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Implement shifts and tilts as properties #15

Merged
merged 21 commits into from
Oct 30, 2024
Merged

Implement shifts and tilts as properties #15

merged 21 commits into from
Oct 30, 2024

Commits on Oct 25, 2024

  1. Minor housekeeping: retry linkcheck 3 times; update .gitignore; 

    update version to dev version; add script to run tests with conditional
coverage depending on presence of CUDA.
    @jat255
    jat255 committed Oct 25, 2024
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  2. TomoStack API changes: 

      - store tilts/shifts in stack.tilts and stack.shifts properties
  - create Signal1D subclasses for TomoTilts and TomoShifts with shape validation and custom slicers
  - remove io.create_stack and implement in CommonStack constructor
  - override copy and deepcopy for CommonStack so tilts and shifts are copied
  - override save for CommonStack so tilts and shits are stashed in the metadata when writing to disk
    @jat255
    jat255 committed Oct 25, 2024
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  3. Minor changes and fixes to x/y docs confusion

    @jat255
    jat255 committed Oct 25, 2024
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  4. Improve SerialEM io handling and documentation

    @jat255
    jat255 committed Oct 25, 2024
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  5. Tests for new property API and 100% coverage (excluding CUDA code)

    @jat255
    jat255 committed Oct 25, 2024
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  6. Update docs to match changes and fix some links

    @jat255
    jat255 committed Oct 25, 2024
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  7. add placeholder test multitilt single file mrc

    @jat255
    jat255 committed Oct 25, 2024
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  8. add missing cupy dependency

    @jat255
    jat255 committed Oct 25, 2024
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Commits on Oct 26, 2024

  1. - fix cuda tests 

    - add more tests for tilts and shifts
- get to 100% coverage
- fix CommonStack signal constructor
- better support for multiframe stacks
- fix save_movie dimensions
- fix plot_sinos due to new tilts property
- make run_test.sh script remove existing coverage reports
    @jat255
    jat255 committed Oct 26, 2024
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  2. add ffmpeg to conda environment, remove cupy from poetry github actions

    @jat255
    jat255 committed Oct 26, 2024
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  3. add ffmpeg to github action

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

  1. add macos environment without cupy; 

    make workflow choice of conda environment condtional
    @jat255
    jat255 committed Oct 27, 2024
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  2. maybe fix GH action always using MacOS; pin astra to <=2.1

    @jat255
    jat255 committed Oct 27, 2024
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Commits on Oct 29, 2024

  1. try to fix conda envs

    @jat255
    jat255 committed Oct 29, 2024
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  2. undo astra version downgrade

    @jat255
    jat255 committed Oct 29, 2024
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  3. no cudapy builds for astra on osx

    @jat255
    jat255 committed Oct 29, 2024
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  4. split conda envs into GPU and non-GPU

    @jat255
    jat255 committed Oct 29, 2024
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  5. fix test warnings and some cuda coverage

    @jat255
    jat255 committed Oct 29, 2024
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  6. revert numpy 1.X dep

    @jat255
    jat255 committed Oct 29, 2024
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  7. Update example notebook

    @jat255
    jat255 committed Oct 29, 2024
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  8. update version number

    @jat255
    jat255 committed Oct 29, 2024
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