Bump the pip group across 6 directories with 5 updates

[dependabot]

Bumps the pip group with 1 update in the /cli directory: pydantic.
Bumps the pip group with 1 update in the /examples/ChestXRay/metrics/project directory: scikit-learn.
Bumps the pip group with 1 update in the /examples/SurgMLCube/surg_metrics/project directory: scikit-learn.
Bumps the pip group with 2 updates in the /examples/chestxray_tutorial/data_preparator/project directory: pillow and tqdm.
Bumps the pip group with 1 update in the /examples/chestxray_tutorial/model_custom_cnn/project directory: tqdm.
Bumps the pip group with 1 update in the /server directory: gunicorn.

Updates pydantic from 1.10.2 to 1.10.13

Release notes

Sourced from pydantic's releases.

V1.10.13 2023-09-27

What's Changed

• Update pip commands to install 1.10 by @​chbndrhnns in pydantic/pydantic#6930
• Make the v1 mypy plugin work with both v1 and v2 by @​dmontagu in pydantic/pydantic#6920
• [Backport] Add max length check to validate_email by @​hramezani in pydantic/pydantic#7673

Full Changelog: pydantic/pydantic@v1.10.12...v1.10.13

V1.10.12

What's Changed

• Deque's maxlen property dropped on V1 validation by @​maciekglowka in pydantic/pydantic#6586
• Prepare release 1.10.12 by @​hramezani in pydantic/pydantic#6825

New Contributors

• @​maciekglowka made their first contribution in pydantic/pydantic#6586

Full Changelog: pydantic/pydantic@v1.10.11...v1.10.12

V1.10.11

What's Changed

• Fix import of create_model in tools.py by @​SharathHuddar in pydantic/pydantic#6364
• Prepare for 1.10.11 by @​hramezani in pydantic/pydantic#6420

New Contributors

• @​SharathHuddar made their first contribution in pydantic/pydantic#6364

Full Changelog: pydantic/pydantic@v1.10.10...v1.10.11

V1.10.10

What's Changed

• Fix racy doctests by @​K900 in pydantic/pydantic#6103
• ✅ Update FastAPI test script by @​Kludex in pydantic/pydantic#6117
• add roadmap to annoucement by @​samuelcolvin in pydantic/pydantic#6120
• Fixed literal validator errors for unhashable values by @​markus1978 in pydantic/pydantic#6194
• Bug fix for forward refs in generics by @​mark-todd in pydantic/pydantic#6157
• Add Pydantic Json field support to settings management by @​hramezani in pydantic/pydantic#6250

New Contributors

• @​K900 made their first contribution in pydantic/pydantic#6103
• @​markus1978 made their first contribution in pydantic/pydantic#6194

Full Changelog: pydantic/pydantic@v1.10.9...v1.10.10

V1.10.9

What's Changed

• Add Pydantic classifier by @​hramezani in pydantic/pydantic#5847
• 📌 Use Cython < v3 by @​lig in pydantic/pydantic#5845
• [cherry-pick] Fix mypy plugin for 1.4.0 (#5927) by @​cdce8p in pydantic/pydantic#5928
• Add future and past date hypothesis strategies by @​bschoenmaeckers in pydantic/pydantic#5850

... (truncated)

Changelog

Sourced from pydantic's changelog.

v1.10.13 (2023-09-27)

• Fix: Add max length check to pydantic.validate_email, #7673 by @​hramezani
• Docs: Fix pip commands to install v1, #6930 by @​chbndrhnns

v1.10.12 (2023-07-24)

• Fixes the maxlen property being dropped on deque validation. Happened only if the deque item has been typed. Changes the _validate_sequence_like func, #6581 by @​maciekglowka

v1.10.11 (2023-07-04)

• Importing create_model in tools.py through relative path instead of absolute path - so that it doesn't import V2 code when copied over to V2 branch, #6361 by @​SharathHuddar

v1.10.10 (2023-06-30)

