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Add "datastores" to represent input data from zarr, npy, etc #66

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Add "datastores" to represent input data from zarr, npy, etc #66

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Commits on May 9, 2024

  1. ar_steps for training and eval

    Simon Adamov committed May 9, 2024
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  2. smaller ammendments

    Simon Adamov committed May 9, 2024
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  3. Dummy mask was inverted - fixed

    Simon Adamov committed May 9, 2024
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  4. replace hardcoded normalization path

    Simon Adamov committed May 9, 2024
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Commits on May 13, 2024

  1. wip on simplifying pre-commit setup

    @leifdenby
    leifdenby committed May 13, 2024
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  2. setup pylint version

    @leifdenby
    leifdenby committed May 13, 2024
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  3. remove external deps install in cicd linting

    @leifdenby
    leifdenby committed May 13, 2024
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  4. create project

    @leifdenby
    leifdenby committed May 13, 2024
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  5. replace absolute imports with relative

    @leifdenby
    leifdenby committed May 13, 2024
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  6. simplify black config

    @leifdenby
    leifdenby committed May 13, 2024
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  7. headers for import sections no longer needed

    @leifdenby
    leifdenby committed May 13, 2024
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  8. minor fixes

    @leifdenby
    leifdenby committed May 13, 2024
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  9. run on all branch pushes

    @leifdenby
    leifdenby committed May 13, 2024
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  10. rename action to "lint"

    @leifdenby
    leifdenby committed May 13, 2024
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  11. add ci/cd test for imports

    @leifdenby
    leifdenby committed May 13, 2024
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  12. py version must be quoted

    @leifdenby
    leifdenby committed May 13, 2024
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  13. fix torch install url

    @leifdenby
    leifdenby committed May 13, 2024
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  14. use pdm in ci/cd

    @leifdenby
    leifdenby committed May 13, 2024
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  15. disable cache for now

    @leifdenby
    leifdenby committed May 13, 2024
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  16. check in lock file

    @leifdenby
    leifdenby committed May 13, 2024
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  17. add pytest

    @leifdenby
    leifdenby committed May 13, 2024
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  18. cache in cicd

    @leifdenby
    leifdenby committed May 13, 2024
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  19. add torch-geometric to deps

    @leifdenby
    leifdenby committed May 13, 2024
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  20. fix import and more tests

    @leifdenby
    leifdenby committed May 13, 2024
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  21. Merge branch 'maint/simplify-precommit-setup' into maint/refactor-as-… 

    …package
    @leifdenby
    leifdenby committed May 13, 2024
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  22. pdm to sync to requirements.txt

    @leifdenby
    leifdenby committed May 13, 2024
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  23. update requirements.txt

    @leifdenby
    leifdenby committed May 13, 2024
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  24. more import tests

    @leifdenby
    leifdenby committed May 13, 2024
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Commits on May 22, 2024

  1. move deps to projects and add import tests

    @leifdenby
    leifdenby committed May 22, 2024
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  2. add cicd testing workflow

    @leifdenby
    leifdenby committed May 22, 2024
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  3. test both with pdm and pip install

    @leifdenby
    leifdenby committed May 22, 2024
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  4. clean up test cicd

    @leifdenby
    leifdenby committed May 22, 2024
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Commits on May 23, 2024

  1. remove requirements.txt

    @leifdenby
    leifdenby committed May 23, 2024
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  2. create 3D mesh objects for schol AR

    Simon Adamov committed May 23, 2024
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Commits on May 28, 2024

  1. fixed math writing

    @sadamov
    sadamov committed May 28, 2024
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  2. Merge branch 'feature_dataset_yaml' of https://github.com/joeloskarss… 

    …on/neural-lam into feature_dataset_yaml
    @sadamov
    sadamov committed May 28, 2024
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  3. cherry-pick with main

    @sadamov
    sadamov committed May 28, 2024
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  4. bugfixes

    @sadamov
    sadamov committed May 28, 2024
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  5. pre_commits

