Bump the poetry-dependencies group with 12 updates

[dependabot]

Bumps the poetry-dependencies group with 12 updates:

Package	From	To
biopython	1.81	1.82
black	23.12.0	23.12.1
coverage	7.3.2	7.4.0
mypy	1.7.1	1.8.0
ruff	0.1.7	0.1.9
pytest	7.4.3	7.4.4
ipykernel	6.27.1	6.28.0
importlib-metadata	7.0.0	7.0.1
jupyter-core	5.5.0	5.5.1
prompt-toolkit	3.0.42	3.0.43
psutil	5.9.6	5.9.7
setuptools	69.0.2	69.0.3

Updates biopython from 1.81 to 1.82

Changelog

Sourced from biopython's changelog.

22 December 2023: Biopython 1.82

This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.8 v7.3.11.

The inplace argument of complement and reverse_complement in Bio.Seq now always default to False both for Seq and MutableSeq objects. To modify a MutableSeq in-place, use inplace=True.

A new class CodonAligner was added to Bio.Align. A CodonAligner object can align a nucleotide sequence to the amino acid sequence it encodes, using a dynamic programming algorithm modeled on PairwiseAligner to take frame shifts into account. The CodonAligner returns Alignment objects. By calling the new mapall method on an Alignment object storing a multiple sequence alignment of amino acid sequences, with nucleotide-to-amino acid alignments generated by CodonAligner as the argument, a codon-by-codon multiple sequence alignment of nucleotide sequences can be obtained. The new submodule Bio.Align.analysis provides functions to estimate synonymous and nonsynonymous mutations and to perform the McDonald-Kreitman test on the codon multiple sequence alignments. Together, this provides the same functionality as the Bio.codonalign module, but uses the standard Alignment class, and does not rely on regular expression searching to align a nucleotide sequence to an amino acid sequence.

The hmmer3-text SearchIO format now also extracts the similarity string of the parsed alignments. This value is available under the 'similarity' key of the aln_annotation attribute of each HSP, the same as how it is done in other SearchIO formats.

HMMER results with the full path to the hmmer executable in the banner are now parsed correctly. This should help Windows users and users with python installations in non-default locations.

We now have basic type hint annotations in various modules including Seq, SeqRecord, and SeqIO. This should help anyone using an editor or IDE with type-aware autocomplete, or in conjunction with mypy as a pre-commit check this can catch passing the wrong types to Biopython functions/methods.

Calling iter on a PairwiseAlignments object returned by a PairwiseAigner previously reset the iterator such that it will start from the first alignment when iterating. As a side effect, this will cause all other iterators of the alignments to reset as well, which is bug prone. Instead, calling iter on a PairwiseAlignments object will now return itself. The iterator can be reset by calling the rewind method.

Calling secondary_structure_fraction() on a ProtParam.ProteinAnalysis object historically returned (sheet, turn, helix) while claiming to return (helix, turn, sheet). This was fixed to correctly return (helix, turn, sheet). Additionally, the amino acids considered were revised as per recent literature.

... (truncated)

Commits

• See full diff in compare view

Updates black from 23.12.0 to 23.12.1

Release notes

Sourced from black's releases.

23.12.1

Fixed a bug that included dependencies from the d extra by default (#4108)

Changelog

Sourced from black's changelog.

23.12.1

Packaging

• Fixed a bug that included dependencies from the d extra by default (#4108)

Commits

• ec91a2b Prepare release 23.12.1 (#4124)
• 8fec1c3 Adds paren to deps for hidden extra constraint (#4108)
• 35ce37d Add new changelog template
• See full diff in compare view

Updates coverage from 7.3.2 to 7.4.0

Changelog

Sourced from coverage's changelog.

Version 7.4.0 — 2023-12-27

• In Python 3.12 and above, you can try an experimental core based on the new :mod:sys.monitoring <python:sys.monitoring> module by defining a COVERAGE_CORE=sysmon environment variable. This should be faster for line coverage, but not for branch coverage, and plugins and dynamic contexts are not yet supported with it. I am very interested to hear how it works (or doesn't!) for you.

