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alexdaniel654 / Renal_Segmentor

An application to segment kidneys from renal MRI data using a convolutional neural network.
GNU General Public License v3.0
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Bump nibabel from 4.0.2 to 5.0.1 #286

Closed dependabot[bot] closed 1 year ago

dependabot[bot] commented 1 year ago

Bumps nibabel from 4.0.2 to 5.0.1.

Release notes

Sourced from nibabel's releases.

5.0.1

DOI

Bug-fix release in the 5.0.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

References like "pr/298" refer to github pull request numbers.

Bug fixes

  • Support ragged voxel arrays in ParcelsAxis (pr/1194) (Michiel Cottaar, reviewed by CM)
  • Return to cwd on exception in InTemporaryDirectory (pr/1184) (CM)

Maintenance

  • Add py.typed to module root to enable use of types in downstream projects (pr/1196) (CM, reviewed by Fernando Pérez-Garcia)
  • Cache git-archive separately from Python packages in GitHub Actions (pr/1186) (CM, reviewed by Zvi Baratz)

5.0.0

DOI

New feature release in the 5.0.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).

New features

  • SerializableImage now has to_stream() and from_stream() methods to read/write streams implementing the io.IOBase interface. A from_url() method enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
  • TrkFile supports TRKv3, an undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)

Enhancements

  • Support multiline header fields in TCKFile (pr/1175) (CM, reviewed by Matt Cieslak)
  • Make layout order an initialization parameter of ArrayProxy (pr/1131) (CM, reviewed by MB)
  • Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by Zvi Baratz)

Bug fixes

  • Handle extension/file-format mismatches implemented incompletely in pr/1013 (pr/1138) (CM, reviewed by Thomas Phil)
  • Improve handling of invalid TCK files, which could sometimes cause an infinite loop (pr/1140) (Anibal Solon, reviewed by CM)
  • Clean up ECAT test case that left filehandle open and failed to use class variables (pr/1155) (Dimitri Papadopoulos, reviewed by CM)

Maintenance

  • Simplify TCK reading code by assuming files are open in binary mode (pr/1142) (Anibal Solon, reviewed by MC, CM)
  • Code support for tests covering deprecated functionality (pr/1159) (CM)
  • Miscellaneous code cleanups (pr/1148, pr/1149, pr/1153, pr/1154, pr/1156) (Dimitri Papadopoulos, reviewed by CM)
  • Update CI to build, test and deploy PyPI artifacts (pr/1134) (CM, reviewed by MB)
  • Transition from setup.cfg to pyproject.toml package configuration (pr/1133) (CM, reviewed by MB)

... (truncated)

Changelog

Sourced from nibabel's changelog.

5.0.1 (Sunday 12 February 2023)

Bug-fix release in the 5.0.x series.

Bug fixes

  • Support ragged voxel arrays in :class:~nibabel.cifti2.cifti2_axes.ParcelsAxis (pr/1194) (Michiel Cottaar, reviewed by CM)
  • Return to cwd on exception in :class:~nibabel.tmpdirs.InTemporaryDirectory (pr/1184) (CM)

Maintenance

  • Add py.typed to module root to enable use of types in downstream projects (CM, reviewed by Fernando Pérez-Garcia)
  • Cache git-archive separately from Python packages in GitHub Actions (pr/1186) (CM, reviewed by Zvi Baratz)

5.0.0 (Monday 9 January 2023)

New feature release in the 5.0.x series.

New features

  • :class:~nibabel.filebasedimages.SerializableImage now has :meth:~nibabel.filebasedimages.SerializableImage.to_stream() and :meth:~nibabel.filebasedimages.SerializableImage.from_stream() methods to read/write streams implementing the :class:~io.IOBase interface. A :meth:~nibabel.filebasedimages.SerializableImage.from_url() method enables loading images from URLs. (pr/1129) (CM, reviewed by MB)
  • :class:~nibabel.streamlines.trk.TrkFile supports TRKv3, an undocumented but generally compatible variant of TRKv2. (pr/1125) (CM)

Enhancements

  • Support multiline header fields in :class:~nibabel.streamlines.tck.TCKFile (pr/1175) (CM, reviewed by Matt Cieslak)
  • Make layout order an initialization parameter of :class:~nibabel.arrayproxy.ArrayProxy (pr/1131) (CM, reviewed by MB)
  • Initial support for type annotations. (pr/1115, pr/1178) (CM, reviewed by Zvi Baratz)

Bug fixes

  • Handle extension/file-format mismatches implemented incompletely in pr/1013 (pr/1138) (CM, reviewed by Thomas Phil)
  • Improve handling of invalid TCK files, which could sometimes cause an

... (truncated)

Commits
  • c0be346 DOC: 5.0.1 changelog
  • 6464fb4 MNT: Ignore nibabel-data when building sdists
  • 91cf8d6 MNT: Add py.typed to module root
  • 7a7385e BF: Support ragged voxel arrays in ParcelsAxis
  • 90bcd83 MNT: Update pre-commit hooks
  • 4fd5e30 Merge pull request #1186 from effigies/ci/fix_archive
  • 62daa84 CI: Reorder if constraints to follow step names
  • 6083235 CI: Cache git-archive separately from Python packages
  • b9c5451 Merge pull request #1184 from effigies/fix/tmpdir_finally
  • bb374f1 FIX: Return to cwd on exception in InTemporaryDirectory
  • Additional commits viewable in compare view


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codecov[bot] commented 1 year ago

Codecov Report

Base: 94.76% // Head: 94.76% // No change to project coverage :thumbsup:

Coverage data is based on head (b768e40) compared to base (ffc2ae8). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #286 +/- ## ======================================= Coverage 94.76% 94.76% ======================================= Files 12 12 Lines 478 478 ======================================= Hits 453 453 Misses 25 25 ``` | [Impacted Files](https://codecov.io/gh/alexdaniel654/Renal_Segmentor/pull/286?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alex+Daniel) | Coverage Δ | | |---|---|---| | [segment/segment.py](https://codecov.io/gh/alexdaniel654/Renal_Segmentor/pull/286?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alex+Daniel#diff-c2VnbWVudC9zZWdtZW50LnB5) | `90.57% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alex+Daniel). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Alex+Daniel)

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