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UMEssen / Body-and-Organ-Analysis

BOA is a segmentation tool of CT scans by the SHIP-AI group (https://ship-ai.ikim.nrw/). Combining the TotalSegmentator and the Body Composition Analysis, this tool is capable of analyzing medical images and identifying the different structures within the human body, including bones, muscles, organs, and blood vessels.
Apache License 2.0
22 stars 5 forks source link

Bump the pip group across 1 directory with 7 updates #36

Open dependabot[bot] opened 4 months ago

dependabot[bot] commented 4 months ago

Bumps the pip group with 7 updates in the / directory:

Package From To
requests 2.31.0 2.32.2
tqdm 4.65.2 4.66.3
black 22.12.0 24.3.0
cryptography 41.0.3 42.0.4
idna 3.4 3.7
pillow 10.2.0 10.3.0
urllib3 2.0.7 2.2.2

Updates requests from 2.31.0 to 2.32.2

Release notes

Sourced from requests's releases.

v2.32.2

2.32.2 (2024-05-21)

Deprecations

  • To provide a more stable migration for custom HTTPAdapters impacted by the CVE changes in 2.32.0, we've renamed _get_connection to a new public API, get_connection_with_tls_context. Existing custom HTTPAdapters will need to migrate their code to use this new API. get_connection is considered deprecated in all versions of Requests>=2.32.0.

    A minimal (2-line) example has been provided in the linked PR to ease migration, but we strongly urge users to evaluate if their custom adapter is subject to the same issue described in CVE-2024-35195. (#6710)

v2.32.1

2.32.1 (2024-05-20)

Bugfixes

  • Add missing test certs to the sdist distributed on PyPI.

v2.32.0

2.32.0 (2024-05-20)

🐍 PYCON US 2024 EDITION 🐍

Security

Improvements

  • verify=True now reuses a global SSLContext which should improve request time variance between first and subsequent requests. It should also minimize certificate load time on Windows systems when using a Python version built with OpenSSL 3.x. (#6667)
  • Requests now supports optional use of character detection (chardet or charset_normalizer) when repackaged or vendored. This enables pip and other projects to minimize their vendoring surface area. The Response.text() and apparent_encoding APIs will default to utf-8 if neither library is present. (#6702)

Bugfixes

  • Fixed bug in length detection where emoji length was incorrectly calculated in the request content-length. (#6589)
  • Fixed deserialization bug in JSONDecodeError. (#6629)
  • Fixed bug where an extra leading / (path separator) could lead urllib3 to unnecessarily reparse the request URI. (#6644)

... (truncated)

Changelog

Sourced from requests's changelog.

2.32.2 (2024-05-21)

Deprecations

  • To provide a more stable migration for custom HTTPAdapters impacted by the CVE changes in 2.32.0, we've renamed _get_connection to a new public API, get_connection_with_tls_context. Existing custom HTTPAdapters will need to migrate their code to use this new API. get_connection is considered deprecated in all versions of Requests>=2.32.0.

    A minimal (2-line) example has been provided in the linked PR to ease migration, but we strongly urge users to evaluate if their custom adapter is subject to the same issue described in CVE-2024-35195. (#6710)

2.32.1 (2024-05-20)

Bugfixes

  • Add missing test certs to the sdist distributed on PyPI.

2.32.0 (2024-05-20)

Security

Improvements

  • verify=True now reuses a global SSLContext which should improve request time variance between first and subsequent requests. It should also minimize certificate load time on Windows systems when using a Python version built with OpenSSL 3.x. (#6667)
  • Requests now supports optional use of character detection (chardet or charset_normalizer) when repackaged or vendored. This enables pip and other projects to minimize their vendoring surface area. The Response.text() and apparent_encoding APIs will default to utf-8 if neither library is present. (#6702)

Bugfixes

  • Fixed bug in length detection where emoji length was incorrectly calculated in the request content-length. (#6589)
  • Fixed deserialization bug in JSONDecodeError. (#6629)
  • Fixed bug where an extra leading / (path separator) could lead urllib3 to unnecessarily reparse the request URI. (#6644)

