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Consolidated v4 fixes #9

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Consolidated v4 fixes #9

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Commits on Jan 28, 2022

  1. Integrated code developed at ESS, so far

    @nitrosx
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  2. REL: v0.2.1

    @dylanmcreynolds
    dylanmcreynolds committed Jan 28, 2022
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  3. url fix

    @dylanmcreynolds
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  4. REL: v0.2.2

    @dylanmcreynolds
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Commits on Jan 31, 2022

  1. Merge pull request SciCatProject#8 from dylanmcreynolds/easy_url 

    Easy url
    @dylanmcreynolds
    dylanmcreynolds authored Jan 31, 2022
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Commits on Feb 2, 2022

  1. Merge branch 'main' of https://github.com/SciCatProject/pyscicat into… 

    … ESS-adding-in-house-functionalities
    @nitrosx
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Commits on Feb 17, 2022

  1. Merge branch 'als-computing:main' into ESS-adding-in-house-functional… 

    …ities
    @nitrosx
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  2. Fixed linting issues

    @nitrosx
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  3. Merge branch 'ESS-adding-in-house-functionalities' of https://github.… 

    …com/SciCatProject/pyscicat into ESS-adding-in-house-functionalities
    @nitrosx
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Commits on Feb 24, 2022

  1. Fixed issue in update_dataset_origdatablock

    @nitrosx
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Commits on Mar 8, 2022

  1. added documentation and example

    @nitrosx
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Commits on Mar 9, 2022

  1. fixed linting

    @nitrosx
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Commits on Mar 10, 2022

  1. updated documentation, included new documentation under how-to sectio… 

    …n of documentation, updated example. Added packages in requirements to requirements-dev.
    @nitrosx
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Commits on Mar 11, 2022

  1. removed production packages from requirements-dev

    @nitrosx
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Commits on Mar 14, 2022

  1. Renamed example script, added test for new functions

    @nitrosx
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  2. Fixed linting

    @nitrosx
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  3. Merge pull request SciCatProject#10 from SciCatProject/ESS-adding-in-… 

    …house-functionalities

Ess adding in house functionalities
    @dylanmcreynolds
    dylanmcreynolds authored Mar 14, 2022
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Commits on Mar 28, 2022

  1. Added function to delete dataset by pid

    @nitrosx
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Commits on Apr 13, 2022

  1. Added raw and derived upsert functions

    @abigailalexander
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Commits on Apr 19, 2022

  1. added functions to load dataset by id and related orig_datablocks

    @nitrosx
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Commits on Apr 21, 2022

  1. Added upsert_dataset. Fixed bug in upsert funcs

    @abigailalexander
    abigailalexander committed Apr 21, 2022
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  2. Removed unneeded f in log/error statements causing bug

    @abigailalexander
    abigailalexander committed Apr 21, 2022
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Commits on Apr 26, 2022

  1. Added initial upsert test

    @abigailalexander
    abigailalexander committed Apr 26, 2022
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  2. Added model and method for PublishedData

    @nitrosx
    nitrosx committed Apr 26, 2022
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  3. Fixing bugs in published data functions

    @nitrosx
    nitrosx committed Apr 26, 2022
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Commits on Apr 27, 2022

  1. Fixed urls for upsert func and test

    @abigailalexander
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  2. remove pre-commit and re-add flake8

    @dylanmcreynolds
    dylanmcreynolds authored Apr 27, 2022
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  3. More remove pre-commit files

    @dylanmcreynolds
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  4. remove pre-commit

    @dylanmcreynolds
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  5. Merge pull request SciCatProject#15 from dylanmcreynolds/remove-pre-c… 

    …ommit

remove pre-commit
    @dylanmcreynolds
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Commits on Apr 28, 2022

  1. Black formatting fixes

    @abigailalexander
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  2. Raise ValueError in upsert_dataset

    @abigailalexander
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Commits on Apr 29, 2022

  1. Added additional upsert test case

    @abigailalexander
    abigailalexander committed Apr 29, 2022
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  2. Removed generic upsert, use raw/derived instead

    @abigailalexander
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  3. Upsert inserts if dataset doesnt exist yet

    @abigailalexander
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Commits on May 4, 2022

  1. Merge remote-tracking branch 'pyscicat-main/remove-precommit' into up… 

    …sert-dataset
    @abigailalexander
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Commits on May 9, 2022

  1. Black format fix

    @abigailalexander
    abigailalexander committed May 9, 2022
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  2. Fixed indentation causing merge conflict

    @abigailalexander
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  3. Merge remote-tracking branch 'origin/main' into upsert-dataset

    @abigailalexander
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Commits on May 13, 2022

