search

NOAA-GSL / VxIngest

Other
2 stars 0 forks source link

Bump the python-dependencies group across 1 directory with 8 updates #391

Closed dependabot[bot] closed 3 months ago

dependabot[bot] commented 3 months ago

Bumps the python-dependencies group with 8 updates in the / directory:

Package From To
xarray 2024.3.0 2024.6.0
netcdf4 1.6.5 1.7.1.post1
cfgrib 0.9.11.0 0.9.13.0
couchbase 4.2.1 4.3.0
numpy 1.26.4 2.0.0
pytest 8.2.0 8.2.2
ruff 0.4.3 0.5.1
coverage 7.5.1 7.6.0

Updates xarray from 2024.3.0 to 2024.6.0

Release notes

Sourced from xarray's releases.

v2024.06.0

This release brings compatibility with numpy 2 and various performance optimizations.

Thanks to the 22 contributors to this release: Alfonso Ladino, David Hoese, Deepak Cherian, Eni Awowale, Ilan Gold, Jessica Scheick, Joe Hamman, Justus Magin, Kai Mühlbauer, Mark Harfouche, Mathias Hauser, Matt Savoie, Maximilian Roos, Mike Thramann, Nicolas Karasiak, Owen Littlejohns, Paul Ockenfuß, Philippe THOMY, Scott Henderson, Spencer Clark, Stephan Hoyer and Tom Nicholas

What's Changed

New Contributors

... (truncated)

Commits


Updates netcdf4 from 1.6.5 to 1.7.1.post1

Changelog

Sourced from netcdf4's changelog.

version 1.7.2 (tag v1.7.2rel)

  • add static type hints (PR #1302)

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).
Commits


Updates cfgrib from 0.9.11.0 to 0.9.13.0

Release notes

Sourced from cfgrib's releases.

0.9.13.0

Changelog

Sourced from cfgrib's changelog.

0.9.13.0 (2024-06-27)

  • Allow users to pass of list of values to filter a key by. See [#384](https://github.com/ecmwf/cfgrib/issues/384) <https://github.com/ecmwf/cfgrib/pull/384>_.

  • Functionality to ignore keys when reading a grib file See [#382](https://github.com/ecmwf/cfgrib/issues/382) <https://github.com/ecmwf/cfgrib/pull/382>_.

  • Preserve coordinate encoding in cfgrib.open_datasets See [#381](https://github.com/ecmwf/cfgrib/issues/381) <https://github.com/ecmwf/cfgrib/pull/381>_.

0.9.12.0 (2024-05-26)

  • fixed issue where GRIB messages with non-hourly steps could not be read See [#370](https://github.com/ecmwf/cfgrib/issues/370) <https://github.com/ecmwf/cfgrib/pull/370>_.
Commits


Updates couchbase from 4.2.1 to 4.3.0

Commits
  • b92c82d Update C++ core to 1.0.0
  • 1207880 PYCBC-1588: Add support for importing FTS index from JSON
  • 11a2040 Bump Vector Search to committed stability level.
  • 388682b Update pre-commit hooks and clang-format
  • c3e29d6 Update C++ core
  • 4e0beea PYCBC-1603: Handle empty VectorQuery field name
  • f630b04 PYCBC-1597: Support for base64 encoded vector types
  • d7391bc Update C++ core
  • 539679d PYCBC-1583: Fix BucketType.COUCHBASE being ignored from bucket settings
  • e86af1c PYCBC-1596: Fix AnalyticsStatus Enum values
  • Additional commits viewable in compare view


Updates numpy from 1.26.4 to 2.0.0

Release notes

Sourced from numpy's releases.

v2.0.0

NumPy 2.0.0 Release Notes

NumPy 2.0.0 is the first major release since 2006. It is the result of 11 months of development since the last feature release and is the work of 212 contributors spread over 1078 pull requests. It contains a large number of exciting new features as well as changes to both the Python and C APIs.