Deprecations

... (truncated)

Commits
  • 88dce9d v2.32.2
  • c98e4d1 Merge pull request #6710 from nateprewitt/api_rename
  • 92075b3 Add deprecation warning
  • aa1461b Move _get_connection to get_connection_with_tls_context
  • 970e8ce v2.32.1
  • d6ebc4a v2.32.0
  • 9a40d12 Avoid reloading root certificates to improve concurrent performance (#6667)
  • 0c030f7 Merge pull request #6702 from nateprewitt/no_char_detection
  • 555b870 Allow character detection dependencies to be optional in post-packaging steps
  • d6dded3 Merge pull request #6700 from franekmagiera/update-redirect-to-invalid-uri-test
  • Additional commits viewable in compare view


Updates tqdm from 4.65.2 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)
  • 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)
Commits


Updates black from 22.12.0 to 24.3.0

Release notes

Sourced from black's releases.

24.3.0

Highlights

This release is a milestone: it fixes Black's first CVE security vulnerability. If you run Black on untrusted input, or if you habitually put thousands of leading tab characters in your docstrings, you are strongly encouraged to upgrade immediately to fix CVE-2024-21503.

This release also fixes a bug in Black's AST safety check that allowed Black to make incorrect changes to certain f-strings that are valid in Python 3.12 and higher.

Stable style

  • Don't move comments along with delimiters, which could cause crashes (#4248)
  • Strengthen AST safety check to catch more unsafe changes to strings. Previous versions of Black would incorrectly format the contents of certain unusual f-strings containing nested strings with the same quote type. Now, Black will crash on such strings until support for the new f-string syntax is implemented. (#4270)
  • Fix a bug where line-ranges exceeding the last code line would not work as expected (#4273)

Performance

  • Fix catastrophic performance on docstrings that contain large numbers of leading tab characters. This fixes CVE-2024-21503. (#4278)

Documentation

  • Note what happens when --check is used with --quiet (#4236)

24.2.0

Stable style

  • Fixed a bug where comments where mistakenly removed along with redundant parentheses (#4218)

Preview style

  • Move the hug_parens_with_braces_and_square_brackets feature to the unstable style due to an outstanding crash and proposed formatting tweaks (#4198)
  • Fixed a bug where base expressions caused inconsistent formatting of ** in tenary expression (#4154)
  • Checking for newline before adding one on docstring that is almost at the line limit (#4185)
  • Remove redundant parentheses in case statement if guards (#4214).

Configuration

... (truncated)

Changelog

Sourced from black's changelog.

24.3.0

Highlights

This release is a milestone: it fixes Black's first CVE security vulnerability. If you run Black on untrusted input, or if you habitually put thousands of leading tab characters in your docstrings, you are strongly encouraged to upgrade immediately to fix CVE-2024-21503.

This release also fixes a bug in Black's AST safety check that allowed Black to make incorrect changes to certain f-strings that are valid in Python 3.12 and higher.

Stable style

  • Don't move comments along with delimiters, which could cause crashes (#4248)
  • Strengthen AST safety check to catch more unsafe changes to strings. Previous versions of Black would incorrectly format the contents of certain unusual f-strings containing nested strings with the same quote type. Now, Black will crash on such strings until support for the new f-string syntax is implemented. (#4270)
  • Fix a bug where line-ranges exceeding the last code line would not work as expected (#4273)

Performance

  • Fix catastrophic performance on docstrings that contain large numbers of leading tab characters. This fixes CVE-2024-21503. (#4278)

Documentation

  • Note what happens when --check is used with --quiet (#4236)

24.2.0

Stable style

  • Fixed a bug where comments where mistakenly removed along with redundant parentheses (#4218)

Preview style

  • Move the hug_parens_with_braces_and_square_brackets feature to the unstable style due to an outstanding crash and proposed formatting tweaks (#4198)
  • Fixed a bug where base expressions caused inconsistent formatting of ** in tenary expression (#4154)
  • Checking for newline before adding one on docstring that is almost at the line limit (#4185)
  • Remove redundant parentheses in case statement if guards (#4214).

