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[bad PR] #90

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wants to merge 103 commits into from
Closed

[bad PR] #90

wants to merge 103 commits into from

Commits on Apr 4, 2024

  1. added suds and pandas conversion libraries

    Aleksejs Fomins authored and Aleksejs Fomins committed Apr 4, 2024
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  2. minor

    Aleksejs Fomins committed Apr 4, 2024
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  3. updated to main

    Aleksejs Fomins committed Apr 4, 2024
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Commits on Apr 8, 2024

  1. made example usage for read

    Aleksejs Fomins committed Apr 8, 2024
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  2. paginator impl as lib+example

    Aleksejs Fomins committed Apr 8, 2024
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  3. skeleton BFabricPy_V2.0000001, engines for suds and zeep, resultsCont… 

    …ainer
    Aleksejs Fomins committed Apr 8, 2024
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  4. Merge branch 'dev-bfabric-2' into feat_response_formats

    Aleksejs Fomins committed Apr 8, 2024
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  5. applied SUDS->Dict to ResultContainer

    Aleksejs Fomins committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. Update bfabric/src/pandas_helper.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  2. Update bfabric/src/pandas_helper.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  3. Update bfabric/src/pandas_helper.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  4. Update bfabric/examples/suds_to_listdict.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  5. Update bfabric/examples/suds_to_listdict.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  6. Update bfabric/src/suds_format.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  7. Update bfabric/src/result_container.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 9, 2024
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  8. Merge pull request #66 from fgcz/feat_response_formats 

    Feat response formats
    @aleksejs-fomins
    aleksejs-fomins authored Apr 9, 2024
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  9. converted some names to to PEP8

    Aleksejs Fomins committed Apr 9, 2024
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  10. Merge branch 'feat_response_formats' into dev-bfabric-2

    Aleksejs Fomins committed Apr 9, 2024
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  11. minor

    Aleksejs Fomins committed Apr 9, 2024
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  12. Merge branch 'dev-bfabric-2' into feature-pagination

    Aleksejs Fomins committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. implementation of pagination and multi-query functionality for BFabric2

    Aleksejs Fomins committed Apr 10, 2024
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  2. Merge branch 'main' into dev-bfabric-2

    Aleksejs Fomins committed Apr 10, 2024
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  3. Merge branch 'main' into feature-pagination

    Aleksejs Fomins committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. using auth class, minor bug in engines, added __repr__ etc to Resourc… 

    …eContainer
    Aleksejs Fomins committed Apr 11, 2024
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  2. Merge branch 'main' into dev-bfabric-2

    Aleksejs Fomins committed Apr 11, 2024
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  3. Merge branch 'main' into feature-pagination

    Aleksejs Fomins committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. minor naming, progress on testing of consistency between Zeep and SUDS

    Aleksejs Fomins committed Apr 12, 2024
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Commits on Apr 16, 2024

  1. rewrote test script in a more readable way

    Aleksejs Fomins committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. reformulated comparison examples closer to test-like, added comments,… 

    … added dict-sorting by key feature for easier comparison of Zeep and Suds
    Aleksejs Fomins committed Apr 17, 2024
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  2. minor naming improvement

    Aleksejs Fomins committed Apr 17, 2024
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  3. added bfabric.exists() to check if objects with requested ids exist. … 

    …Modularized pagination iterator
    Aleksejs Fomins committed Apr 17, 2024
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  4. extended exists interface to arbitrary key. Makes sense to also query… 

    … it by name
    Aleksejs Fomins committed Apr 17, 2024
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  5. experimenting with exists-save-delete pipeline

    Aleksejs Fomins committed Apr 17, 2024
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Commits on Apr 19, 2024

  1. unit and integration tests. Not full coverage, but hopefully will do … 

    …for now
    Aleksejs Fomins committed Apr 19, 2024
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Commits on Apr 22, 2024

  1. Update bfabric/tests/unit/test_results_container.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  2. test naming, moved dict_helper into same file

    Aleksejs Fomins committed Apr 22, 2024
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  3. Merge branch 'feature-pagination' of github.com:fgcz/bfabricPy into f… 

