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feat: added support for Pydantic V2 #487

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wants to merge 59 commits into from
Closed

feat: added support for Pydantic V2 #487

wants to merge 59 commits into from

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camilovelezr
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@camilovelezr camilovelezr commented Nov 24, 2023 •
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This was superseded by #505

This PR:

  • Adds parallel support for Pydantic V2 and Pydantic V1.
  • Improves submit_plugin(manifest) function: before, when trying to submit a plugin from a local manifest, only manifest as a pathlib.Path was allowed. Now, manifest can also be a str of the path.

@camilovelezr
build: removed exclude src in pre-commit-config
be01c39
@camilovelezr
refactor: added docstrings to top of scripts
79fd117
@camilovelezr
refactor: addressed most of flake8
f726f80
@camilovelezr
Merge branch 'nickupdate' of github.com:camilovelezr/polus-plugins in…
c782ef0 
…to nickupdate
@camilovelezr
refactor: refactored to pass flake8 and remove plugins class
b32c4a5
@camilovelezr
refactor: fixed isort and black conflicts
cd70c77
@camilovelezr
refactor: removed unused code in __init__.py
77c09b7
@camilovelezr
refactor: removed extra comments
d4088b1
@camilovelezr
fix: fixed missing character in pyproject.toml
5aea47e
@camilovelezr
feat: improved error handling of manifests' validation errors
4f09101
@camilovelezr
refactor: removed logger config
6c62833
@camilovelezr
feat: added cwl methods
604b530
@camilovelezr
build: modified authors in pyproject.toml
5f87610
@camilovelezr
build: modified authors in pyproject.toml
6cae5c6
@camilovelezr
Merge branch 'nickupdate' into err2
378484a
@camilovelezr
Merge branch 'err2' into cwl3
b417cc7
@camilovelezr
refactor: removed 'files' from outputbinding
08ef8f5
@camilovelezr
Merge branch 'master' into err2
18a1b78
@camilovelezr
Merge branch 'err2' into cwl3
d827d67
@camilovelezr
fix: fixed Union operator for Python <3.10
1f14b0a
@camilovelezr
refactor: removed global var invalid_manifest
95ec314
@camilovelezr
fix: fixed collection not as directory type
30a96d1
@camilovelezr
fix: fixed lower case d in Directory output
e4e6cd4
@camilovelezr
refactor: refactored enums in CLT to str for compat with workflows
51f3814
@camilovelezr
Merge branch 'err2' into cwl3
e622e19
@camilovelezr
build: added cwltool to pyproject.toml
49f76cc
@camilovelezr
Merge branch 'cwl3' into rm1
02b0687
@camilovelezr
fix: removed | for unions
f2ec33a
@camilovelezr
Merge branch 'cwl3' into rm1
a6e92e0
@camilovelezr
feat: added methods to remove plugins
11282b5
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sweep-ai bot commented Nov 24, 2023

Apply Sweep Rules to your PR?

  • Apply: All new business logic should have corresponding unit tests.
  • Apply: Refactor large functions to be more modular.
  • Apply: Add docstrings to all functions and file headers.

@camilovelezr camilovelezr marked this pull request as draft November 27, 2023 14:32
@camilovelezr camilovelezr marked this pull request as ready for review December 5, 2023 23:20
@camilovelezr camilovelezr mentioned this pull request Jan 26, 2024
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@bengtl bengtl bengtl approved these changes

@Nicholas-Schaub Nicholas-Schaub Awaiting requested review from Nicholas-Schaub Nicholas-Schaub is a code owner

@NHotaling NHotaling Awaiting requested review from NHotaling NHotaling is a code owner

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