.. _changes_7-3-4:

Version 7.3.4 — 2023-12-20

• Fix: the change for multi-line signature exclusions in 7.3.3 broke other forms of nested clauses being excluded properly. This is now fixed, closing issue 1713_.

• Fix: in the HTML report, selecting code for copying won't select the line numbers also. Thanks, Robert Harris <pull 1717_>_.

.. _issue 1713: nedbat/coveragepy#1713 .. _pull 1717: nedbat/coveragepy#1717

.. _changes_7-3-3:

Version 7.3.3 — 2023-12-14

• Fix: function definitions with multi-line signatures can now be excluded by matching any of the lines, closing issue 684. Thanks, Jan Rusak, Maciej Kowalczyk and Joanna Ejzel <pull 1705_>.

• Fix: XML reports could fail with a TypeError if files had numeric components that were duplicates except for leading zeroes, like file1.py and file001.py. Fixes issue 1709_.

• The coverage annotate command used to announce that it would be removed in a future version. Enough people got in touch to say that they use it, so it will stay. Don't expect it to keep up with other new features though.

• Added new :ref:debug options <cmd_run_debug>:

  • pytest writes the pytest test name into the debug output.

  • dataop2 writes the full data being added to CoverageData objects.

... (truncated)

Commits

• 23a015c docs: sample HTML for 7.4.0
• 4f020d4 docs: prep for 7.4.0
• 5bb88c3 build: temporarily disable metacov, it's flaky now with sysmon support
• 3879b97 docs: mention sys.monitoring support
• 9a84eeb style: environment variable names should be monospace
• 7882b8c refactor: clean lint and mypy for sysmon et al
• 5dad1a1 test: test which core we get
• b7e0c34 fix: don't default to sysmon yet
• e5babcf docs: explain the COVERAGE_*_CORE testing variables
• ebdc277 fix: use core more consistently than tracer
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Updates mypy from 1.7.1 to 1.8.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next release

Mypy 1.8

We’ve just uploaded mypy 1.8 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance improvements and bug fixes. You can install it as follows:

python3 -m pip install -U mypy

You can read the full documentation for this release on Read the Docs.

Type-checking Improvements

• Do not intersect types in isinstance checks if at least one is final (Christoph Tyralla, PR 16330)
• Detect that @final class without __bool__ cannot have falsey instances (Ilya Priven, PR 16566)
• Do not allow TypedDict classes with extra keywords (Nikita Sobolev, PR 16438)
• Do not allow class-level keywords for NamedTuple (Nikita Sobolev, PR 16526)
• Make imprecise constraints handling more robust (Ivan Levkivskyi, PR 16502)
• Fix strict-optional in extending generic TypedDict (Ivan Levkivskyi, PR 16398)
• Allow type ignores of PEP 695 constructs (Shantanu, PR 16608)
• Enable type_check_only support for TypedDict and NamedTuple (Nikita Sobolev, PR 16469)

Performance Improvements

• Add fast path to analyzing special form assignments (Jukka Lehtosalo, PR 16561)

Improvements to Error Reporting

• Don't show documentation links for plugin error codes (Ivan Levkivskyi, PR 16383)
• Improve error messages for super checks and add more tests (Nikita Sobolev, PR 16393)
• Add error code for mutable covariant override (Ivan Levkivskyi, PR 16399)

Stubgen Improvements

• Preserve simple defaults in function signatures (Ali Hamdan, PR 15355)
• Include __all__ in output (Jelle Zijlstra, PR 16356)
• Fix stubgen regressions with pybind11 and mypy 1.7 (Chad Dombrova, PR 16504)

Stubtest Improvements

• Improve handling of unrepresentable defaults (Jelle Zijlstra, PR 16433)
• Print more helpful errors if a function is missing from stub (Alex Waygood, PR 16517)
• Support @type_check_only decorator (Nikita Sobolev, PR 16422)
• Warn about missing __del__ (Shantanu, PR 16456)
• Fix crashes with some uses of final and deprecated (Shantanu, PR 16457)