• Add Pydantic Json field support to settings management, #6250 by @​hramezani
• Fixed literal validator errors for unhashable values, #6188 by @​markus1978
• Fixed bug with generics receiving forward refs, #6130 by @​mark-todd
• Update install method of FastAPI for internal tests in CI, #6117 by @​Kludex

v1.10.9 (2023-06-07)

• Fix trailing zeros not ignored in Decimal validation, #5968 by @​hramezani
• Fix mypy plugin for v1.4.0, #5928 by @​cdce8p
• Add future and past date hypothesis strategies, #5850 by @​bschoenmaeckers
• Discourage usage of Cython 3 with Pydantic 1.x, #5845 by @​lig

v1.10.8 (2023-05-23)

• Fix a bug in Literal usage with typing-extension==4.6.0, #5826 by @​hramezani
• This solves the (closed) issue #3849 where aliased fields that use discriminated union fail to validate when the data contains the non-aliased field name, #5736 by @​benwah
• Update email-validator dependency to >=2.0.0post2, #5627 by @​adriangb
• update AnyClassMethod for changes in python/typeshed#9771, #5505 by @​ITProKyle

v1.10.7 (2023-03-22)

• Fix creating schema from model using ConstrainedStr with regex as dict key, #5223 by @​matejetz
• Address bug in mypy plugin caused by explicit_package_bases=True, #5191 by @​dmontagu
• Add implicit defaults in the mypy plugin for Field with no default argument, #5190 by @​dmontagu
• Fix schema generated for Enum values used as Literals in discriminated unions, #5188 by @​javibookline
• Fix mypy failures caused by the pydantic mypy plugin when users define from_orm in their own classes, #5187 by @​dmontagu
• Fix InitVar usage with pydantic dataclasses, mypy version 1.1.1 and the custom mypy plugin, #5162 by @​cdce8p

v1.10.6 (2023-03-08)

• Implement logic to support creating validators from non standard callables by using defaults to identify them and unwrapping functools.partial and functools.partialmethod when checking the signature, #5126 by @​JensHeinrich
• Fix mypy plugin for v1.1.1, and fix dataclass_transform decorator for pydantic dataclasses, #5111 by @​cdce8p
• Raise ValidationError, not ConfigError, when a discriminator value is unhashable, #4773 by @​kurtmckee

v1.10.5 (2023-02-15)

... (truncated)

Commits

• 8822578 Prepare release 1.10.13 (#7674)
• 59d8f38 [Backport] Add max length check to validate_email (#7673)
• 69b92b5 Make the v1 mypy plugin work with both v1 and v2 (#6920)
• 87bf417 Update pip commands to install 1.10 (#6930)
• d9c2af3 Prepare release 1.10.12 (#6825)
• 2aaddf6 Deque's maxlen property dropped on V1 validation (#6586)
• 15c82d9 Prepare for 1.10.11 (#6420)
• 8750c37 no longer tag docs release as latest
• 2c0e2a6 Fix import of create_model in tools.py (#6364)
• 0e8a387 Prepare for 1.10.10 (#6308)
• Additional commits viewable in compare view

Updates scikit-learn from 0.24.2 to 1.0.1

Release notes

Sourced from scikit-learn's releases.

scikit-learn 1.0.1

We're happy to announce the 1.0.1 release with several bugfixes:

You can see the changelog here: https://scikit-learn.org/dev/whats_new/v1.0.html#version-1-0-1

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds will be available shortly, which you can then install using:

conda install -c conda-forge scikit-learn

scikit-learn 1.0

We're happy to announce the 1.0 release. You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_1_0_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v1.0.html#changes-1-0

This version supports Python versions 3.7 to 3.9.