... (truncated)

Commits


Updates cryptography from 41.0.3 to 42.0.4

Changelog

Sourced from cryptography's changelog.

42.0.4 - 2024-02-20


* Fixed a null-pointer-dereference and segfault that could occur when creating
  a PKCS#12 bundle. Credit to **Alexander-Programming** for reporting the
  issue. **CVE-2024-26130**
* Fixed ASN.1 encoding for PKCS7/SMIME signed messages. The fields ``SMIMECapabilities``
  and ``SignatureAlgorithmIdentifier`` should now be correctly encoded according to the
  definitions in :rfc:`2633` :rfc:`3370`.

.. _v42-0-3:


42.0.3 - 2024-02-15

  • Fixed an initialization issue that caused key loading failures for some users.

.. _v42-0-2:

42.0.2 - 2024-01-30


* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.2.1.
* Fixed an issue that prevented the use of Python buffer protocol objects in
  ``sign`` and ``verify`` methods on asymmetric keys.
* Fixed an issue with incorrect keyword-argument naming with ``EllipticCurvePrivateKey``
  :meth:`~cryptography.hazmat.primitives.asymmetric.ec.EllipticCurvePrivateKey.exchange`,
  ``X25519PrivateKey``
  :meth:`~cryptography.hazmat.primitives.asymmetric.x25519.X25519PrivateKey.exchange`,
  ``X448PrivateKey``
  :meth:`~cryptography.hazmat.primitives.asymmetric.x448.X448PrivateKey.exchange`,
  and ``DHPrivateKey``
  :meth:`~cryptography.hazmat.primitives.asymmetric.dh.DHPrivateKey.exchange`.

.. _v42-0-1:


42.0.1 - 2024-01-24

  • Fixed an issue with incorrect keyword-argument naming with EllipticCurvePrivateKey :meth:~cryptography.hazmat.primitives.asymmetric.ec.EllipticCurvePrivateKey.sign.
  • Resolved compatibility issue with loading certain RSA public keys in :func:~cryptography.hazmat.primitives.serialization.load_pem_public_key.

.. _v42-0-0:

42.0.0 - 2024-01-22


</tr></table>

... (truncated)

Commits


Updates idna from 3.4 to 3.7

Release notes

Sourced from idna's releases.

v3.7

What's Changed

  • Fix issue where specially crafted inputs to encode() could take exceptionally long amount of time to process. [CVE-2024-3651]

Thanks to Guido Vranken for reporting the issue.

Full Changelog: https://github.com/kjd/idna/compare/v3.6...v3.7

Changelog

Sourced from idna's changelog.

3.7 (2024-04-11) ++++++++++++++++

  • Fix issue where specially crafted inputs to encode() could take exceptionally long amount of time to process. [CVE-2024-3651]

Thanks to Guido Vranken for reporting the issue.

3.6 (2023-11-25) ++++++++++++++++

  • Fix regression to include tests in source distribution.

3.5 (2023-11-24) ++++++++++++++++

  • Update to Unicode 15.1.0
  • String codec name is now "idna2008" as overriding the system codec "idna" was not working.
  • Fix typing error for codec encoding
  • "setup.cfg" has been added for this release due to some downstream lack of adherence to PEP 517. Should be removed in a future release so please prepare accordingly.
  • Removed reliance on a symlink for the "idna-data" tool to comport with PEP 517 and the Python Packaging User Guide for sdist archives.
  • Added security reporting protocol for project

Thanks Jon Ribbens, Diogo Teles Sant'Anna, Wu Tingfeng for contributions to this release.

Commits
  • 1d365e1 Release v3.7
  • c1b3154 Merge pull request #172 from kjd/optimize-contextj
  • 0394ec7 Merge branch 'master' into optimize-contextj
  • cd58a23 Merge pull request #152 from elliotwutingfeng/dev
  • 5beb28b More efficient resolution of joiner contexts
  • 1b12148 Update ossf/scorecard-action to v2.3.1
  • d516b87 Update Github actions/checkout to v4
  • c095c75 Merge branch 'master' into dev
  • 60a0a4c Fix typo in GitHub Actions workflow key
  • 5918a0e Merge branch 'master' into dev
  • Additional commits viewable in compare view


Updates pillow from 10.2.0 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

... (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 urllib3 from 2.0.7 to 2.2.2

Release notes

Sourced from urllib3's releases.

