[dependabot]

Bumps the python-dependencies group with 7 updates in the / directory:

Package	From	To
curies	0.15.4	0.15.5
duckdb	1.5.6	2.0.0
pyoxigraph	0.5.12	0.5.13
pytest	9.1.1	9.2.0
snakemake	9.27.0	9.27.1
ruff	0.17.1	0.17.3
rumdl	0.3.0	0.3.2

Updates curies from 0.15.4 to 0.15.5

Commits

• e8186c0 Bump version: 0.15.5-dev → 0.15.5
• 5cb6710 Add regular expression for fully qualified CURIE (#248)
• 42d3597 Update CURIE regex (#247)
• aee3518 Bump version: 0.15.4 → 0.15.5-dev
• See full diff in compare view

Updates duckdb from 1.5.6 to 2.0.0

Release notes

Sourced from duckdb's releases.

DuckDB v2.0.0

duckdb-python 2.0.0 is the Python package for DuckDB 2.0. It supports Python >= 3.11 and drops Python 3.10. From Python 3.12 on, one wheel per platform serves every Python version. The binding layer was rewritten on nanobind, query results stream instead of being collected up front, the relational API was rebuilt on SQL text, and the way DataFrames, Arrow data and polars frames are read was replaced. Many long-standing bugs are fixed, and moving data in and out of Python is much faster. The engine is DuckDB 2.0.0; see its release notes for what changed in SQL and storage.

Highlights

• Moving data is much faster. Numeric exports to numpy, pandas, Arrow and polars take a quarter to two fifths of the 1.5 time; in-memory Arrow, polars and pandas 3 inputs are scanned on all threads, 8x to 20x faster; Arrow UDFs run about 20x faster; draining an Arrow reader on 16 threads takes an eighth of the time. (#693, #697, #700)
• Results stream. con.execute() starts the query and you read rows as you fetch them; con.complete() and con.abort() finish or cancel an open result, and an open result or Arrow reader owns the connection until it is done.
• The relational API is rebuilt on SQL text. A relation is a lazy query, bound at every step so its schema is known; rel.sql_query() shows exactly what will run. Many new methods and expression helpers (col, lit, when, window functions). One semantic change: a plain string in an expression is a value, not a column name. (#697)
• A new Appender for fast bulk inserts: with con.appender("t") as a: a.append_row(...), under a microsecond per row. (#661)
• One stable ABI wheel per platform for Python 3.12 and later, so a new Python release works on day one. Python 3.15 is supported. (#672, #673, #684)
• Arrow export on con.execute() results changed: fetch_arrow_table, fetch_record_batch and arrow(n) are gone; use con.sql(query).to_arrow_table() or .to_arrow_reader(). (#702)
• The experimental Spark API is brought up to date: it is now compatible with PySpark 4.2.0 and 3.5.9 (#686). We would love your input on whether to continue support or to drop it in future releases.

Upgrading from 1.x: what to check

1. Make sure you run Python 3.11 or later.
2. If you call fetch_arrow_table, fetch_record_batch, arrow(n) or pl() on the result of con.execute(), switch to con.sql(query).to_arrow_table(), to_arrow_reader() or pl(). Libraries that call the removed names on an execute result need an update. (#702)
3. If you call fetchone(), fetchmany(), fetch_df_chunk() or execute() on a relation, use rel.limit(n).fetchall(), rel.to_arrow_reader(), rel.materialize(), or run the query through con.execute(). (#697)
4. If you compare a relation column with a plain string, col("s") == "x" now compares with the text x. Wrap column names in col(). (#697)
5. If you rely on import duckdb having opened the default database, note that it happens on the first duckdb.sql() or duckdb.connect() call instead. (#680)
6. If you pass Decimal values with a positive exponent, such as Decimal("1E+2"), they now arrive as the number they denote, 100, where 1.5 produced 1.00. (#654)
7. If you write files with overwrite=False, an existing file is now refused instead of replaced. (#668)
8. If a test or script depends on str(rel) being free, note that it runs the query each time now.

Breaking changes

Arrow export on DB-API results (#702)

Results of con.execute() are now read row by row and are not kept in memory, so they cannot hand their data to Arrow for free. fetch_arrow_table, fetch_record_batch, arrow(rows_per_batch) and pl() on a DB-API result are removed; they had been deprecated. to_arrow_table() and to_arrow_reader() remain, also as duckdb.to_arrow_table() and duckdb.to_arrow_reader(), but they materialize the rows twice, once as the result and once as Arrow, and emit a UserWarning pointing at the relational path, con.sql(query).to_arrow_table(), which we recommend instead. The reader no longer streams: its first batch arrives after the whole query ran. After a partial fetchone or fetchmany the Arrow call returns the remaining rows instead of raising. With preserve_insertion_order off, the row order can differ between calls. duckdb.arrow(n) with an integer is gone; duckdb.arrow(arrow_object) still builds a relation.