Fixes to Crashes

• Fix crash with type alias to Callable[[Unpack[Tuple[Any, ...]]], Any] (Alex Waygood, PR 16541)
• Fix crash on TypeGuard in __call__ (Ivan Levkivskyi, PR 16516)
• Fix crash on invalid enum in method (Ivan Levkivskyi, PR 16511)
• Fix crash on unimported Any in TypedDict (Ivan Levkivskyi, PR 16510)

Documentation Updates

• Update soft-error-limit default value to -1 (Sveinung Gundersen, PR 16542)

... (truncated)

Commits

• 3b46750 remove +dev suffix from version
• c9bc833 Fix tests broken by hatchling (#16655)
• 60d30e3 Fix crash with type alias to Callable[[Unpack[Tuple[Any, ...]]], Any] (#16541)
• f53f422 Allow type ignores of PEP 695 constructs (#16608)
• 7c33e7c @​final class without bool cannot have falsey instances (#16566)
• c224da5 Do not intersect types in isinstance checks if at least one is final (#16330)
• d54cc35 Change example in test cases with no stubs available (#16513)
• eb1ee97 Update hashes in sync-typeshed.py following recent typeshed sync (#16600)
• 344298e Revert use of ParamSpec for functools.wraps
• 3e5d813 Revert typeshed ctypes change
• Additional commits viewable in compare view

Updates ruff from 0.1.7 to 0.1.9

Release notes

Sourced from ruff's releases.

v0.1.9

Changes

Breaking changes

• Add site-packages to default exclusions (#9188)

Preview features

• Fix: Avoid parenthesizing subscript targets and values (#9209)
• [pylint] Implement too-many-locals (PLR0914) (#9163)
• Implement reimplemented_operator (FURB118) (#9171)
• Add a rule to detect string members in runtime-evaluated unions (#9143)
• Implement no_blank_line_before_class_docstring preview style (#9154)

Rule changes

• CONSTANT_CASE variables are improperly flagged for yoda violation (SIM300) (#9164)
• [flake8-pyi] Cover ParamSpecs and TypeVarTuples (PYI018) (#9198)
• [flake8-bugbear] Add fix for zip-without-explicit-strict (B905) (#9176)
• Add fix to automatically remove print and pprint statements (T201, T203) (#9208)
• Prefer Never to NoReturn in auto-typing in Python >= 3.11 (ANN201) (#9213)

Formatter

• can_omit_optional_parentheses: Exit early for unparenthesized expressions (#9125)
• Fix dynamic mode with doctests so that it doesn't exceed configured line width (#9129)
• Fix can_omit_optional_parentheses for expressions with a right most fstring (#9124)
• Add target_version to formatter options (#9220)

CLI

• Update ruff format --check to display message for already formatted files (#9153)

Bug fixes

• Reverse order of arguments for operator.contains (#9192)
• Iterate over lambdas in deferred type annotations (#9175)
• Fix panic in D208 with multibyte indent (#9147)
• Add support for NoReturn in auto-return-typing (#9206)
• Allow removal of typing from exempt-modules (#9214)
• Avoid mutable-class-default violations for Pydantic subclasses (#9187)
• Fix dropped union expressions for piped non-types in PYI055 autofix (#9161)
• Enable annotation quoting for multi-line expressions (#9142)
• Deduplicate edits when quoting annotations (#9140)
• Prevent invalid utf8 indexing in cell magic detection (#9146)
• Avoid nested quotations in auto-quoting fix (#9168)
• Add base-class inheritance detection to flake8-django rules (#9151)
• Avoid asyncio-dangling-task violations on shadowed bindings (#9215)

... (truncated)

Changelog

Sourced from ruff's changelog.

