi now
    @jat255
    jat255 committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. update README and add some context to API reference page

    @jat255
    jat255 committed Oct 4, 2024
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  2. fix various sphinx warnings to ensure a clean doc build 

    and other minor documentation edits (fix circular TomoStack import)
    @jat255
    jat255 committed Oct 4, 2024
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  3. Make recon.run take numpy array to be consistent with the rest of the… 

    … recon methods
    @jat255
    jat255 committed Oct 4, 2024
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  4. Make CommonStack explicitly abstract so it cannot be instantiated dir… 

    …ectly

(better for API clarity that TomoStack and RecStack should be used instead)
    @jat255
    jat255 committed Oct 4, 2024
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  5. add typing_extensions for 3.10 support

    @jat255
    jat255 committed Oct 4, 2024
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Commits on Oct 5, 2024

  1. First attempt at rendering notebook in documentation

    @jat255
    jat255 committed Oct 5, 2024
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  2. update example notebook with CUDA outputs

    @jat255
    jat255 committed Oct 5, 2024
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  3. add some fancy badges and a section for developer installation

    @jat255
    jat255 committed Oct 5, 2024
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  4. update pystackreg to 0.2.8 and numpy to 2.0

    @jat255
    jat255 committed Oct 5, 2024
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  5. add missing cuda argument to stack_register

    @jat255
    jat255 committed Oct 5, 2024
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Commits on Oct 8, 2024

  1. update README with updated test information

    @jat255
    jat255 committed Oct 8, 2024
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  2. add coverage, pytest-cov, and pytest-mpl, and improve test running

    @jat255
    jat255 committed Oct 8, 2024
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Commits on Oct 11, 2024

  1. update align.py to 100% (without CUDA)

    @jat255
    jat255 committed Oct 11, 2024
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  2. Remove pytest-mpl since I couldn't get it to work reliably on CI/CD

    @jat255
    jat255 committed Oct 11, 2024
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  3. bump version and add version check to test

    @jat255
    jat255 committed Oct 11, 2024
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  4. pin sphinx due to jbms/sphinx-immaterial#394 and make version dynamic… 

    … in docs
    @jat255
    jat255 committed Oct 11, 2024
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  5. retrigger checks

    @jat255
    jat255 committed Oct 11, 2024
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  6. try to limit doc deploy to master branch only on main repo

    @jat255
    jat255 committed Oct 11, 2024
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  7. run test suite on PRs also

    @jat255
    jat255 committed Oct 11, 2024
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