2.2.2

🚀 urllib3 is fundraising for HTTP/2 support

urllib3 is raising ~$40,000 USD to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support for 2023. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects please consider contributing financially to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.

Thank you for your support.

Changes

  • Added the Proxy-Authorization header to the list of headers to strip from requests when redirecting to a different host. As before, different headers can be set via Retry.remove_headers_on_redirect.
  • Allowed passing negative integers as amt to read methods of http.client.HTTPResponse as an alternative to None. (#3122)
  • Fixed return types representing copying actions to use typing.Self. (#3363)

Full Changelog: https://github.com/urllib3/urllib3/compare/2.2.1...2.2.2

2.2.1

🚀 urllib3 is fundraising for HTTP/2 support

urllib3 is raising ~$40,000 USD to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support for 2023. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects please consider contributing financially to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.

Thank you for your support.

Changes

  • Fixed issue where InsecureRequestWarning was emitted for HTTPS connections when using Emscripten. (#3331)
  • Fixed HTTPConnectionPool.urlopen to stop automatically casting non-proxy headers to HTTPHeaderDict. This change was premature as it did not apply to proxy headers and HTTPHeaderDict does not handle byte header values correctly yet. (#3343)
  • Changed ProtocolError to InvalidChunkLength when response terminates before the chunk length is sent. (#2860)
  • Changed ProtocolError to be more verbose on incomplete reads with excess content. (#3261)

2.2.0

🖥️ urllib3 now works in the browser

:tada: This release adds experimental support for using urllib3 in the browser with Pyodide! :tada:

Thanks to Joe Marshall (@​joemarshall) for contributing this feature. This change was possible thanks to work done in urllib3 v2.0 to detach our API from http.client. Please report all bugs to the urllib3 issue tracker.

🚀 urllib3 is fundraising for HTTP/2 support

urllib3 is raising ~$40,000 USD to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support for 2023. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects please consider contributing financially to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.

Thank you for your support.

Changes

  • Added support for Emscripten and Pyodide, including streaming support in cross-origin isolated browser environments where threading is enabled. (#2951)
  • Added support for HTTPResponse.read1() method. (#3186)
  • Added rudimentary support for HTTP/2. (#3284)
  • Fixed issue where requests against urls with trailing dots were failing due to SSL errors when using proxy. (#2244)
  • Fixed HTTPConnection.proxy_is_verified and HTTPSConnection.proxy_is_verified to be always set to a boolean after connecting to a proxy. It could be None in some cases previously. (#3130)

... (truncated)

Changelog

Sourced from urllib3's changelog.

2.2.2 (2024-06-17)

  • Added the Proxy-Authorization header to the list of headers to strip from requests when redirecting to a different host. As before, different headers can be set via Retry.remove_headers_on_redirect.
  • Allowed passing negative integers as amt to read methods of http.client.HTTPResponse as an alternative to None. ([#3122](https://github.com/urllib3/urllib3/issues/3122) <https://github.com/urllib3/urllib3/issues/3122>__)
  • Fixed return types representing copying actions to use typing.Self. ([#3363](https://github.com/urllib3/urllib3/issues/3363) <https://github.com/urllib3/urllib3/issues/3363>__)

2.2.1 (2024-02-16)

