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version 0.4.0 #31

Merged
merged 38 commits into from
Sep 26, 2024
Merged

version 0.4.0 #31

merged 38 commits into from
Sep 26, 2024

Commits on Sep 26, 2024

  1. initial POTGNN implementation

    @wolearyc
    wolearyc committed Sep 26, 2024
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  2. organized torch dir, refactored, added some exceptions

    @wolearyc
    wolearyc committed Sep 26, 2024
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  3. check for empty paths, fixed mps testing 

    mps used only if not in github actions
    @wolearyc
    wolearyc committed Sep 26, 2024
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  4. added read_structure_and_polarizability for vasprun.xml

    @wolearyc
    wolearyc committed Sep 26, 2024
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  5. improved dataset: properties, io, and tests

    @wolearyc
    wolearyc committed Sep 26, 2024
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  6. updated build system for readthedocs compatability (#23) 

    added pip options to top of requirements files
    @wolearyc
    wolearyc committed Sep 26, 2024
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  7. added [torch] install option

    @wolearyc
    wolearyc committed Sep 26, 2024
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  8. annotation-based type checking for PolarizabilityDataset

    @wolearyc
    wolearyc committed Sep 26, 2024
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  9. refactor and doc updates

    @wolearyc
    wolearyc committed Sep 26, 2024
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  10. make PotGNN a subclass of PolarizabilityModel

    @wolearyc
    wolearyc committed Sep 26, 2024
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  11. added train function

    @wolearyc
    wolearyc committed Sep 26, 2024
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  12. dataset now works with single lattice, atomic_numbers

    @wolearyc
    wolearyc committed Sep 26, 2024
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  13. parameter validation and private classes

    @wolearyc
    wolearyc committed Sep 26, 2024
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  14. fix dimension of output of mean_polarizability and std_polarizability

    @wolearyc
    wolearyc committed Sep 26, 2024
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  15. fixed scale_polarizabilities implementation

    @wolearyc
    wolearyc committed Sep 26, 2024
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  16. renamed tensor<->vector utilities

    @wolearyc
    wolearyc committed Sep 26, 2024
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  17. added batching to potgnn calc_polarizabilities

    @wolearyc
    wolearyc committed Sep 26, 2024
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  18. dataset and potgnn internally scales polarizability

    @wolearyc
    wolearyc committed Sep 26, 2024
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  19. added progress bar for trajectory.get_spectrum

    @wolearyc
    wolearyc committed Sep 26, 2024
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  20. refactor UsageError -> UserError

    @wolearyc
    wolearyc committed Sep 26, 2024
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  21. refactor np.isclose(...).all() -> np.allclose(...)

    @wolearyc
    wolearyc committed Sep 26, 2024
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  22. documentation improvements

    @wolearyc
    wolearyc committed Sep 26, 2024
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  23. renamed most *_utils.py to utils.py, globals.py to constants.py

    @wolearyc
    wolearyc committed Sep 26, 2024
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  24. renamed polarizability model to pmodel

    @wolearyc
    wolearyc committed Sep 26, 2024
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  25. moved PolarizabilityDataset to its own package 

    this should avoid circular imports
    @wolearyc
    wolearyc committed Sep 26, 2024
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  26. moved abstract classes to their own file 

    this should help avoid circular imports
    @wolearyc
    wolearyc committed Sep 26, 2024
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  27. added imports to all __init__.py files 

    this allows access to ramannoodle's functionality from base package
    @wolearyc
    wolearyc committed Sep 26, 2024
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  28. changed recommended imports in docs

    @wolearyc
    wolearyc committed Sep 26, 2024
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  29. bump sphinx

    @wolearyc
    wolearyc committed Sep 26, 2024
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  30. removed sphinx-rtd-theme from doc dependencies

    @wolearyc
    wolearyc committed Sep 26, 2024
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  31. added and refactored tests

    @wolearyc
    wolearyc committed Sep 26, 2024
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  32. moved robots.txt to conf directory

    @wolearyc
    wolearyc committed Sep 26, 2024
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  33. Bump the action-packages group across 1 directory with 4 updates (#19) 

    Bumps the action-packages group with 4 updates in the / directory: [actions/setup-python](https://github.com/actions/setup-python), [actions/upload-artifact](https://github.com/actions/upload-artifact), [actions/download-artifact](https://github.com/actions/download-artifact) and [sigstore/gh-action-sigstore-python](https://github.com/sigstore/gh-action-sigstore-python).


Updates `actions/setup-python` from 3 to 5
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v3...v5)

Updates `actions/upload-artifact` from 3 to 4
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v3...v4)

Updates `actions/download-artifact` from 4.1.7 to 4.1.8
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v4.1.7...v4.1.8)

Updates `sigstore/gh-action-sigstore-python` from 2.1.1 to 3.0.0
- [Release notes](https://github.com/sigstore/gh-action-sigstore-python/releases)
- [Changelog](https://github.com/sigstore/gh-action-sigstore-python/blob/main/CHANGELOG.md)
- [Commits](sigstore/gh-action-sigstore-python@v2.1.1...v3.0.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: action-packages
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: action-packages
- dependency-name: actions/download-artifact
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: action-packages
- dependency-name: sigstore/gh-action-sigstore-python
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: action-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    @dependabot
    dependabot[bot] authored Sep 26, 2024
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  34. changed dependabot target branch to dev

    @wolearyc
    wolearyc committed Sep 26, 2024
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  35. refreshed doc sources

    @wolearyc
    wolearyc committed Sep 26, 2024
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  36. version bump

    @wolearyc
    wolearyc committed Sep 26, 2024
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  37. added too-many-positional-arguments pylint ignores

    @wolearyc
    wolearyc committed Sep 26, 2024
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  38. bump pylint to 3.3.1

    @wolearyc
    wolearyc committed Sep 26, 2024
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