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Bump the python-dependencies group with 7 updates #441

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@dependabot dependabot bot commented on behalf of github Nov 1, 2024

Bumps the python-dependencies group with 7 updates:

Package From To
xarray 2024.9.0 2024.10.0
netcdf4 1.7.1.post2 1.7.2
couchbase 4.3.2 4.3.3
pyproj 3.6.1 3.7.0
numpy 2.1.1 2.1.2
ruff 0.6.8 0.7.1
coverage 7.6.1 7.6.4

Updates xarray from 2024.9.0 to 2024.10.0

Release notes

Sourced from xarray's releases.

v2024.10.0

This release brings official support for xarray.DataTree, and compatibility with zarr-python v3!

Aside from these two huge features, it also improves support for vectorised interpolation and fixes various bugs.

Thanks to the 31 contributors to this release: Alfonso Ladino, DWesl, Deepak Cherian, Eni, Etienne Schalk, Holly Mandel, Ilan Gold, Illviljan, Joe Hamman, Justus Magin, Kai Mühlbauer, Karl Krauth, Mark Harfouche, Martey Dodoo, Matt Savoie, Maximilian Roos, Patrick Hoefler, Peter Hill, Renat Sibgatulin, Ryan Abernathey, Spencer Clark, Stephan Hoyer, Tom Augspurger, Tom Nicholas, Vecko, Virgile Andreani, Yvonne Fröhlich, carschandler, joseph nowak, mgunyho and owenlittlejohns

What's Changed

... (truncated)

Commits
  • 165177e v2024.10.0 release summary (#9678)
  • fbe73ef drop the length from numpy's fixed-width string dtypes (#9586)
  • f24cae3 fixing behaviour for group parameter in open_datatree (#9666)
  • 519f05e Use zarr v3 dimension_names (#9669)
  • 5b2e6f1 fix(zarr): use inplace array.resize for zarr 2 and 3 (#9673)
  • 1f5889a implement dask methods on DataTree (#9670)
  • 521b087 support chunks in open_groups and open_datatree (#9660)
  • b133fdc Compatibility for zarr-python 3.x (#9552)
  • 4798707 Update to_dataframe doc to match current behavior (#9662)
  • 5632c8e Reduce graph size through writing indexes directly into graph for ``map_block...
  • Additional commits viewable in compare view

Updates netcdf4 from 1.7.1.post2 to 1.7.2

Changelog

Sourced from netcdf4's changelog.

since version 1.7.2 release

  • fix type hint for createEnumType (issue #1378)
  • add python 3.13 to windows wheel builds (PR #1377)

version 1.7.2 (tag v1.7.2rel)

  • add static type hints (PRs #1302, #1349)
  • Expose nc_rc_set, nc_rc_get (via rc_set, rc_get module functions). (PR #1348)
  • Add Variable.get_fill_value and allow fill_value='default' to set _FillValue attribute using default fill values. (issue #1374, PR #1375).
  • Fix NETCDF3 endian error (issue #1373, PR #1355).

version 1.7.1 (tag v1.7.1rel)

  • include nc_complex source code from v0.2.0 tag (instead of using submodule).
  • add aarch64 wheels.

version 1.7.0 (tag v1.7.0rel)

  • add support for complex numbers via auto_complex keyword to Dataset (PR #1295)
  • fix for deprecated Cython DEF and IF statements using compatibility header with shims for unavailable functionality (PR #1277)
  • use szip as the library name on Windows (PR #1304)
  • add support for MS-MPI MPI_Message detection (PR #1305)
  • fix for issue #1306 - surprising result when indexing vlen str with non-contiguous indices.
  • Fix bug in set_collective introduced in PR #1277 (collective mode was always set).

version 1.6.5 (tag v1.6.5rel)

  • fix for issue #1271 (mask ignored if bool MA assigned to uint8 var)
  • include information on specific object when reporting errors from netcdf-c
  • python 3.12 wheels added, support for python 3.7 removed.

version 1.6.4 (tag v1.6.4rel)

  • set path to SSL certificates internally, so https DAP URLs work with wheels (issue #1246, requires nc_rc_set function available starting with netcdf-c 4.9.1, plus bugfix in netcdf-c PR #2690). Added certifi as a dependency.
  • Added isopen method to MFDataset object to check if underlying files are open.

version 1.6.3 (tag v1.6.3rel)

  • Use nc_put_vars for strided writes for netcdf-c >= 4.6.2 (issue #1222).
  • _Unsigned="false" should be same as not having _Unsigned set (issue #1232). _Unsigned now must be set to "true" or "True" for variable to be interpreted as unsigned, instead of just having _Unsigned be set (to anything).