    @sadamov
    sadamov committed May 28, 2024
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Commits on May 31, 2024

  1. Merge remote-tracking branch 'origin/main' into feature_dataset_yaml

    @sadamov
    sadamov committed May 31, 2024
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  2. config.py is ready for danra

    @sadamov
    sadamov committed May 31, 2024
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Commits on Jun 1, 2024

  1. streamlined multi-zarr workflow

    @sadamov
    sadamov committed Jun 1, 2024
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  2. xarray zarr based data normalization

    @sadamov
    sadamov committed Jun 1, 2024
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Commits on Jun 2, 2024

  1. adjusted pre-processing scripts to new data config workflow

    @sadamov
    sadamov committed Jun 2, 2024
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  2. plotting update with latest get_xy() function

    @sadamov
    sadamov committed Jun 2, 2024
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  3. making data config more modular

    @sadamov
    sadamov committed Jun 2, 2024
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  4. removing boundaries for now

    @sadamov
    sadamov committed Jun 2, 2024
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  5. small updates

    @sadamov
    sadamov committed Jun 2, 2024
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  6. improved stats and units retrieval

    @sadamov
    sadamov committed Jun 2, 2024
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Commits on Jun 3, 2024

  1. add GPU-based runner on cirun.io

    @leifdenby
    leifdenby committed Jun 3, 2024
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  2. improved zarr-based normalization

    @sadamov
    sadamov committed Jun 3, 2024
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  3. pdm install with cpu torch

    @leifdenby
    leifdenby committed Jun 3, 2024
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  4. ensure exec in pdm venv

    @leifdenby
    leifdenby committed Jun 3, 2024
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  5. ensure exec in pdm venv

    @leifdenby
    leifdenby committed Jun 3, 2024
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  6. check version #2

    @leifdenby
    leifdenby committed Jun 3, 2024
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  7. check version no 3

    @leifdenby
    leifdenby committed Jun 3, 2024
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  8. check versions

    @leifdenby
    leifdenby committed Jun 3, 2024
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  9. merge main

    @sadamov
    sadamov committed Jun 3, 2024
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  10. Introduced datetime forcing calculation as seperate script

    @sadamov
    sadamov committed Jun 3, 2024
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  11. Fixed order of y and x dims to adhere to mllam#52

    @sadamov
    sadamov committed Jun 3, 2024
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  12. fix for pip install

    @leifdenby
    leifdenby committed Jun 3, 2024
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  13. switch cirun instance type

    @leifdenby
    leifdenby committed Jun 3, 2024
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  14. install py39 on cirun runner

    @leifdenby
    leifdenby committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. cleanup: boundary_mask, zarr-opening, utils

    @sadamov
    sadamov committed Jun 4, 2024
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  2. Merge remote-tracking branch 'origin/main' into feature_dataset_yaml

    @sadamov
    sadamov committed Jun 4, 2024
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  3. change ami image to gpu

    @leifdenby
    leifdenby committed Jun 4, 2024
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  4. Merge remote-tracking branch 'upstream/main' into maint/deps-in-pypro… 

    …ject-toml
    @leifdenby
    leifdenby committed Jun 4, 2024
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  5. use cheaper gpu instance

    @leifdenby
    leifdenby committed Jun 4, 2024
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  6. adapted tests for zarr-analysis data

    @sadamov
    sadamov committed Jun 4, 2024
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  7. Readme adapted for yaml zarr analysis workflow

    @sadamov
    sadamov committed Jun 4, 2024
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  8. samller bugfixes and improvements

    @sadamov
    sadamov committed Jun 4, 2024
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  9. Added fixed data config file for testing on Danra

    @sadamov
    sadamov committed Jun 4, 2024
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  10. reducing runtime of tests with smaller sample

    @sadamov
    sadamov committed Jun 4, 2024
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Commits on Jun 6, 2024

  1. download danra data for test and example (streaming not possible)

    @sadamov
    sadamov committed Jun 6, 2024
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  2. bugfixes after real-life testcase