0.1.9

Breaking changes

• Add site-packages to default exclusions (#9188)

Preview features

• Fix: Avoid parenthesizing subscript targets and values (#9209)
• [pylint] Implement too-many-locals (PLR0914) (#9163)
• Implement reimplemented_operator (FURB118) (#9171)
• Add a rule to detect string members in runtime-evaluated unions (#9143)
• Implement no_blank_line_before_class_docstring preview style (#9154)

Rule changes

• CONSTANT_CASE variables are improperly flagged for yoda violation (SIM300) (#9164)
• [flake8-pyi] Cover ParamSpecs and TypeVarTuples (PYI018) (#9198)
• [flake8-bugbear] Add fix for zip-without-explicit-strict (B905) (#9176)
• Add fix to automatically remove print and pprint statements (T201, T203) (#9208)
• Prefer Never to NoReturn in auto-typing in Python >= 3.11 (ANN201) (#9213)

Formatter

• can_omit_optional_parentheses: Exit early for unparenthesized expressions (#9125)
• Fix dynamic mode with doctests so that it doesn't exceed configured line width (#9129)
• Fix can_omit_optional_parentheses for expressions with a right most fstring (#9124)
• Add target_version to formatter options (#9220)

CLI

• Update ruff format --check to display message for already formatted files (#9153)

Bug fixes

• Reverse order of arguments for operator.contains (#9192)
• Iterate over lambdas in deferred type annotations (#9175)
• Fix panic in D208 with multibyte indent (#9147)
• Add support for NoReturn in auto-return-typing (#9206)
• Allow removal of typing from exempt-modules (#9214)
• Avoid mutable-class-default violations for Pydantic subclasses (#9187)
• Fix dropped union expressions for piped non-types in PYI055 autofix (#9161)
• Enable annotation quoting for multi-line expressions (#9142)
• Deduplicate edits when quoting annotations (#9140)
• Prevent invalid utf8 indexing in cell magic detection (#9146)
• Avoid nested quotations in auto-quoting fix (#9168)
• Add base-class inheritance detection to flake8-django rules (#9151)
• Avoid asyncio-dangling-task violations on shadowed bindings (#9215)

Documentation

... (truncated)

Commits

• 0263f27 Bump version to v0.1.9 (#9231)
• c6d8076 Set target versions in Black tests (#9221)
• 8cb7950 Add target_version to formatter options (#9220)
• ef4bd8d Fix: Avoid parenthesizing subscript targets and values (#9209)
• 5d41c84 SIM300: CONSTANT_CASE variables are improperly flagged for yoda violation (#9...
• cbe3bf9 Avoid asyncio-dangling-task violations on shadowed bindings (#9215)
• 4b4160e Allow removal of typing from exempt-modules (#9214)
• 29846f5 Prefer Never to NoReturn in auto-typing (#9213)
• 07b293d Add fix to automatically remove print and pprint statements (#9208)
• 5ccc21a Add support for NoReturn in auto-return-typing (#9206)
• Additional commits viewable in compare view

Updates pytest from 7.4.3 to 7.4.4

Release notes

Sourced from pytest's releases.

pytest 7.4.4 (2023-12-31)

Bug Fixes

• #11140: Fix non-string constants at the top of file being detected as docstrings on Python>=3.8.
• #11572: Handle an edge case where sys.stderr{.interpreted-text role="data"} and sys.__stderr__{.interpreted-text role="data"} might already be closed when faulthandler{.interpreted-text role="ref"} is tearing down.
• #11710: Fixed tracebacks from collection errors not getting pruned.
• #7966: Removed unhelpful error message from assertion rewrite mechanism when exceptions are raised in __iter__ methods. Now they are treated un-iterable instead.

Improved Documentation

• #11091: Updated documentation to refer to hyphenated options: replaced --junitxml with --junit-xml and --collectonly with --collect-only.

Commits

• 33f694f Prepare release version 7.4.4
• 76c107c Merge pull request #11751 from bluetech/backport-11143-to-7.4.x
• 531d76d [7.4.x] Improve reporting from iter exceptions (#11749)
• a0f58fa Merge pull request #11143 from tushar-deepsource/patch-1
• b1f3387 [7.4.x] #11091: documentation should use hypthonated properties (#11750)
• 2cdd619 Merge pull request #11747 from pytest-dev/backport-11711-to-7.4.x
• d06c05b [7.4.x] nodes: fix tracebacks from collection errors are not getting pruned
• 5582bfc [7.4.x] Improves clarity in Sphinx documentation for function signature. (#11...
• 13024ef [7.4.x] Fix for operation on closed file in faulthandler teardown (#11631)
• a40dacf [7.4.x] XFAIL TestLocalPath.test_make_numbered_dir_multiprocess_safe (#11616)
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Updates ipykernel from 6.27.1 to 6.28.0