# 1.5
table = con.execute("SELECT * FROM t").fetch_arrow_table()
reader = con.execute("SELECT * FROM t").fetch_record_batch(10_000)
2.0
table = con.sql("SELECT * FROM t").to_arrow_table()
reader = con.sql("SELECT * FROM t").to_arrow_reader(10_000)

Relations are SQL text (#697)

The relational API is a query building API, not an execution API. A relation is a piece of SQL text with a schema bound once when it is built, so every step knows its columns and types. It runs nothing until you ask for data, and it runs again on every read; rel.sql_query() returns exactly the text that runs, as one SELECT per group of steps and a common table expression where the order of clauses breaks. The engine's binder decides every column name and type; nothing is renamed by the client.

What you are most likely to notice:

• A bare string operand of an expression is a value, not a column. For one release a warning is raised when the string matches a column name; the warning goes in 2.1. A dotted string is not split into parts; pass the parts separately.

... (truncated)

Commits

• 83c7199 Build the dictionary test's indices with a 64 bit arange (#705)
• b12fd55 Build the dictionary test's indices with a 64 bit arange
• 6aa2ce3 Build the Linux and macOS wheels with clang and ThinLTO (#703)
• 2f0ac79 Pin submodule to v2.0.0 hash
• f7826ad Fix wrong values and lost parallelism in the pandas, numpy and Arrow input sc...
• 2f2a0dd Bring back to_arrow_table and to_arrow_reader on DB-API results over a re-fee...
• 6086a15 Keep the macOS wheels native, like the engine's release
• 07ee3e2 Build the Linux and macOS wheels with clang and ThinLTO
• a2c151f Register the linked extensions when the module loads, not only on import (#701)
• dd2a3e9 Read numpy masks a word at a time
• Additional commits viewable in compare view

Updates pyoxigraph from 0.5.12 to 0.5.13

Release notes

Sourced from pyoxigraph's releases.

v0.5.13

• SPARQL: improve join cost estimates and OPTIONAL planning to avoid quadratic scaling for joins on foreign keys.
• SPARQL: preserve input bindings during type inference for subqueries, fixing joins that lost their keys after a LATERAL subquery.
• SPARQL: allow for-loop left joins for nested OPTIONAL patterns while preserving input-dependent BIND expressions and conflicting bindings.
• RocksDB: fix copying read options with recent RocksDB versions.

Changelog

Sourced from pyoxigraph's changelog.

[0.5.13] - 2026-10-22

Fixed

• SPARQL: improve join cost estimates and OPTIONAL planning to avoid quadratic scaling for joins on foreign keys.
• SPARQL: preserve input bindings during type inference for subqueries, fixing joins that lost their keys after a LATERAL subquery.
• SPARQL: allow for-loop left joins for nested OPTIONAL patterns while preserving input-dependent BIND expressions and conflicting bindings.
• RocksDB: fix copying read options with recent RocksDB versions.

Commits

• 2837810 Releases v0.5.13
• e83d941 Wait for bulk loader workers before rollback cleanup
• 57b0d56 Fix oxrocksdb_readoptions_create_copy on recent RocksDB versions
• aadee62 sparopt: preserve input-dependent bindings when checking OPTIONAL rewrites
• 3cdb017 sparopt: fix three query optimization bugsOptimizer/1 fixes (#1986)
• c9ed035 CI: improve RocksDB installation script
• 6caac53 bugfix/optimizer: fix quadratic scaling of OPTIONAL in a JOIN on FK (#1733)
• See full diff in compare view

Updates pytest from 9.1.1 to 9.2.0

Release notes

Sourced from pytest's releases.

9.2.0

pytest 9.2.0 (2026-10-27)

Removals and backward incompatible breaking changes

• #14716: -c now raises a usage error for a path that does not exist, is a directory, or is in a format pytest has no loader for. Such paths were previously either ignored or reported as an unhandled FileNotFoundError.

• #8593: The indirect, ids and scope arguments of Metafunc.parametrize() <pytest.Metafunc.parametrize> -- and therefore of @pytest.mark.parametrize <pytest.mark.parametrize ref> -- are now keyword-only.

  Passing them positionally was a common source of confusing errors, e.g. parametrize("arg1", "arg2", [(1, 2)]) made the argvalues land in indirect and failed with indirect fixture '(1, 2)' doesn't exist; such mistakes now fail with an understandable TypeError. The type annotations have always declared these arguments as keyword-only.