    @sadamov
    sadamov committed Jun 6, 2024
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  3. Merge remote-tracking branch 'origin/main' into feature_dataset_yaml

    @sadamov
    sadamov committed Jun 6, 2024
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  4. organize .zarr in /data

    @sadamov
    sadamov committed Jun 6, 2024
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  5. cleanup

    @sadamov
    sadamov committed Jun 6, 2024
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  6. linter

    @sadamov
    sadamov committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. static dataset doesn't have time dim

    @sadamov
    sadamov committed Jun 7, 2024
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  2. making two complex functions more modular

    @sadamov
    sadamov committed Jun 7, 2024
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Commits on Jun 8, 2024

  1. chunk dataset by time

    @sadamov
    sadamov committed Jun 8, 2024
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  2. create list first for performance

    @sadamov
    sadamov committed Jun 8, 2024
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  3. converting to_array is very slow 

    the behavior of xr.Dataset.dims will change soon
    @sadamov
    sadamov committed Jun 8, 2024
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  4. allow for forcings to not be normalized

    @sadamov
    sadamov committed Jun 8, 2024
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  5. allow non_normalized_vars to be null

    @sadamov
    sadamov committed Jun 8, 2024
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  6. fixed coastlines using new xy_extent function

    @sadamov
    sadamov committed Jun 8, 2024
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Commits on Jun 9, 2024

  1. Some projections return inverted axes (rotatedPole)

    @sadamov
    sadamov committed Jun 9, 2024
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Commits on Jun 13, 2024

  1. Docstrings added

    @sadamov
    sadamov committed Jun 13, 2024
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Commits on Jun 26, 2024

  1. wip

    @leifdenby
    leifdenby committed Jun 26, 2024
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Commits on Jul 6, 2024

  1. npy mllam nearly done

    @leifdenby
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Commits on Jul 7, 2024

  1. minor adjustment

    @leifdenby
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Commits on Jul 11, 2024

  1. Merge branch 'main' of https://github.com/mllam/neural-lam into maint… 

    …/deps-in-pyproject-toml
    @leifdenby
    leifdenby committed Jul 11, 2024
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  2. add pooch and tweak pip cicd testing

    @leifdenby
    leifdenby committed Jul 11, 2024
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  3. combine cicd tests with caching

    @leifdenby
    leifdenby committed Jul 11, 2024
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  4. linting

    @leifdenby
    leifdenby committed Jul 11, 2024
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  5. add pyg dep

    @leifdenby
    leifdenby committed Jul 11, 2024
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  6. set cirun aws region to frankfurt

    @leifdenby
    leifdenby committed Jul 11, 2024
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  7. adapt image

    @leifdenby
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  8. set image

    @leifdenby
    leifdenby committed Jul 11, 2024
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  9. try different image

    @leifdenby
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  10. add pooch to cicd

    @leifdenby
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Commits on Jul 16, 2024

  1. add pdm gpu test

    @leifdenby
    leifdenby committed Jul 16, 2024
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  2. start work on readme

    @leifdenby
    leifdenby committed Jul 16, 2024
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  3. Merge branch 'maint/deps-in-pyproject-toml' into datastore

    @leifdenby
    leifdenby committed Jul 16, 2024
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  4. Merge branch 'main' into maint/refactor-as-package

    @leifdenby
    leifdenby committed Jul 16, 2024
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  5. Merge branch 'main' of https://github.com/mllam/neural-lam into maint… 

    …/refactor-as-package
    @leifdenby
    leifdenby committed Jul 16, 2024
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  6. turn meps testdata download into pytest fixture

    @leifdenby
    leifdenby committed Jul 16, 2024
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  7. adapt README for package

    @leifdenby
    leifdenby committed Jul 16, 2024
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  8. remove pdm cicd test (will be in separate PR)

    @leifdenby
    leifdenby committed Jul 16, 2024
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  9. remove pdm in gitignore