... (truncated)

Commits

Updates couchbase from 4.3.2 to 4.3.3

Commits
  • 465027c Update C++ core to 1.0.3
  • 8717eec Changes for PYCBC-1625 and PYCBC-1628
  • 846a9ca PYCBC-1619: Enable use of C++ file logger
  • 0a10904 PYCBC-1629: Update array_addunique to adhere to RFC
  • 2625e34 PYCBC-1569: Provide way in increment/decrement to not create document if it d...
  • See full diff in compare view

Updates pyproj from 3.6.1 to 3.7.0

Release notes

Sourced from pyproj's releases.

3.7.0 Release

What's Changed

Dependencies:

Enhancements:

Bug fixes:

Maintenance:

New Contributors

Other contributions:

Full Changelog: pyproj4/pyproj@3.6.1...3.7.0

3.7.0rc0

No release notes provided.

Changelog

Sourced from pyproj's changelog.

3.7.0

  • WHL: Wheels contain PROJ 9.4.1 (pull #1423)
  • DEP: Minimum supported Python version 3.10 (pull #1357)
  • DEP: Minimum PROJ version 9.2 (pull #1394)
  • ENH: Add :meth:CRS.is_deprecated and :meth:CRS.get_non_deprecated (pull #1383)
  • PERF: thread local context (issue #1133)
  • ENH: Add runtime & compiled PROJ versions (discussion #1420)
  • BUG: Handle changes to HotineObliqueMercatorBConversion (issue #1429)
Commits

Updates numpy from 2.1.1 to 2.1.2

Release notes

Sourced from numpy's releases.

2.1.2 (Oct 5, 2024)

NumPy 2.1.2 Release Notes

NumPy 2.1.2 is a maintenance release that fixes bugs and regressions discovered after the 2.1.1 release.

The Python versions supported by this release are 3.10-3.13.

Contributors

A total of 11 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Charles Harris
  • Chris Sidebottom
  • Ishan Koradia +
  • João Eiras +
  • Katie Rust +
  • Marten van Kerkwijk
  • Matti Picus
  • Nathan Goldbaum
  • Peter Hawkins
  • Pieter Eendebak
  • Slava Gorloff +

Pull requests merged

A total of 14 pull requests were merged for this release.

  • #27333: MAINT: prepare 2.1.x for further development
  • #27400: BUG: apply critical sections around populating the dispatch cache
  • #27406: BUG: Stub out get_build_msvc_version if distutils.msvccompiler...
  • #27416: BUILD: fix missing include for std::ptrdiff_t for C++23 language...
  • #27433: BLD: pin setuptools to avoid breaking numpy.distutils
  • #27437: BUG: Allow unsigned shift argument for np.roll
  • #27439: BUG: Disable SVE VQSort
  • #27471: BUG: rfftn axis bug
  • #27479: BUG: Fix extra decref of PyArray_UInt8DType.
  • #27480: CI: use PyPI not scientific-python-nightly-wheels for CI doc...
  • #27481: MAINT: Check for SVE support on demand
  • #27484: BUG: initialize the promotion state to be weak
  • #27501: MAINT: Bump pypa/cibuildwheel from 2.20.0 to 2.21.2
  • #27506: BUG: avoid segfault on bad arguments in ndarray.__array_function__

Checksums

MD5

4aae28b7919b126485c1aaccee37a6ba  numpy-2.1.2-cp310-cp310-macosx_10_9_x86_64.whl
172614423a82ef73d8752ad8a59cbafc  numpy-2.1.2-cp310-cp310-macosx_11_0_arm64.whl

... (truncated)

Commits
  • f5afe3d Merge pull request #27507 from charris/prepare-2.1.2
  • 6b9ef48 REL: Prepare for the NumPy 2.1.2 release [wheel build]
  • 6d85a24 MAINT: Pin setuptools for Python < 3.12 [wheel build]
  • 7f327d8 Merge pull request #27506 from charris/backport-27503
  • 09e9cd9 BUG: avoid segfault on bad arguments in ndarray.array_function
  • 06b4793 Merge pull request #27501 from charris/backport-27495
  • 364efb5 MAINT: Bump pypa/cibuildwheel from 2.21.1 to 2.21.2
  • df0e261 Merge pull request #27484 from ngoldbaum/use-weak-default
  • fa61bc6 Merge pull request #27481 from charris/backport-27472
  • d6d06ae Merge pull request #27480 from charris/backport-27475
  • Additional commits viewable in compare view

Updates ruff from 0.6.8 to 0.7.1

Release notes

Sourced from ruff's releases.