Commits

• 0d37891 Trigger wheel builder workflow: [cd build]
• 7737cb9 DOC update the News section in website (#21417)
• 8971a19 DOC Ensures that MultiTaskElasticNetCV passes numpydoc validation (#21405)
• d6e24ee DOC Ensures that LabelSpreading passes numpydoc validation (#21414)
• 14fda2f DOC Ensures that PassiveAggressiveRegressor passes numpydoc validation (#21413)
• 112ae4e DOC Ensures that OrthogonalMatchingPursuitCV passes numpydoc validation (#21412)
• cd927c0 FIX delete feature_names_in_ when refitting on a ndarray (#21389)
• ae223ee bumpversion to 1.0.1
• 9227162 MNT remove 1.1 changelog due to rebase conflict
• 5d75547 MNT fix changelog 1.0.1 (#21416)
• Additional commits viewable in compare view

Updates scikit-learn from 0.24.2 to 1.0.1

Release notes

Sourced from scikit-learn's releases.

scikit-learn 1.0.1

We're happy to announce the 1.0.1 release with several bugfixes:

You can see the changelog here: https://scikit-learn.org/dev/whats_new/v1.0.html#version-1-0-1

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds will be available shortly, which you can then install using:

conda install -c conda-forge scikit-learn

scikit-learn 1.0

We're happy to announce the 1.0 release. You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_1_0_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v1.0.html#changes-1-0

This version supports Python versions 3.7 to 3.9.

Commits

• 0d37891 Trigger wheel builder workflow: [cd build]
• 7737cb9 DOC update the News section in website (#21417)
• 8971a19 DOC Ensures that MultiTaskElasticNetCV passes numpydoc validation (#21405)
• d6e24ee DOC Ensures that LabelSpreading passes numpydoc validation (#21414)
• 14fda2f DOC Ensures that PassiveAggressiveRegressor passes numpydoc validation (#21413)
• 112ae4e DOC Ensures that OrthogonalMatchingPursuitCV passes numpydoc validation (#21412)
• cd927c0 FIX delete feature_names_in_ when refitting on a ndarray (#21389)
• ae223ee bumpversion to 1.0.1
• 9227162 MNT remove 1.1 changelog due to rebase conflict
• 5d75547 MNT fix changelog 1.0.1 (#21416)
• Additional commits viewable in compare view

Updates pillow from 9.5.0 to 10.3.0

Release notes

Sourced from pillow's releases.