    @leifdenby
    leifdenby committed Jul 16, 2024
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  10. remove pdm and pyproject files (will be sep PR)

    @leifdenby
    leifdenby committed Jul 16, 2024
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  11. add pyproject.toml from main

    @leifdenby
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  12. clean out tests

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  13. fix linting

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  14. add cli entrypoints import test

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  15. Merge branch 'maint/refactor-as-package' into datastore

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  16. tweak cicd pytest execution

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  17. Merge branch 'maint/refactor-as-package' into datastore

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Commits on Jul 17, 2024

  1. Update tests/test_mllam_dataset.py 

    Co-authored-by: SimonKamuk <[email protected]>
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    leifdenby and SimonKamuk authored Jul 17, 2024
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  2. grid-shape ok

    @leifdenby
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  3. get_vars_names and units

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  4. get_vars_names and units 2

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Commits on Jul 23, 2024

  1. test for stats

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Commits on Jul 24, 2024

  1. get_dataarray test

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  2. get_dataarray test

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  3. boundary_mask

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  4. get_xy

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  5. remove TrainingSample dataclass

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  6. test for WeatherDataset.__getitem__

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  7. test for graph creation

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  8. more graph creation tests

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  9. check for consistency of num features across splits

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  10. test for single batch from mllam through model

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  11. Add init files to expose classes in editable package

    @joeloskarsson
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  12. Linting

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Commits on Jul 25, 2024

  1. working training_step with datastores!

    Leif Denby committed Jul 25, 2024
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  2. remove superfluous tests

    Leif Denby committed Jul 25, 2024
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  3. fix for dataset length

    Leif Denby committed Jul 25, 2024
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  4. step length should be int

    Leif Denby committed Jul 25, 2024
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  5. step length should be int

    Leif Denby committed Jul 25, 2024
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  6. training working with mllam datastore!

    Leif Denby committed Jul 25, 2024
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  7. adapt neural_lam.train_model for datastores

    Leif Denby committed Jul 25, 2024
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  8. fixes for npy

    Leif Denby committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. npyfiles datastore complete

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  2. cleanup for datastore examples

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  3. training on ohm with danra!

    Leif Denby committed Jul 26, 2024
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Commits on Aug 5, 2024

  1. use mllam-data-prep v0.2.0

    Leif Denby committed Aug 5, 2024
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  2. remove py3.12 from pre-commit

    Leif Denby committed Aug 5, 2024
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Commits on Aug 8, 2024

  1. cleanup

    Leif Denby committed Aug 8, 2024
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Commits on Aug 12, 2024

  1. all tests passing!

    Leif Denby committed Aug 12, 2024
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  2. use mllam-data-prep v0.3.0

    Leif Denby committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. delete requirements.txt

    Leif Denby committed Aug 13, 2024
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  2. remove .DS_Store

    Leif Denby committed Aug 13, 2024
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  3. use tmate in gpu pdm cicd

    Leif Denby committed Aug 13, 2024
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  4. remove requirements

    Leif Denby committed Aug 13, 2024
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  5. update pdm gpu cicd setup to pdm venv on nvme drive

    Leif Denby committed Aug 13, 2024
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  6. don't try to use pdm venv in-project

    Leif Denby committed Aug 13, 2024
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  7. remove tmate

    Leif Denby committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. update README with install instructions

    Leif Denby committed Aug 14, 2024
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  2. changelog

    Leif Denby committed Aug 14, 2024
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  3. update ci/cd badges to include gpu + gpu

    Leif Denby committed Aug 14, 2024
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  4. Merge pull request #1 from mllam/package_inits 

    Package inits
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  5. add pyproject-flake8 to precommit config

    Leif Denby committed Aug 14, 2024
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  6. use Flake8-pyproject instead

    Leif Denby committed Aug 14, 2024
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  7. update README

    Leif Denby committed Aug 14, 2024
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  8. Merge branch 'maint/deps-in-pyproject-toml' into feat/datastores