Release notes

Sourced from ipykernel's releases.

v6.28.0

6.28.0

(Full Changelog)

Enhancements made

• Enable ProactorEventLoop on windows for ipykernel #1184 (@​NewUserHa)
• Adds a flag in debug_info for the copyToGlobals support #1099 (@​brichet)

Maintenance and upkeep improvements

• Support python 3.12 #1185 (@​blink1073)
• Bump actions/setup-python from 4 to 5 #1181 (@​dependabot)
• chore: update pre-commit hooks #1179 (@​pre-commit-ci)
• Refactor execute_request to reduce redundancy and improve consistency #1177 (@​jjvraw)

Documentation improvements

• Update pytest commands in README #1178 (@​ianthomas23)

Contributors to this release

(GitHub contributors page for this release)

@​blink1073 | @​brichet | @​dependabot | @​ianthomas23 | @​jjvraw | @​NewUserHa | @​pre-commit-ci

Changelog

Sourced from ipykernel's changelog.

6.28.0

(Full Changelog)

Enhancements made

• Enable ProactorEventLoop on windows for ipykernel #1184 (@​NewUserHa)
• Adds a flag in debug_info for the copyToGlobals support #1099 (@​brichet)

Maintenance and upkeep improvements

• Support python 3.12 #1185 (@​blink1073)
• Bump actions/setup-python from 4 to 5 #1181 (@​dependabot)
• chore: update pre-commit hooks #1179 (@​pre-commit-ci)
• Refactor execute_request to reduce redundancy and improve consistency #1177 (@​jjvraw)

Documentation improvements

• Update pytest commands in README #1178 (@​ianthomas23)

Contributors to this release

(GitHub contributors page for this release)

@​blink1073 | @​brichet | @​dependabot | @​ianthomas23 | @​jjvraw | @​NewUserHa | @​pre-commit-ci

Commits

• 69967dc Publish 6.28.0
• de45c7a Support python 3.12 (#1185)
• 07f7437 Enable ProactorEventLoop on windows for ipykernel (#1184)
• 4001f8a Adds a flag in debug_info for the copyToGlobals support (#1099)
• 6d18054 Bump actions/setup-python from 4 to 5 (#1181)
• e9ddcf5 chore: update pre-commit hooks (#1179)
• 6154ba3 Update pytest commands in README (#1178)
• e35e2f5 Refactor execute_request to reduce redundancy and improve consistency (#1177)
• See full diff in compare view

Updates importlib-metadata from 7.0.0 to 7.0.1

Changelog

Sourced from importlib-metadata's changelog.

v7.0.1

Bugfixes

• Corrected the interface for SimplePath to encompass the expectations of locate_file and PackagePath.
• Fixed type annotations to allow strings.

Commits

• f2e84e3 Finalize
• e9e9f77 Merge commit '98196a'
• 98196a7 Fixed type annotations to allow strings.
• f38e051 Add Python 3.13 to compatibility matrix. Ref python/cpython#113174.
• 0c1d32e Inline os.PathLike using future annotations.
• b99c9d6 Refine SimplePath to allow for os.PathLike on input and SimplePath on output.
• 200cf45 Merge pull request #480 from python/bugfix/distribution-simplepath
• ac243d3 Include _meta in docs to fix doc build failures.
• 1b3f272 Corrected the interface for SimplePath to encompass the expectations of locat...
• fc4df51 Rely on read_text and read_bytes from located paths.
• Additional commits viewable in compare view

Updates jupyter-core from 5.5.0 to 5.5.1

Release notes

Sourced from jupyter-core's releases.

v5.5.1

5.5.1

(Full Changelog)

Bugs fixed

• Account for read only file systems in migration #379 (@​blink1073)

Maintenance and upkeep improvements

• Update ruff and typings #376 (@​blink1073)
• chore: update pre-commit hooks #374 (@​pre-commit-ci)
• Clean up lint and add downstream checks #373 (@​blink1073)

Contributors to this release

(GitHub contributors page for this release)

@​blink1073 | @​mtelka | @​pre-commit-ci

Changelog

Sourced from jupyter-core's changelog.