  1. Removed unneeded as_posix causing bug

    @abigailalexander
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  2. Merge pull request #2 from rosalindfranklininstitute/modify-setup 

    Modified setup.py
    @LAShemilt
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  3. Merge pull request SciCatProject#17 from rosalindfranklininstitute/mo… 

    …dify-setup

modify setup.py to remove filename.as_posix causing bug
    @dylanmcreynolds
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Commits on Jun 1, 2022

  1. Merge pull request SciCatProject#12 from rosalindfranklininstitute/up… 

    …sert-dataset

Upsert dataset
    @dylanmcreynolds
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Commits on Jun 3, 2022

  1. wip right before finalizing th ecode for the PR

    @nitrosx
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  2. Fixed naming convention on few functions, added test on published data

    @nitrosx
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  3. merged with master. Fixed naming according to CRUD/mongodb convention

    @nitrosx
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  4. fixed linting and code styling

    @nitrosx
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Commits on Jun 14, 2022

  1. Do not log username and token

    @jl-wynen
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  2. Turn into non-f-string

    @jl-wynen
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  3. Merge pull request SciCatProject#21 from jl-wynen/do-not-log-credentials 

    Security: Do not log username and token
    @dylanmcreynolds
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Commits on Jun 15, 2022

  1. Merge pull request #3 from SciCatProject/main 

    Updating our main with Scicat Project
    @LAShemilt
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  2. Added update dataset method with patch

    @abigailalexander
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  3. Added update dataset mock test

    @abigailalexander
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  4. Modified update dataset test

    @abigailalexander
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Commits on Jun 16, 2022

  1. Removed upsert method and tests

    @abigailalexander
    abigailalexander committed Jun 16, 2022
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  2. modified update dataset format and url encoding

    @abigailalexander
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  3. flake8 linting changes

    @abigailalexander
    abigailalexander committed Jun 16, 2022
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  4. Changed functions names according to what agreed on PR SciCatProject#20

    @nitrosx
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Commits on Jun 17, 2022

  1. Implemented new naming

    @nitrosx
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  2. Merge branch 'main' of https://github.com/SciCatProject/pyscicat into… 

    … ESS
    @nitrosx
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Commits on Jun 30, 2022

  1. Add more model fields

    @jl-wynen
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Commits on Jul 5, 2022

  1. add logo 

    design by Max
approved by PSF
    @zjttoefs
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Commits on Jul 6, 2022

  1. fix sphynx build

    @dylanmcreynolds
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Commits on Aug 7, 2022

  1. Merge pull request SciCatProject#24 from SciCatProject/ESS 

    Latest ESS functionalities and naming coinvention
    @dylanmcreynolds
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  2. Merge branch 'update-dataset' of github.com:rosalindfranklininstitute… 

    …/pyscicat into rosalindfranklininstitute-update-dataset
    @dylanmcreynolds
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  3. fix merge

    @dylanmcreynolds
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  4. Merge branch 'rosalindfranklininstitute-update-dataset'

    @dylanmcreynolds
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Commits on Aug 10, 2022

  1. Update model.py 

    modify according comments in PR
    @nitrosx
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  2. Update model.py 

    switch order of MongoQueryable and Ownable
    @nitrosx
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  3. Merge pull request SciCatProject#25 from jl-wynen/model-missing-fields 

    Add more model fields
    @dylanmcreynolds
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  4. REL: v0.2.3

    @dylanmcreynolds
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Commits on Aug 17, 2022

  1. Remove code duplication in client

    @jl-wynen
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  2. Remove log call in client constructor

    @jl-wynen
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Commits on Sep 29, 2022

  1. Log in via either Users/login or auth/msad

    @jl-wynen
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Commits on Nov 8, 2022

  1. Merge pull request SciCatProject#31 from jl-wynen/user-auth 

    Log in via either Users/login or auth/msad
    @dylanmcreynolds
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  2. Merge branch 'main' into client-refactor

    @dylanmcreynolds
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Commits on Nov 9, 2022

  1. Fix call to urljoin

    @jl-wynen
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  2. Merge pull request SciCatProject#27 from jl-wynen/client-refactor 

    Remove code duplication in client
    @dylanmcreynolds
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Commits on Nov 10, 2022

  1. small fixes to model and search

    @toqduj
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  2. Merge branch 'SciCatProject:main' into main

    @toqduj
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Commits on Nov 11, 2022

  1. Merge pull request SciCatProject#32 from BAMresearch/main 

    small fixes
    @nitrosx
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Commits on Jan 27, 2023

  1. Implement upload functions for proposals, samples and instruments

    Martin Voigt committed Jan 27, 2023
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  2. Test upload functions for proposals, samples and instruments

    Martin Voigt committed Jan 27, 2023
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  3. Update data model

    Martin Voigt committed Jan 27, 2023
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  4. Update documentation

    Martin Voigt committed Jan 27, 2023
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  5. Implement update functions for proposals, samples and instruments

    Martin Voigt committed Jan 27, 2023
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  6. Fix documentation

    Martin Voigt committed Jan 27, 2023
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  7. Flake8 compliance

    Martin Voigt committed Jan 27, 2023
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Commits on Jan 30, 2023

  1. Update-function of the form <api-endpoint>_update

    Martin Voigt committed Jan 30, 2023
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  2. Rename update_dataset() to datasets_update() in client.