This major release includes breaking changes that could not happen in a regular minor (feature) release - including an ABI break, changes to type promotion rules, and API changes which may not have been emitting deprecation warnings in 1.26.x. Key documents related to how to adapt to changes in NumPy 2.0, in addition to these release notes, include:

Highlights

Highlights of this release include:

  • New features:
    • A new variable-length string dtype, numpy.dtypes.StringDType and a new numpy.strings namespace with performant ufuncs for string operations,
    • Support for float32 and longdouble in all numpy.fft functions,
    • Support for the array API standard in the main numpy namespace.
  • Performance improvements:
    • Sorting functions sort, argsort, partition, argpartition have been accelerated through the use of the Intel x86-simd-sort and Google Highway libraries, and may see large (hardware-specific) speedups,
    • macOS Accelerate support and binary wheels for macOS >=14, with significant performance improvements for linear algebra operations on macOS, and wheels that are about 3 times smaller,
    • numpy.char fixed-length string operations have been accelerated by implementing ufuncs that also support numpy.dtypes.StringDType in addition to the fixed-length string dtypes,
    • A new tracing and introspection API, numpy.lib.introspect.opt_func_info, to determine which hardware-specific kernels are available and will be dispatched to.
    • numpy.save now uses pickle protocol version 4 for saving arrays with object dtype, which allows for pickle objects larger than 4GB and improves saving speed by about 5% for large arrays.
  • Python API improvements:

... (truncated)

Commits
  • 1d49c7f Merge pull request #26698 from charris/prepare-2.0.0
  • 2103511 DOC: Remove duplicate in author list.
  • db8030e BUG: Change cibuildwheel version [wheel build]
  • 1a68264 REL: Prepare for the NumPy 2.0.0 release [wheel build]
  • c8665ba Merge pull request #26696 from charris/backport-26582
  • 103f4dd Merge pull request #26697 from charris/backport-25963
  • c193dcd Merge pull request #26695 from charris/backport-26667
  • 8fa8191 BUG: Fix bug in numpy.pad() (#25963)
  • ece3559 BUG: weighted nanpercentile, nanquantile and multi-dim q (#26582)
  • b31e195 BUG: Adds asanyarray to start of linalg.cross (#26667)
  • Additional commits viewable in compare view


Updates pytest from 8.2.0 to 8.2.2

Release notes

Sourced from pytest's releases.

8.2.2

pytest 8.2.2 (2024-06-04)

Bug Fixes

  • #12355: Fix possible catastrophic performance slowdown on a certain parametrization pattern involving many higher-scoped parameters.
  • #12367: Fix a regression in pytest 8.2.0 where unittest class instances (a fresh one is created for each test) were not released promptly on test teardown but only on session teardown.
  • #12381: Fix possible "Directory not empty" crashes arising from concurent cache dir (.pytest_cache) creation. Regressed in pytest 8.2.0.

Improved Documentation

  • #12290: Updated Sphinx theme to use Furo instead of Flask, enabling Dark mode theme.
  • #12356: Added a subsection to the documentation for debugging flaky tests to mention lack of thread safety in pytest as a possible source of flakyness.
  • #12363: The documentation webpages now links to a canonical version to reduce outdated documentation in search engine results.

8.2.1

pytest 8.2.1 (2024-05-19)

Improvements

  • #12334: Support for Python 3.13 (beta1 at the time of writing).

Bug Fixes

  • #12120: Fix [PermissionError]{.title-ref} crashes arising from directories which are not selected on the command-line.
  • #12191: Keyboard interrupts and system exits are now properly handled during the test collection.
  • #12300: Fixed handling of 'Function not implemented' error under squashfuse_ll, which is a different way to say that the mountpoint is read-only.
  • #12308: Fix a regression in pytest 8.2.0 where the permissions of automatically-created .pytest_cache directories became rwx------ instead of the expected rwxr-xr-x.