• #993: Plugin import failures at startup are now reported and classified instead of escaping as a raw traceback with the accidental exit code 1:

  • a plugin that cannot be found -- via -p, pytest_plugins or PYTEST_PLUGINS -- exits with pytest.ExitCode USAGE_ERROR (4), like a conftest.py that fails to import;
  • a plugin that is found but raises while importing -- including a broken pytest11 entry point or a missing plugin dependency -- exits with pytest.ExitCode INTERNAL_ERROR (3), with the traceback preserved.

  pytest.main now returns these codes instead of raising ImportError. Also fixed an IndexError from pytest's own internals when the plugin raised an exception with no arguments.

Deprecations (removal in next major release)

• #14742: The private _pytest.python.CallSpec2 name has been renamed to CallSpec. The old CallSpec2 alias remains available for now and will be removed in pytest 10 or 11.

• #14755: Schedule yield_fixture decorator for removal in pytest 10 or 11.

• #14774: Similarly to the deprecation of class-scoped fixtures defined as instance methods in pytest 9.1, all higher-scoped fixtures (module, package, and session) defined as instance methods are now deprecated.

  They suffer from the same issue the original deprecation only fixed for class-scoped fixtures, see 10819 and 14011.

• #14808: Passing a non-string value to a string-typed ini option now emits a pytest.PytestRemovedIn10Warning. This affects [tool.pytest.ini_options] in pyproject.toml. In pytest 10 this will raise a TypeError, matching the behavior of the corresponding TOML config path.

• #7323: Passing bytes to TerminalReporter.write_line() is now deprecated, pass a str instead.

New features

• #14743: Full diff: now contains a legend explaining the + & - symbols in diff output.
• #2781: When strict_markers is enabled, marker names used in -m expressions are now validated against registered markers.
• #6881: Added the parametrize_long_str_id_strategy configuration option to control how long str/bytes parameter values are handled in auto-generated test IDs. Explicit IDs set via ids=[...] or pytest.param(..., id=...) are not affected. Available strategies: short (default, values over 100 chars fall back to argname+index), sha256 (SHA-256 hex digest), legacy (keep full value), and disallow (error requesting explicit IDs).

Improvements in existing functionality

• #10745: A RecursionError whose recursion origin cannot be located now shows only the first and last 10 stack frames, matching what pytest already did when locating the origin failed outright. Previously the full traceback -- often around a thousand near-identical frames -- was rendered, which was both slow and unreadable. Pass --full-trace to see every frame.

... (truncated)

Commits

• ae1d0ff Prepare release version 9.2.0
• 143ce31 pre-commit: exclude codespell on generated release announcements
• 532dc5f tox: add attrs dependency to regen, needed in reportingdemo.rst
• a7b2446 Merge pull request #15245 from pytest-dev/claude/project-thread-9jcf91
• 679d09c [pre-commit.ci] pre-commit autoupdate (#15266)
• 41d12cd docs: clarify typing for yield fixtures
• b9022ba Merge pull request #15182 from 1871698/docs/improve-getting-started-description
• 16f87a7 docs: improve getting-started.rst test execution description
• 082ed70 Merge pull request #15255 from pytest-dev/claude/project-thread-eoi3d6
• ae37a01 Merge pull request #15227 from pytest-dev/claude/project-thread-4etye4
• Additional commits viewable in compare view

Updates snakemake from 9.27.0 to 9.27.1

Release notes

Sourced from snakemake's releases.

v9.27.1

9.27.1 (2026-10-21)

Bug Fixes

• handle emudhra incident in dockerfile (1a8fa42)

Changelog

Sourced from snakemake's changelog.

9.27.1 (2026-10-21)

Bug Fixes

• handle emudhra incident in dockerfile (1a8fa42)

Commits

• f79d9eb chore(v9_backports): release 9.27.1 (#4350)
• 47136b3 release handling
• 1a8fa42 fix: handle emudhra incident in dockerfile
• See full diff in compare view

Updates ruff from 0.17.1 to 0.17.3

Release notes

Sourced from ruff's releases.

0.17.3

Release Notes

Released on 2026-10-26.