10.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/10.3.0.html

Changes

• CVE-2024-28219: Use strncpy to avoid buffer overflow #7928 [@​hugovk]
• Use functools.lru_cache for hopper() #7912 [@​hugovk]
• Raise ValueError if seeking to greater than offset-sized integer in TIFF #7883 [@​radarhere]
• Improve speed of loading QOI images #7925 [@​radarhere]
• Added RGB to I;16N conversion #7920 [@​radarhere]
• Add --report argument to main.py to omit supported formats #7818 [@​nulano]
• Added RGB to I;16, I;16L and I;16B conversion #7918 [@​radarhere]
• Fix editable installation with custom build backend and configuration options #7658 [@​nulano]
• Fix putdata() for I;16N on big-endian #7209 [@​Yay295]
• Determine MPO size from markers, not EXIF data #7884 [@​radarhere]
• Improved conversion from RGB to RGBa, LA and La #7888 [@​radarhere]
• Support FITS images with GZIP_1 compression #7894 [@​radarhere]
• Use I;16 mode for 9-bit JPEG 2000 images #7900 [@​scaramallion]
• Raise ValueError if kmeans is negative #7891 [@​radarhere]
• Remove TIFF tag OSUBFILETYPE when saving using libtiff #7893 [@​radarhere]
• Raise ValueError for negative values when loading P1-P3 PPM images #7882 [@​radarhere]
• Added reading of JPEG2000 palettes #7870 [@​radarhere]
• Added alpha_quality argument when saving WebP images #7872 [@​radarhere]
• Fixed joined corners for ImageDraw rounded_rectangle() non-integer dimensions #7881 [@​radarhere]
• Removed Python and NumPy pinning on Cygwin #7880 [@​radarhere]
• Update UnidentifiedImageError and version imports #7644 [@​radarhere]
• Stop reading EPS image at EOF marker #7753 [@​radarhere]
• PSD layer co-ordinates may be negative #7706 [@​radarhere]
• Use subprocess with CREATE_NO_WINDOW flag in ImageShow WindowsViewer #7791 [@​radarhere]
• When saving GIF frame that restores to background color, do not fill identical pixels #7788 [@​radarhere]
• Fixed reading PNG iCCP compression method #7823 [@​radarhere]
• Allow writing IFDRational to UNDEFINED tag #7840 [@​radarhere]
• Fix logged tag name when loading Exif data #7842 [@​radarhere]
• Use maximum frame size in IHDR chunk when saving APNG images #7821 [@​radarhere]
• Prevent opening P TGA images without a palette #7797 [@​radarhere]
• Use palette when loading ICO images #7798 [@​radarhere]
• Use consistent arguments for load_read and load_seek #7713 [@​radarhere]
• Turn off nullability warnings for macOS SDK #7827 [@​radarhere]
• Fix shift-sign issue in Convert.c #7838 [@​r-barnes]
• winbuild: Refactor dependency versions into constants #7843 [@​hugovk]
• Build macOS arm64 wheels natively #7852 [@​radarhere]
• Fixed typo #7855 [@​radarhere]
• Open 16-bit grayscale PNGs as I;16 #7849 [@​radarhere]
• Handle truncated chunks at the end of PNG images #7709 [@​lajiyuan]
• Match mask size to pasted image size in GifImagePlugin #7779 [@​radarhere]
• Changed SupportsGetMesh protocol to be public #7841 [@​radarhere]
• Release GIL while calling WebPAnimDecoderGetNext #7782 [@​evanmiller]
• Fixed reading FLI/FLC images with a prefix chunk #7804 [@​twolife]
• Updated package name for Tidelift #7810 [@​radarhere]
• Removed unused code #7744 [@​radarhere]

... (truncated)

Changelog

Sourced from pillow's changelog.

10.3.0 (2024-04-01)

• CVE-2024-28219: Use strncpy to avoid buffer overflow #7928 [radarhere, hugovk]

• Deprecate eval(), replacing it with lambda_eval() and unsafe_eval() #7927 [radarhere, hugovk]

• Raise ValueError if seeking to greater than offset-sized integer in TIFF #7883 [radarhere]

• Add --report argument to __main__.py to omit supported formats #7818 [nulano, radarhere, hugovk]

• Added RGB to I;16, I;16L, I;16B and I;16N conversion #7918, #7920 [radarhere]

• Fix editable installation with custom build backend and configuration options #7658 [nulano, radarhere]

• Fix putdata() for I;16N on big-endian #7209 [Yay295, hugovk, radarhere]

• Determine MPO size from markers, not EXIF data #7884 [radarhere]

• Improved conversion from RGB to RGBa, LA and La #7888 [radarhere]

• Support FITS images with GZIP_1 compression #7894 [radarhere]

• Use I;16 mode for 9-bit JPEG 2000 images #7900 [scaramallion, radarhere]

• Raise ValueError if kmeans is negative #7891 [radarhere]

• Remove TIFF tag OSUBFILETYPE when saving using libtiff #7893 [radarhere]

• Raise ValueError for negative values when loading P1-P3 PPM images #7882 [radarhere]

• Added reading of JPEG2000 palettes #7870 [radarhere]

• Added alpha_quality argument when saving WebP images #7872 [radarhere]

... (truncated)

Commits

• 5c89d88 10.3.0 version bump
• 63cbfcf Update CHANGES.rst [ci skip]
• 2776126 Merge pull request #7928 from python-pillow/lcms
• aeb51cb Merge branch 'main' into lcms
• 5beb0b6 Update CHANGES.rst [ci skip]
• cac6ffa Merge pull request #7927 from python-pillow/imagemath
• f5eeeac Name as 'options' in lambda_eval and unsafe_eval, but '_dict' in deprecated eval
• facf3af Added release notes
• 2a93aba Use strncpy to avoid buffer overflow
• a670597 Update CHANGES.rst [ci skip]
• Additional commits viewable in compare view