Trivial/Internal Changes

  • #12333: pytest releases are now attested using the recent Artifact Attestation support from GitHub, allowing users to verify the provenance of pytest's sdist and wheel artifacts.
Commits
  • 329d371 Prepare release version 8.2.2
  • 214d098 Merge pull request #12414 from bluetech/backport-12409
  • 153a436 [8.2.x] fixtures: fix catastrophic performance problem in reorder_items
  • b41d5a5 Merge pull request #12412 from pytest-dev/backport-12408-to-8.2.x
  • 9bb73d7 [8.2.x] cacheprovider: fix "Directory not empty" crash from cache directory c...
  • 4569a01 [8.2.x] doc: Update trainings/events (#12402)
  • 1d103e5 [8.2.x] Clarify pytest_ignore_collect docs (#12386)
  • 240a252 [8.2.x] Add html_baseurl to sphinx conf.py (#12372)
  • a5ee3c4 Merge pull request #12370 from pytest-dev/backport-12368-to-8.2.x
  • f7358ae [8.2.x] unittest: fix class instances no longer released on test teardown sin...
  • Additional commits viewable in compare view


Updates ruff from 0.4.3 to 0.5.1

Release notes

Sourced from ruff's releases.

0.5.1

Release Notes

Preview features

  • [flake8-bugbear] Implement mutable-contextvar-default (B039) (#12113)
  • [pycodestyle] Whitespace after decorator (E204) (#12140)
  • [pytest] Reverse PT001 and PT0023 defaults (#12106)

Rule changes

  • Enable token-based rules on source with syntax errors (#11950)
  • [flake8-bandit] Detect httpx for S113 (#12174)
  • [numpy] Update NPY201 to include exception deprecations (#12065)
  • [pylint] Generate autofix for duplicate-bases (PLE0241) (#12105)

Server

  • Avoid syntax error notification for source code actions (#12148)
  • Consider the content of the new cells during notebook sync (#12203)
  • Fix replacement edit range computation (#12171)

Bug fixes

  • Disable auto-fix when source has syntax errors (#12134)
  • Fix cache key collisions for paths with separators (#12159)
  • Make requires-python inference robust to == (#12091)
  • Use char-wise width instead of str-width (#12135)
  • [pycodestyle] Avoid E275 if keyword followed by comma (#12136)
  • [pycodestyle] Avoid E275 if keyword is followed by a semicolon (#12095)
  • [pylint] Skip dummy variables for PLR1704 (#12190)

Performance

  • Remove allocation in parse_identifier (#12103)
  • Use CompactString for Identifier AST node (#12101)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.5.1

Preview features

  • [flake8-bugbear] Implement mutable-contextvar-default (B039) (#12113)
  • [pycodestyle] Whitespace after decorator (E204) (#12140)
  • [pytest] Reverse PT001 and PT0023 defaults (#12106)

Rule changes

  • Enable token-based rules on source with syntax errors (#11950)
  • [flake8-bandit] Detect httpx for S113 (#12174)
  • [numpy] Update NPY201 to include exception deprecations (#12065)
  • [pylint] Generate autofix for duplicate-bases (PLE0241) (#12105)

Server

  • Avoid syntax error notification for source code actions (#12148)
  • Consider the content of the new cells during notebook sync (#12203)
  • Fix replacement edit range computation (#12171)

Bug fixes

  • Disable auto-fix when source has syntax errors (#12134)
  • Fix cache key collisions for paths with separators (#12159)
  • Make requires-python inference robust to == (#12091)
  • Use char-wise width instead of str-width (#12135)
  • [pycodestyle] Avoid E275 if keyword followed by comma (#12136)
  • [pycodestyle] Avoid E275 if keyword is followed by a semicolon (#12095)
  • [pylint] Skip dummy variables for PLR1704 (#12190)

Performance

  • Remove allocation in parse_identifier (#12103)
  • Use CompactString for Identifier AST node (#12101)

0.5.0

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

Breaking changes

See also, the "Remapped rules" section which may result in disabled rules.

  • Follow the XDG specification to discover user-level configurations on macOS (same as on other Unix platforms)
  • Selecting ALL now excludes deprecated rules
  • The released archives now include an extra level of nesting, which can be removed with --strip-components=1 when untarring.
  • The release artifact's file name no longer includes the version tag. This enables users to install via /latest URLs on GitHub.
  • The diagnostic ranges for some flake8-bandit rules were modified (#10667).