    Leif Denby committed Aug 14, 2024
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  9. Merge branch 'maint/refactor-as-package' into maint/deps-in-pyproject… 

    …-toml
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  10. Merge branch 'maint/deps-in-pyproject-toml' into feat/datastores

    Leif Denby committed Aug 14, 2024
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  11. linting fixes

    Leif Denby committed Aug 14, 2024
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  12. train only 1 epoch in cicd and print to stdout

    Leif Denby committed Aug 14, 2024
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  13. log datastore config

    Leif Denby committed Aug 14, 2024
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Commits on Aug 15, 2024

  1. cleanup doctrings

    Leif Denby committed Aug 15, 2024
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Commits on Aug 19, 2024

  1. Merge branch 'maint/refactor-as-package' into datastore

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  2. Merge branch 'main' of https://github.com/mllam/neural-lam into maint… 

    …/deps-in-pyproject-toml
    @leifdenby
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  3. update changelog

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Commits on Aug 20, 2024

  1. move dev deps optional dependencies group

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  2. update cicd tests to install dev deps

    @leifdenby
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  3. update readme with new dev deps group

    @leifdenby
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  4. quote the skip step the install readme

    @leifdenby
    leifdenby committed Aug 20, 2024
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  5. remove unused files

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  6. Merge branch 'feat/datastores' of https://github.com/leifdenby/neural… 

    …-lam into feat/datastores
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  7. revert to line length of 80

    @leifdenby
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  8. revert docstring formatting changes

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  9. pin numpy to <2.0.0

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  10. Merge branch 'maint/deps-in-pyproject-toml' into feat/datastores

    @leifdenby
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  11. Merge branch 'main' into feat/datastores

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  12. fix flake8 linting errors

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    leifdenby committed Aug 20, 2024
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Commits on Sep 8, 2024

  1. Update neural_lam/weather_dataset.py 

    Clarify that for forecast datasets the training sample always starts with the first timestep, rather than creating samples from all lead times (as it was before)

Co-authored-by: Joel Oskarsson <[email protected]>
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  2. Update neural_lam/datastore/multizarr/create_normalization_stats.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  3. Update neural_lam/datastore/npyfiles/store.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  4. Update neural_lam/datastore/npyfiles/store.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  5. Update neural_lam/datastore/npyfiles/store.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  6. Update tests/test_training.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  7. Update tests/test_datasets.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 8, 2024
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  8. Update README.md 

    Co-authored-by: Joel Oskarsson <[email protected]>
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Commits on Sep 10, 2024

  1. update README

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  2. Merge branch 'main' of https://github.com/mllam/neural-lam into feat/… 

    …datastores
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  3. Merge branch 'feat/datastores' of https://github.com/leifdenby/neural… 

    …-lam into feat/datastores
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  4. column_water -> open_water_fraction

    @leifdenby
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  5. fix linting

    @leifdenby
    leifdenby committed Sep 10, 2024
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  6. static data same for all splits

    @leifdenby
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  7. forcing_window_size from args

    @leifdenby
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  8. Update neural_lam/datastore/base.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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  9. only use first ensemble member in datastores

    @leifdenby
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  10. Merge branch 'feat/datastores' of https://github.com/leifdenby/neural… 

    …-lam into feat/datastores
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  11. Update neural_lam/datastore/base.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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  12. Update neural_lam/datastore/base.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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  13. Update neural_lam/datastore/base.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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  14. remove all multizarr functionality

    @leifdenby
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  15. cleanup and test fixes for recent changes

    @leifdenby
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  16. Merge branch 'feat/datastores' of https://github.com/leifdenby/neural… 

    …-lam into feat/datastores
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  17. fix linting

    @leifdenby
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  18. remove multizar example files

    @leifdenby
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  19. normalization -> standardization

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  20. fix import for tests

    @leifdenby
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  21. Update neural_lam/datastore/base.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
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    leifdenby and joeloskarsson authored Sep 10, 2024
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Commits on Sep 12, 2024