Updates tqdm from 4.65.0 to 4.66.3

Release notes

Sourced from tqdm's releases.

tqdm v4.66.3 stable

• cli: eval safety (fixes CVE-2024-34062, GHSA-g7vv-2v7x-gj9p)

tqdm v4.66.2 stable

• pandas: add DataFrame.progress_map (#1549)
• notebook: fix HTML padding (#1506)
• keras: fix resuming training when verbose>=2 (#1508)
• fix format_num negative fractions missing leading zero (#1548)
• fix Python 3.12 DeprecationWarning on import (#1519)
• linting: use f-strings (#1549)
• update tests (#1549)
  • fix pandas warnings
  • fix asv (airspeed-velocity/asv#1323)
  • fix macos notebook docstring indentation
• CI: bump actions (#1549)

tqdm v4.66.1 stable

• fix utils.envwrap types (#1493 <- #1491, #1320 <- #966, #1319)
  • e.g. cloudwatch & kubernetes workaround: export TQDM_POSITION=-1
• drop mentions of unsupported Python versions

tqdm v4.66.0 stable

• environment variables to override defaults (TQDM_*) (#1491 <- #1061, #950 <- #614, #1318, #619, #612, #370)
  • e.g. in CI jobs, export TQDM_MININTERVAL=5 to avoid log spam
  • add tests & docs for tqdm.utils.envwrap
• fix & update CLI completion
• fix & update API docs
• minor code tidy: replace os.path => pathlib.Path
• fix docs image hosting
• release with CI bot account again (cli/cli#6680)

tqdm v4.65.2 stable

• exclude examples from distributed wheel (#1492)

tqdm v4.65.1 stable

• migrate setup.{cfg,py} => pyproject.toml (#1490)
  • fix asv benchmarks
  • update docs
• fix snap build (#1490)
• fix & update tests (#1490)
  • fix flaky notebook tests
  • bump pre-commit
  • bump workflow actions

Commits

• 4e613f8 Merge pull request from GHSA-g7vv-2v7x-gj9p
• b53348c cli: eval safety
• cc372d0 bump version, merge pull request #1549 from tqdm/devel
• e9f0c05 use PyPI trusted publishing
• 7323d5b slight makefile clean
• 5306125 tests: bump pre-commit
• 4a6fd4f fix datetime.utcfromtimestamp py3.12 warning (#1519)
• 6f13759 tests: fix macos notebook indentation
• 3abcd2a tests: fix asv
• a4d15c8 tests: fix pandas warnings
• Additional commits viewable in compare view

Updates tqdm from 4.65.0 to 4.66.3

Release notes

Sourced from tqdm's releases.

tqdm v4.66.3 stable

• cli: eval safety (fixes CVE-2024-34062, GHSA-g7vv-2v7x-gj9p)

tqdm v4.66.2 stable

• pandas: add DataFrame.progress_map (#1549)
• notebook: fix HTML padding (#1506)
• keras: fix resuming training when verbose>=2 (#1508)
• fix format_num negative fractions missing leading zero (#1548)
• fix Python 3.12 DeprecationWarning on import (#1519)
• linting: use f-strings (#1549)
• update tests (#1549)
  • fix pandas warnings
  • fix asv (airspeed-velocity/asv#1323)
  • fix macos notebook docstring indentation
• CI: bump actions (#1549)

tqdm v4.66.1 stable

• fix utils.envwrap types (#1493 <- #1491, #1320 <- #966, #1319)
  • e.g. cloudwatch & kubernetes workaround: export TQDM_POSITION=-1
• drop mentions of unsupported Python versions