5.5.1

(Full Changelog)

Bugs fixed

• Account for read only file systems in migration #379 (@​blink1073)

Maintenance and upkeep improvements

• Update ruff and typings #376 (@​blink1073)
• chore: update pre-commit hooks #374 (@​pre-commit-ci)
• Clean up lint and add downstream checks #373 (@​blink1073)

Contributors to this release

(GitHub contributors page for this release)

@​blink1073 | @​mtelka | @​pre-commit-ci

Commits

• 29a9aaa Publish 5.5.1
• 4e387a4 Account for read only file systems in migration (#379)
• 257b483 Update ruff and typings (#376)
• 6921356 chore: update pre-commit hooks (#374)
• 82f3e2a Clean up lint and add downstream checks (#373)
• See full diff in compare view

Updates prompt-toolkit from 3.0.42 to 3.0.43

Release notes

Sourced from prompt-toolkit's releases.

3.0.43

Fixes regression from 3.0.42:

• Fix regression on Pypy: Don't use ctypes.pythonapi to restore SIGINT if not available.

Other changes from 3.0.42:

• Fix line wrapping in patch_stdout on Windows.
• Make formatted_text.split_lines() accept an iterable instead of lists only.
• Disable the IPython workaround (from 3.0.41) for IPython >= 8.18.
• Restore signal.SIGINT handler between prompts

Changelog

Sourced from prompt-toolkit's changelog.

3.0.43: 2023-12-13

Fixes:

• Fix regression on Pypy: Don't use ctypes.pythonapi to restore SIGINT if not available.

Commits

• 4432d62 Release 3.0.43
• 6a24c99 Fix for pypy: don't use pythonapi on pypy.
• 1c6d094 Use Coroutine instead of Awaitable in type annotations where possible.
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Updates psutil from 5.9.6 to 5.9.7

Changelog

Sourced from psutil's changelog.

5.9.7

2023-12-17

Enhancements

• 2324_: enforce Ruff rule raw-string-in-exception, which helps providing clearer tracebacks when exceptions are raised by psutil.

Bug fixes

• 2325_, [PyPy]: psutil did not compile on PyPy due to missing PyErr_SetExcFromWindowsErrWithFilenameObject cPython API.

Commits

• 8e21684 pre-release
• 3080df4 make pre-release: check if psutil version already exists on PYPI
• 7c10295 micro optimization on python startup ("x in set" instead of "x in list")
• 4407540 Update README.rst (#2330)
• ccdb775 fix #2325: fix compilation on PyPy
• 902fada Enforce ruff rule raw-string-in-exception rule (#2324)
• e9dabbb Include <unistd.h> to avoid implicit-function-declaration for close and sysca...
• 0c3a1c5 users() / Linux: make ":0" -> "localhost" host conversion in C instead of python
• 1b94083 Merge branch 'master' of github.com:giampaolo/psutil
• a7205fc Linux C files refactoring (#2320)
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Updates setuptools from 69.0.2 to 69.0.3

Changelog

Sourced from setuptools's changelog.

v69.0.3

Bugfixes

• Retain valid names with underscores in egg_info.

Commits

• b07d2f5 Fix broken reference from changelog to PyPUG.
• e92440a Bump version: 69.0.2 → 69.0.3
• 5a2eb0c Merge pull request #4159 from pypa/bugfix/2522-retain-valid-name
• d0b0a4d Retain valid names with underscores in egg_info.
• dd5f15a Add attribution for #3659.
• 6bdc74f Merge https://github.com/jaraco/skeleton
• 97a5f44 Update Github Actions badge per actions/starter-workflows#1525.
• 8df868b Merge https://github.com/jaraco/skeleton
• 33dd012 Suppress deprecation warning in dateutil. Workaround for dateutil/dateutil#1284.
• 382e617 Temporarily disable deprecation enforcement (#4142)
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