    Martin Voigt committed Jan 30, 2023
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Commits on Jan 31, 2023

  1. Merge pull request SciCatProject#35 from eilmiv/more_upload_functions 

    More upload functions
    @nitrosx
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Commits on Jun 6, 2023

  1. adding some tests to work against a scicat v4 backend.

    @LAShemilt
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  2. Restructured the code so that we can install the optional requiments … 

    …using `pip install -e ".[option]"`. To add optional requirements add to the [optional.extras_require] in the setup config. All functions and imports work the same way. Restructured the testing suite so it follows a similar pattern. All tests pass.
    @LAShemilt
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  3. moving the extra tests into the new test suite

    @LAShemilt
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  4. reducing the version of python as 3.8 is not the requirment

    @LAShemilt
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  5. porting tests to pyscicat and linting with flake8

    @LAShemilt
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  6. putting the python version to the lowest verions that is built agains… 

    …t. The versioneer part of the set up config will set the version and does not need to be written in the metadata section
    @LAShemilt
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  7. Removing the forward / before Datasets. If this is given in the endpo… 

    …int then this is treated by urllib.parse like a full path.
    @LAShemilt
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  8. testing update dataset now that the getter methods work

    @LAShemilt
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  9. move the integration tests out into their own package so they can be … 

    …ignored by the current actions workflows.
    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  10. first attempt at an actions workflow to do the integration testing.

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  11. changing linting and adding steps

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  12. changing linting and adding steps

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  13. correct name for the scicat backend service

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  14. adding environmental variables

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  15. remove subtests dependency

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  16. solving merge

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  17. removing methods from v4

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  18. remove erroneous line in coverage stage of integration-testing.yml

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  19. replace pip install from requirements-dev.txt with the .[dev] option … 

    …from the setup config.
    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  20. updating the tests mocks to be inline with the new backend

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  21. liniting

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  22. updating deprecated config - license_file to license_files

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  23. excluding continuous_integration folder that is used in workflows but… 

    … is not part of package
    @LAShemilt
    LAShemilt committed Jun 6, 2023
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  24. run just the integration tests

    @LAShemilt
    LAShemilt committed Jun 6, 2023
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Commits on Jun 7, 2023

  1. Merge pull request SciCatProject#40 from rosalindfranklininstitute/v4… 

    …-datasets

V4 datasets
    @dylanmcreynolds
    dylanmcreynolds authored Jun 7, 2023
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Commits on Jun 27, 2023

  1. removing quotation marks that causes pypi to fail

    @LAShemilt
    LAShemilt committed Jun 27, 2023
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  2. Merge pull request SciCatProject#41 from rosalindfranklininstitute/se… 

    …tup-cfg-hotfix

removing quotation marks that causes pypi to fail
    @dylanmcreynolds
    dylanmcreynolds authored Jun 27, 2023
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Commits on Aug 2, 2023

  1. add default value None for all optional parameters

    Martin Voigt committed Aug 2, 2023
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  2. update to flake8-6.1

    Martin Voigt committed Aug 2, 2023
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  3. pydantic v2 no longer converts int to str automatically

    Martin Voigt committed Aug 2, 2023
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  4. Merge pull request SciCatProject#46 from eilmiv/pydantic_v2_compatible 

    Support newer versions of pydantic
    @dylanmcreynolds
    dylanmcreynolds authored Aug 2, 2023
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Commits on Aug 25, 2023

  1. This commit makes a small change with the client in order to better s… 

    …upport the current routes available on the newest version(v4.x) of the scicat backend. It also makes a small change to the OrigDatablock to support what is required in the new backend.
    @JeffreyFG
    JeffreyFG committed Aug 25, 2023
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Commits on Sep 12, 2023

  1. removed unnecessary comment about datasetType

    @JeffreyFG
    JeffreyFG committed Sep 12, 2023
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  2. fixed small comment error about which dataset is default

    @JeffreyFG
    JeffreyFG committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. Update model.py 

    ownerGroup will now longer be required by the pydantic model and because the backend will not accept it
    @JeffreyFG
    JeffreyFG authored Sep 13, 2023
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