tqdm v4.66.0 stable

• environment variables to override defaults (TQDM_*) (#1491 <- #1061, #950 <- #614, #1318, #619, #612, #370)
  • e.g. in CI jobs, export TQDM_MININTERVAL=5 to avoid log spam
  • add tests & docs for tqdm.utils.envwrap
• fix & update CLI completion
• fix & update API docs
• minor code tidy: replace os.path => pathlib.Path
• fix docs image hosting
• release with CI bot account again (cli/cli#6680)

tqdm v4.65.2 stable

• exclude examples from distributed wheel (#1492)

tqdm v4.65.1 stable

• migrate setup.{cfg,py} => pyproject.toml (#1490)
  • fix asv benchmarks
  • update docs
• fix snap build (#1490)
• fix & update tests (#1490)
  • fix flaky notebook tests
  • bump pre-commit
  • bump workflow actions

Commits

• 4e613f8 Merge pull request from GHSA-g7vv-2v7x-gj9p
• b53348c cli: eval safety
• cc372d0 bump version, merge pull request #1549 from tqdm/devel
• e9f0c05 use PyPI trusted publishing
• 7323d5b slight makefile clean
• 5306125 tests: bump pre-commit
• 4a6fd4f fix datetime.utcfromtimestamp py3.12 warning (#1519)
• 6f13759 tests: fix macos notebook indentation
• 3abcd2a tests: fix asv
• a4d15c8 tests: fix pandas warnings
• Additional commits viewable in compare view

Updates gunicorn from 21.2.0 to 22.0.0

Release notes

Sourced from gunicorn's releases.

Gunicorn 22.0 has been released

Gunicorn 22.0.0 has been released. This version fix the numerous security vulnerabilities. You're invited to upgrade asap your own installation.

Changes:

22.0.0 - 2024-04-17
===================

use utime to notify workers liveness
migrate setup to pyproject.toml
fix numerous security vulnerabilities in HTTP parser (closing some request smuggling vectors)
parsing additional requests is no longer attempted past unsupported request framing
on HTTP versions < 1.1 support for chunked transfer is refused (only used in exploits)
requests conflicting configured or passed SCRIPT_NAME now produce a verbose error
Trailer fields are no longer inspected for headers indicating secure scheme
support Python 3.12

** Breaking changes **

minimum version is Python 3.7
the limitations on valid characters in the HTTP method have been bounded to Internet Standards
requests specifying unsupported transfer coding (order) are refused by default (rare)
HTTP methods are no longer casefolded by default (IANA method registry contains none affected)
HTTP methods containing the number sign (#) are no longer accepted by default (rare)
HTTP versions < 1.0 or >= 2.0 are no longer accepted by default (rare, only HTTP/1.1 is supported)
HTTP versions consisting of multiple digits or containing a prefix/suffix are no longer accepted
HTTP header field names Gunicorn cannot safely map to variables are silently dropped, as in other software
HTTP headers with empty field name are refused by default (no legitimate use cases, used in exploits)
requests with both Transfer-Encoding and Content-Length are refused by default (such a message might indicate an attempt to perform request smuggling)
empty transfer codings are no longer permitted (reportedly seen with really old & broken proxies)

** SECURITY **

fix CVE-2024-1135

1. Documentation is available there: https://docs.gunicorn.org/en/stable/news.html
2. Packages: https://pypi.org/project/gunicorn/

Commits

• f63d59e bump to 22.0
• 4ac81e0 Merge pull request #3175 from e-kwsm/typo
• 401cecf Merge pull request #3179 from dhdaines/exclude-eventlet-0360
• 0243ec3 fix(deps): exclude eventlet 0.36.0
• 628a0bc chore: fix typos
• 88fc4a4 Merge pull request #3131 from pajod/patch-py12-rebased
• deae2fc CI: back off the agressive timeout
• f470382 docs: promise 3.12 compat
• 5e30bfa add changelog to project.urls (updated for PEP621)
• 481c3f9 remove setup.cfg - overridden by pyproject.toml
• Additional commits viewable in compare view

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Superseded by #599.