  1. fix coord issues and add datastore example plotting cli

    @leifdenby
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  2. add lru_cache to get_xy_extent

    @leifdenby
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  3. MLLAMDatastore -> MDPDatastore

    @leifdenby
    leifdenby committed Sep 12, 2024
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  4. missed renames for MDPDatastore

    @leifdenby
    leifdenby committed Sep 12, 2024
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  5. update graph plot for datastores

    @leifdenby
    leifdenby committed Sep 12, 2024
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  6. use relative import

    @leifdenby
    leifdenby committed Sep 12, 2024
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  7. add long_names and refactor npyfiles create weights

    @leifdenby
    leifdenby committed Sep 12, 2024
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Commits on Sep 23, 2024

  1. Update neural_lam/weather_dataset.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
    @leifdenby @joeloskarsson
    leifdenby and joeloskarsson authored Sep 23, 2024
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  2. Update neural_lam/weather_dataset.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
    @leifdenby @joeloskarsson
    leifdenby and joeloskarsson authored Sep 23, 2024
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Commits on Sep 27, 2024

  1. Update neural_lam/models/ar_model.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
    @leifdenby @joeloskarsson
    leifdenby and joeloskarsson authored Sep 27, 2024
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  2. Update neural_lam/weather_dataset.py 

    Co-authored-by: Joel Oskarsson <[email protected]>
    @leifdenby @joeloskarsson
    leifdenby and joeloskarsson authored Sep 27, 2024
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  3. read projection from datastore config extra section

    @leifdenby
    leifdenby committed Sep 27, 2024
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  4. NpyFilesDatastore -> NpyFilesDatastoreMEPS

    @leifdenby
    leifdenby committed Sep 27, 2024
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  5. revert tp training with 1 AR step by default

    @leifdenby
    leifdenby committed Sep 27, 2024
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  6. add missing kwarg to BaseHiGraphModel.__init__

    @leifdenby
    leifdenby committed Sep 27, 2024
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  7. add missing kwarg to HiLAM.__init__

    @leifdenby
    leifdenby committed Sep 27, 2024
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  8. add missing kwarg to HiLAMParallel

    @leifdenby
    leifdenby committed Sep 27, 2024
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  9. check that for enough forecast steps given ar_steps

    @leifdenby
    leifdenby committed Sep 27, 2024
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  10. remove numpy<2.0.0 version cap

    @leifdenby
    leifdenby committed Sep 27, 2024
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Commits on Oct 1, 2024

  1. tweak print statement working in mdp

    Leif Denby committed Oct 1, 2024
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  2. fix missed removed argument from cli

    Leif Denby committed Oct 1, 2024
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  3. remove wandb config log comment, we log now

    Leif Denby committed Oct 1, 2024
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  4. ensure loading from checkpoint during train possible

    Leif Denby committed Oct 1, 2024
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  5. get step_length from datastore in plot_error_map

    @leifdenby
    leifdenby committed Oct 1, 2024
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  6. remove step_legnth attr in ARModel

    @leifdenby
    leifdenby committed Oct 1, 2024
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  7. remove unused obs_mask arg for vis.plot_prediction

    @leifdenby
    leifdenby committed Oct 1, 2024
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  8. ensure no reference to multizarr "data_config"

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

  1. introduce neural-lam config

    @leifdenby
    leifdenby committed Oct 2, 2024
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  2. include meps neural-lam config example

    @leifdenby
    leifdenby committed Oct 2, 2024
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  3. fix extra space typo in BaseDatastore

    @leifdenby
    leifdenby committed Oct 2, 2024
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  4. add check and print of train/test/val split in MDPDatastore

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

  1. BaseCartesianDatastore -> BaseRegularGridDatastore 

    Rename base class for datastores representating data on a regular grid. Also introduce DummyDatastore in tests that represent data on an irregular grid
    @leifdenby
    leifdenby committed Oct 3, 2024
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Commits on Oct 23, 2024

  1. removed `control_only' arg

    @sadamov
    sadamov committed Oct 23, 2024
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