0.7.1

Release Notes

Preview features

  • Fix E221 and E222 to flag missing or extra whitespace around == operator (#13890)
  • Formatter: Alternate quotes for strings inside f-strings in preview (#13860)
  • Formatter: Join implicit concatenated strings when they fit on a line (#13663)
  • [pylint] Restrict iteration-over-set to only work on sets of literals (PLC0208) (#13731)

Rule changes

  • [flake8-type-checking] Support auto-quoting when annotations contain quotes (#11811)

Server

  • Avoid indexing the workspace for single-file mode (#13770)

Bug fixes

  • Make ARG002 compatible with EM101 when raising NotImplementedError (#13714)

Other changes

  • Introduce more Docker tags for Ruff (similar to uv) (#13274)

Contributors

Install ruff 0.7.1

Install prebuilt binaries via shell script

... (truncated)

Changelog

Sourced from ruff's changelog.

0.7.1

Preview features

  • Fix E221 and E222 to flag missing or extra whitespace around == operator (#13890)
  • Formatter: Alternate quotes for strings inside f-strings in preview (#13860)
  • Formatter: Join implicit concatenated strings when they fit on a line (#13663)
  • [pylint] Restrict iteration-over-set to only work on sets of literals (PLC0208) (#13731)

Rule changes

  • [flake8-type-checking] Support auto-quoting when annotations contain quotes (#11811)

Server

  • Avoid indexing the workspace for single-file mode (#13770)

Bug fixes

  • Make ARG002 compatible with EM101 when raising NotImplementedError (#13714)

Other changes

  • Introduce more Docker tags for Ruff (similar to uv) (#13274)

0.7.0

Check out the blog post for a migration guide and overview of the changes!

Breaking changes

  • The pytest rules PT001 and PT023 now default to omitting the decorator parentheses when there are no arguments (#12838, #13292). This was a change that we attempted to make in Ruff v0.6.0, but only partially made due to an error on our part. See the blog post for more details.
  • The useless-try-except rule (in our tryceratops category) has been recoded from TRY302 to TRY203 (#13502). This ensures Ruff's code is consistent with the same rule in the tryceratops linter.
  • The lint.allow-unused-imports setting has been removed (#13677). Use lint.pyflakes.allow-unused-imports instead.

Formatter preview style

  • Normalize implicit concatenated f-string quotes per part (#13539)

Preview linter features

  • [refurb] implement hardcoded-string-charset (FURB156) (#13530)
  • [refurb] Count codepoints not bytes for slice-to-remove-prefix-or-suffix (FURB188) (#13631)

... (truncated)

Commits
  • 337af83 Bump version to 0.7.1 (#13913)
  • 113ce84 Fix normalize arguments when fstring_formatting is disabled (#13910)
  • 7272f83 Fix preview style name in can_omit_parentheses to is_f_string_formatting_en...
  • 3eb4546 [red-knot] Format mdtest Python snippets more concisely (#13905)
  • 77ae0cc [red-knot] Infer subscript expression types for bytes literals (#13901)
  • 73ee72b Join implicit concatenated strings when they fit on a line (#13663)
  • e402e27 Use referencial equality in traversal helper methods (#13895)
  • de4181d Remove "default" remark from ruff check (#13900)
  • 2c57c2d [red-knot] Type narrowing for isinstance checks (#13894)
  • 72c18c8 Fix E221 and E222 to flag missing or extra whitespace around == operator (#...
  • Additional commits viewable in compare view

Updates coverage from 7.6.1 to 7.6.4

Changelog

Sourced from coverage's changelog.

Version 7.6.4 — 2024-10-20

  • fix: multi-line with statements could cause contained branches to be incorrectly marked as missing (issue 1880_). This is now fixed.

.. _issue 1880: nedbat/coveragepy#1880

.. _changes_7-6-3:

Version 7.6.3 — 2024-10-13

  • Fix: nested context managers could incorrectly be analyzed to flag a missing branch on the last context manager, as described in issue 1876_. This is now fixed.