    …eature-pagination
    Aleksejs Fomins committed Apr 22, 2024
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  4. Update bfabric/bfabric2.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  5. removed save_multi

    Aleksejs Fomins committed Apr 22, 2024
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  6. Merge branch 'feature-pagination' of github.com:fgcz/bfabricPy into f… 

    …eature-pagination
    Aleksejs Fomins committed Apr 22, 2024
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  7. Update bfabric/tests/integration/test_bfabric2_read_pagination.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  8. naming and subtest for read test

    Aleksejs Fomins committed Apr 22, 2024
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  9. Update bfabric/tests/integration/test_bfabric2_read_pagination.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  10. Merge branch 'feature-pagination' of github.com:fgcz/bfabricPy into f… 

    …eature-pagination
    Aleksejs Fomins committed Apr 22, 2024
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  11. Update bfabric/tests/integration/test_bfabric2_save_delete.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  12. Update bfabric/tests/unit/test_results_container.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 22, 2024
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  13. minor naming

    Aleksejs Fomins committed Apr 22, 2024
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  14. minor naming

    Aleksejs Fomins committed Apr 22, 2024
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  15. hack to enable Zeep to read from samples

    Aleksejs Fomins committed Apr 22, 2024
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  16. added deepcopy to Zeep Hack for potential hierarchical queries

    Aleksejs Fomins committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. migrated bfabricpy to .yml config files

    Aleksejs Fomins committed Apr 23, 2024
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  2. Merge pull request #70 from fgcz/feature-pagination 

    Feature pagination
    @aleksejs-fomins
    aleksejs-fomins authored Apr 23, 2024
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  3. docstring for bfabric class

    Aleksejs Fomins committed Apr 23, 2024
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  4. Merge branch 'feat_ini_config' into dev-bfabric-2

    Aleksejs Fomins committed Apr 23, 2024
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  5. added authentication to the actual bfabric2 class, fixed a few minor … 

    …bugs introduced by previous revision
    Aleksejs Fomins committed Apr 23, 2024
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  6. renamed webbase to base_url everywhere

    Aleksejs Fomins committed Apr 23, 2024
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  7. Merge branch 'feat_ini_config' into dev-bfabric-2

    Aleksejs Fomins committed Apr 23, 2024
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  8. merged renaming from main

    Aleksejs Fomins committed Apr 23, 2024
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  9. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  10. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  11. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  12. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  13. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  14. renamed bfabric2 from webbase to base_url

    Aleksejs Fomins committed Apr 23, 2024
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  15. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
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  16. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  17. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  18. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  19. Update bfabric/bfabric_config.py 

    Co-authored-by: Leonardo Schwarz <[email protected]>
    @aleksejs-fomins @leoschwarz
    aleksejs-fomins and leoschwarz authored Apr 23, 2024
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  20. revision changes

    Aleksejs Fomins committed Apr 23, 2024
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  21. Merge branch 'feat_ini_config' of github.com:fgcz/bfabricPy into feat… 

    …_ini_config
    Aleksejs Fomins committed Apr 23, 2024
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  22. warning for old config file

    Aleksejs Fomins committed Apr 23, 2024
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  23. fixed a few bugs in _parse_dict

    Aleksejs Fomins committed Apr 23, 2024
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  24. Merge branch 'feat_ini_config' into dev-bfabric-2

    Aleksejs Fomins committed Apr 23, 2024
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  25. minor fix bad refactor

    Aleksejs Fomins committed Apr 23, 2024
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  26. Merge branch 'dev-bfabric-2' into bugfix_bfabric2_login

    @aleksejs-fomins
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  27. Merge pull request #72 from fgcz/bugfix_bfabric2_login 

    Bugfix bfabric2 login
    @aleksejs-fomins
    aleksejs-fomins authored Apr 23, 2024
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  28. minor test if config file has .yml extension

    Aleksejs Fomins committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. throw exception if explicitly-provided path to the config file is wrong

    Aleksejs Fomins committed Apr 24, 2024
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  2. Handle default None parameters in BfabricConfig

    @leoschwarz
    leoschwarz committed Apr 24, 2024
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Commits on Apr 25, 2024