  • Fixed issue where InsecureRequestWarning was emitted for HTTPS connections when using Emscripten. ([#3331](https://github.com/urllib3/urllib3/issues/3331) <https://github.com/urllib3/urllib3/issues/3331>__)
  • Fixed HTTPConnectionPool.urlopen to stop automatically casting non-proxy headers to HTTPHeaderDict. This change was premature as it did not apply to proxy headers and HTTPHeaderDict does not handle byte header values correctly yet. ([#3343](https://github.com/urllib3/urllib3/issues/3343) <https://github.com/urllib3/urllib3/issues/3343>__)
  • Changed InvalidChunkLength to ProtocolError when response terminates before the chunk length is sent. ([#2860](https://github.com/urllib3/urllib3/issues/2860) <https://github.com/urllib3/urllib3/issues/2860>__)
  • Changed ProtocolError to be more verbose on incomplete reads with excess content. ([#3261](https://github.com/urllib3/urllib3/issues/3261) <https://github.com/urllib3/urllib3/issues/3261>__)

2.2.0 (2024-01-30)

  • Added support for Emscripten and Pyodide <https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html>, including streaming support in cross-origin isolated browser environments where threading is enabled. ([#2951](https://github.com/urllib3/urllib3/issues/2951) <https://github.com/urllib3/urllib3/issues/2951>)
  • Added support for HTTPResponse.read1() method. ([#3186](https://github.com/urllib3/urllib3/issues/3186) <https://github.com/urllib3/urllib3/issues/3186>__)
  • Added rudimentary support for HTTP/2. ([#3284](https://github.com/urllib3/urllib3/issues/3284) <https://github.com/urllib3/urllib3/issues/3284>__)
  • Fixed issue where requests against urls with trailing dots were failing due to SSL errors when using proxy. ([#2244](https://github.com/urllib3/urllib3/issues/2244) <https://github.com/urllib3/urllib3/issues/2244>__)
  • Fixed HTTPConnection.proxy_is_verified and HTTPSConnection.proxy_is_verified to be always set to a boolean after connecting to a proxy. It could be None in some cases previously. ([#3130](https://github.com/urllib3/urllib3/issues/3130) <https://github.com/urllib3/urllib3/issues/3130>__)
  • Fixed an issue where headers passed in a request with json= would be mutated ([#3203](https://github.com/urllib3/urllib3/issues/3203) <https://github.com/urllib3/urllib3/issues/3203>__)
  • Fixed HTTPSConnection.is_verified to be set to False when connecting from a HTTPS proxy to an HTTP target. It was set to True previously. ([#3267](https://github.com/urllib3/urllib3/issues/3267) <https://github.com/urllib3/urllib3/issues/3267>__)
  • Fixed handling of new error message from OpenSSL 3.2.0 when configuring an HTTP proxy as HTTPS ([#3268](https://github.com/urllib3/urllib3/issues/3268) <https://github.com/urllib3/urllib3/issues/3268>__)
  • Fixed TLS 1.3 post-handshake auth when the server certificate validation is disabled ([#3325](https://github.com/urllib3/urllib3/issues/3325) <https://github.com/urllib3/urllib3/issues/3325>__)
  • Note for downstream distributors: To run integration tests, you now need to run the tests a second time with the --integration pytest flag. ([#3181](https://github.com/urllib3/urllib3/issues/3181) <https://github.com/urllib3/urllib3/issues/3181>__)

2.1.0 (2023-11-13)

  • Removed support for the deprecated urllib3[secure] extra. ([#2680](https://github.com/urllib3/urllib3/issues/2680) <https://github.com/urllib3/urllib3/issues/2680>__)
  • Removed support for the deprecated SecureTransport TLS implementation. ([#2681](https://github.com/urllib3/urllib3/issues/2681) <https://github.com/urllib3/urllib3/issues/2681>__)
  • Removed support for the end-of-life Python 3.7. ([#3143](https://github.com/urllib3/urllib3/issues/3143) <https://github.com/urllib3/urllib3/issues/3143>__)
  • Allowed loading CA certificates from memory for proxies. ([#3065](https://github.com/urllib3/urllib3/issues/3065) <https://github.com/urllib3/urllib3/issues/3065>__)
  • Fixed decoding Gzip-encoded responses which specified x-gzip content-encoding. ([#3174](https://github.com/urllib3/urllib3/issues/3174) <https://github.com/urllib3/urllib3/issues/3174>__)
Commits


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