... (truncated)

Commits
  • 3a72400 Rename publish workflow file extension (yaml -> yml) (#12206)
  • 1b3bff0 Bump version to 0.5.1 (#12205)
  • 0f6f73e [red-knot] Require that FileSystem objects implement Debug (#12204)
  • 7910bee Consider the content of the new cells during notebook sync (#12203)
  • f3ccd15 Revert "Remove --preview as a required argument for ruff server (#12053)"...
  • 1e07bfa [pycodestyle] Whitespace after decorator (E204) (#12140)
  • 5e7ba05 docs(*): fix a few typos, consistency issues and links (#12193)
  • d12570e docs(options): fix some typos and improve consistency (#12191)
  • 2f3264e fix(rules): skip dummy variables for PLR1704 (#12190)
  • e2e0889 [red-knot] Add very basic benchmark (#12182)
  • Additional commits viewable in compare view


Updates coverage from 7.5.1 to 7.6.0

Changelog

Sourced from coverage's changelog.

Version 7.6.0 — 2024-07-11

  • Exclusion patterns can now be multi-line, thanks to Daniel Diniz <pull 1807_>. This enables many interesting exclusion use-cases, including those requested in issues 118 <issue 118_> (entire files), 996 <issue 996_>_ (multiple lines only when appearing together), 1741 <issue 1741_>_ (remainder of a function), and 1803 <issue 1803_>_ (arbitrary sequence of marked lines). See the :ref:multi_line_exclude section of the docs for more details and examples.

  • The JSON report now includes per-function and per-class coverage information. Thanks to Daniel Diniz <pull 1809_>_ for getting the work started. This closes issue 1793_ and issue 1532_.

  • Fixed an incorrect calculation of "(no class)" lines in the HTML classes report.

  • Python 3.13.0b3 is supported.

.. _issue 118: nedbat/coveragepy#118 .. _issue 996: nedbat/coveragepy#996 .. _issue 1532: nedbat/coveragepy#1532 .. _issue 1741: nedbat/coveragepy#1741 .. _issue 1793: nedbat/coveragepy#1793 .. _issue 1803: nedbat/coveragepy#1803 .. _pull 1807: nedbat/coveragepy#1807 .. _pull 1809: nedbat/coveragepy#1809

.. _changes_7-5-4:

Version 7.5.4 — 2024-06-22

  • If you attempt to combine statement coverage data with branch coverage data, coverage.py used to fail with the message "Can't combine arc data with line data" or its reverse, "Can't combine line data with arc data." These messages used internal terminology, making it hard for people to understand the problem. They are now changed to mention "branch coverage data" and "statement coverage data."

  • Fixed a minor branch coverage problem with wildcard match/case cases using names or guard clauses.

  • Started testing on 3.13 free-threading (nogil) builds of Python. I'm not claiming full support yet. Closes issue 1799_.

.. _issue 1799: nedbat/coveragepy#1799

... (truncated)

Commits
  • 59a3cd7 docs: sample HTML for 7.6.0
  • 7f27fa7 docs: prep for 7.6.0
  • 6a268b0 docs: issues closed by the json region reporting
  • 5bfe9e7 chore: bump actions/setup-python from 5.1.0 to 5.1.1 (#1814)
  • ab609ef docs: mention json region reporting in the changes
  • 92d96b9 fix: json report needs 'no class' and 'no function' also
  • e47e7e7 refactor: move duplicate code into methods
  • 3d6be2b fix: json format should bump for regions
  • a9992d2 test: add a test of json regions with branches
  • 8b89764 test: json expectations should have explicit format number
  • Additional commits viewable in compare view


Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself) - `@dependabot ignore minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself) - `@dependabot ignore ` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself) - `@dependabot unignore ` will remove all of the ignore conditions of the specified dependency - `@dependabot unignore ` will remove the ignore condition of the specified dependency and ignore conditions
github-actions[bot] commented 3 months ago

Code Coverage

Package Line Rate Branch Rate Health
vxingest 33% 38% ❌
vxingest.builder_common 27% 15% ❌
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% 32% ❌
Summary 16% (490 / 3033) 6% (40 / 712) ❌