  • Fix: the missing branch message about not exiting a module had an extra "didn't," as described in issue 1873_. This is now fixed.

.. _issue 1873: nedbat/coveragepy#1873 .. _issue 1876: nedbat/coveragepy#1876

.. _changes_7-6-2:

Version 7.6.2 — 2024-10-09

  • Dropped support for Python 3.8 and PyPy 3.8.

  • Fix: a final wildcard match/case clause assigning to a name (case _ as value) was incorrectly marked as a missing branch. This is now fixed, closing issue 1860_.

  • Fewer things are considered branches now. Lambdas, comprehensions, and generator expressions are no longer marked as missing branches if they don't complete execution. Closes issue 1852_.

  • Fix: the HTML report didn't properly show multi-line f-strings that end with a backslash continuation. This is now fixed, closing issue 1836, thanks to LiuYinCarl and Marco Ricci <pull 1838_>.

  • Fix: the LCOV report now has correct line numbers (fixing issue 1846) and better branch descriptions for BRDA records (fixing issue 1850). There are other changes to lcov also, including a new configuration option :ref:line_checksums <config_lcov_line_checksums> to control whether line checksums are included in the lcov report. The default is false. To keep checksums set it to true. All this work is thanks to Zack Weinberg

... (truncated)

Commits
  • f24f76b docs: sample HTML for 7.6.4
  • 96e10f7 docs: prep for 7.6.4
  • b8c236a fix: multi-line with-statements exit correctly. #1880
  • 64b7a45 docs: another discord reference
  • 68d7427 docs: Python Discord
  • 43adcea build: include 3.14 in the usual Pythons
  • fb2b49f build: github_releases can update older releases, and pauses to get the sorti...
  • ca550ca 3.0b2 wasn't correctly titled
  • debcc77 build: bump version
  • 342a4cb docs: sample HTML for 7.6.3
  • Additional commits viewable in compare view

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Bumps the python-dependencies group with 7 updates:

| Package | From | To |
| --- | --- | --- |
| [xarray](https://github.com/pydata/xarray) | `2024.9.0` | `2024.10.0` |
| [netcdf4](https://github.com/Unidata/netcdf4-python) | `1.7.1.post2` | `1.7.2` |
| [couchbase](https://github.com/couchbase/couchbase-python-client) | `4.3.2` | `4.3.3` |
| [pyproj](https://github.com/pyproj4/pyproj) | `3.6.1` | `3.7.0` |
| [numpy](https://github.com/numpy/numpy) | `2.1.1` | `2.1.2` |
| [ruff](https://github.com/astral-sh/ruff) | `0.6.8` | `0.7.1` |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.1` | `7.6.4` |


Updates `xarray` from 2024.9.0 to 2024.10.0
- [Release notes](https://github.com/pydata/xarray/releases)
- [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md)
- [Commits](pydata/xarray@v2024.09.0...v2024.10.0)

Updates `netcdf4` from 1.7.1.post2 to 1.7.2
- [Release notes](https://github.com/Unidata/netcdf4-python/releases)
- [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog)
- [Commits](https://github.com/Unidata/netcdf4-python/commits)

Updates `couchbase` from 4.3.2 to 4.3.3
- [Commits](couchbase/couchbase-python-client@4.3.2...4.3.3)

Updates `pyproj` from 3.6.1 to 3.7.0
- [Release notes](https://github.com/pyproj4/pyproj/releases)
- [Changelog](https://github.com/pyproj4/pyproj/blob/main/docs/history.rst)
- [Commits](pyproj4/pyproj@3.6.1...3.7.0)

Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.1.1...v2.1.2)

Updates `ruff` from 0.6.8 to 0.7.1
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.6.8...0.7.1)

Updates `coverage` from 7.6.1 to 7.6.4
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.6.1...7.6.4)

---
updated-dependencies:
- dependency-name: xarray
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: netcdf4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: couchbase
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: pyproj
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Nov 1, 2024
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github-actions bot commented Nov 1, 2024

Code Coverage

Package Line Rate Branch Rate Health
vxingest 32% 27%
vxingest.builder_common 27% 18%
vxingest.ctc_to_cb 12% 1%
vxingest.grib2_to_cb 13% 1%
vxingest.netcdf_to_cb 13% 1%
vxingest.partial_sums_to_cb 12% 1%
vxingest.utilities 30% 35%
Summary 16% (490 / 3044) 5% (32 / 664)

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