  1. Merge pull request #73 from fgcz/config-class-default-params 

    Handle default `None` parameters in BfabricConfig
    @aleksejs-fomins
    aleksejs-fomins authored Apr 25, 2024
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Commits on Apr 26, 2024

  1. Detect error responses in ResultContainer

    @leoschwarz
    leoschwarz committed Apr 26, 2024
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  2. added integration tests for bad queries. added common handling of bad… 

    … endpoints. extended use BfabricRequestError to correctly handle bad delete queries and multiple responses
    @leoschwarz
    Aleksejs Fomins authored and leoschwarz committed Apr 26, 2024
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  3. Minor changes

    @leoschwarz
    leoschwarz committed Apr 26, 2024
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  4. added zeep as a requirement

    Aleksejs Fomins committed Apr 26, 2024
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Commits on Apr 29, 2024

  1. fixed minor bug, added exists test

    Aleksejs Fomins committed Apr 29, 2024
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  2. minor

    Aleksejs Fomins committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Python 3.9 compatibility

    @leoschwarz
    leoschwarz committed Apr 30, 2024
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  2. Merge branch 'main' into dev-bfabric-2

    @leoschwarz
    leoschwarz committed Apr 30, 2024
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  3. fix some test failures

    @leoschwarz
    leoschwarz committed Apr 30, 2024
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Commits on May 2, 2024

  1. Migrate to pyproject.toml (#76) 

    - This migrates the project configuration to `pyproject.toml`.
- In a next step we can update the folder structure as well.
- Scripts can be added once we add a `main` function to them, which will be done in separate PRs.
    @leoschwarz
    leoschwarz authored May 2, 2024
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  2. Extract wrapper creator code (#78) 

    The code itself has not been changed, nor does it use the new API.
    @leoschwarz
    leoschwarz authored May 2, 2024
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Commits on May 3, 2024

  1. Update script bfabric_list_not_available_proteomics_workunits.py

    @leoschwarz
    leoschwarz committed May 3, 2024
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  2. Merge pull request #80 from fgcz/leo-refactor-list-not-available-prot-wu 

    Refactor list not available proteomics workunits
    @cpanse
    cpanse authored May 3, 2024
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  3. adapt 'make install' to toml

    @cpanse
    cpanse committed May 3, 2024
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  4. correct url, better version message

    @leoschwarz
    leoschwarz committed May 3, 2024
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  5. Merge pull request #82 from fgcz/use-configured-url 

    Use configured url
    @cpanse
    cpanse authored May 3, 2024
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Commits on May 7, 2024

  1. cosmetics Makefile

    @cpanse
    cpanse committed May 7, 2024
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  2. Extend PR Checks (#83) 

    - Use `uv`
- Adds:
  - Code style (does not need to pass)
  - License check
    @leoschwarz
    leoschwarz authored May 7, 2024
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  3. Move auth logic to Bfabric class (#79) 

    - Make managing the `BfabricAuth` object the responsibility of the `Bfabric` class. This allows us to implement the contextmanager, which will be useful for the REST-proxy server.
  - Notably this shouldn't change anything about code that already uses the new class.
- Rename `BfabricConfig.with_overrides` to `BfabricConfig.copy_with` for clarity.
- Some unit tests for the Bfabric class, I will add more as I go.
    @leoschwarz
    leoschwarz authored May 7, 2024
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  4. add config field server_timezone (#84)

    @leoschwarz
    leoschwarz authored May 7, 2024
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  5. new pagination interface, more stable reads, Bfabric.from_config (#85) 

    - New pagination logic:
  - Specify max number of items
  - Specify offset of items to skip
- Stable reading
  - Reading passes a `createdbefore` query field (if it's not part of the query) to ensure consistent reads/pagination in the presence of insertions into the database. Deletions are not handled and might require an API feature.
  - It will need to be tested further before releasing, but my idea is that this is a lot more flexible moving forward
- New `Bfabric.from_config` arguably it is a bit redundant with the `get_system_auth` method, however I do feel like 99% of use cases will be handled with this method now and it will be easier to do so. I'm not changing the usage in this PR yet.
    @leoschwarz
    leoschwarz authored May 7, 2024
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  6. Deprecate some scripts

    @leoschwarz
    leoschwarz committed May 7, 2024
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