Preview features

• [suspicious] Add shared-clock-mock (#29074)

Bug fixes

• [pyupgrade] Avoid incorrect conversions to f-strings (UP032) (#25485)

Performance

• Buffer stdout in ruff format (#29631)
• Specialize ASCII identifier lexing (#29503)
• Speed up identifier and keyword lexing (#29463)

Documentation

• [flake8-bandit] Describe what the rule actually checks for httpx (S113) (#27936)

Contributors

• @​itsvedantkumar
• @​charliermarsh
• @​anishgirianish

Install ruff 0.17.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.17.3/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.17.3/ruff-installer.ps1 | iex"

Download ruff 0.17.3

File	Platform	Checksum
ruff-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
ruff-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
ruff-aarch64-pc-windows-msvc.zip	ARM64 Windows	checksum

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.3

Released on 2026-10-26.

Preview features

• [suspicious] Add shared-clock-mock (#29074)

Bug fixes

• [pyupgrade] Avoid incorrect conversions to f-strings (UP032) (#25485)

Performance

• Buffer stdout in ruff format (#29631)
• Specialize ASCII identifier lexing (#29503)
• Speed up identifier and keyword lexing (#29463)

Documentation

• [flake8-bandit] Describe what the rule actually checks for httpx (S113) (#27936)

Contributors

• @​itsvedantkumar
• @​charliermarsh
• @​anishgirianish

0.17.2

Released on 2026-10-22.

Preview features

• [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

• Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
• [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
• [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
• [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
• [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

• Avoid intermediate names in lint name resolution (#29506)
• Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
• Share postfix parsing and reduce expression copies (#29480)

... (truncated)

Commits

• ba65abf Bump version to 0.17.3 (#29745)
• fb2f921 [ty] Fix narrowing of strings and integers compared with enum members (#29743)
• d181287 [ty] Index nominal union alternatives (#29196)
• 07872ad [ty] Preserve string literals in comparisons with LiteralString (#29741)
• 95888b2 [ty] Preserve narrowing after guarded match subject captures (#29558)
• 3c8166b [ty] Fix hang when negating recursive unions of instance types (#29652)
• 3fd20e0 [ty] Preserve generic callback specializations during return refinement (#29667)
• 2f0a29e [ty] Record predicate truthiness alongside expression inference (#29706)
• 60f104a [ty] Honor @​override on overload implementations in stubs (#29470)
• 207ec3a [ty] Add diagnostic baseline support (#27636)
• Additional commits viewable in compare view

Updates rumdl from 0.3.0 to 0.3.2

Release notes

Sourced from rumdl's releases.

v0.3.2

Fixed

• Upgrade pulldown-cmark to fix exponential parser event growth and duplicate diagnostics after empty wikilink labels (RUSTSEC-2026-0414), and upgrade Tokio to address its I/O safety advisory (RUSTSEC-2026-0386). Release publication now requires a fresh dependency security audit, including during recovery runs.

• MD087 recognizes inline suppression of heading-capitalization diagnostics, avoiding false unused-disable warnings (#973).

• MD022 enforces configured spacing below headings before lists and code fences, including when MD031 or MD032 is disabled. Overlapping spacing fixes insert the required blank lines only once (#971).

• MD067 can safely reorder complete footnote definitions to match their first references. Reordering is atomic, preserves surrounding content and directive scope, and leaves ambiguous Markdown or MDX cases report-only (#969).

• MD013 recognizes additional common abbreviations and titles, including numeric references with formatted numbers, while preserving sentence boundaries after ambiguous units and labels. Sentence-spacing checks share this behavior (#966).

• MD013 preserves meaningful indentation inside multiline code spans following a bare list marker when reflowing text.

• security: patch parser dependencies and gate release publication (41d60e1)

• ci: install only the tools required by parity checks (ce014aa)

• MD013: preserve code-span indentation after bare list markers (9cf648f)

Downloads

File	Platform	Checksum
rumdl-v0.3.2-x86_64-unknown-linux-gnu.tar.gz	Linux x86_64	checksum
rumdl-v0.3.2-x86_64-unknown-linux-musl.tar.gz	Linux x86_64 (musl)	checksum
rumdl-v0.3.2-aarch64-unknown-linux-gnu.tar.gz	Linux ARM64	checksum
rumdl-v0.3.2-aarch64-unknown-linux-musl.tar.gz	Linux ARM64 (musl)	checksum
rumdl-v0.3.2-x86_64-apple-darwin.tar.gz	macOS x86_64	checksum
rumdl-v0.3.2-aarch64-apple-darwin.tar.gz	macOS ARM64 (Apple Silicon)	checksum
rumdl-v0.3.2-x86_64-pc-windows-msvc.zip	Windows x86_64	checksum

Installation

Using uv (Recommended)

uv tool install rumdl

Using pip

pip install rumdl

... (truncated)

Changelog

Sourced from rumdl's changelog.

0.3.2 - 2026-10-28

Fixed

• Upgrade pulldown-cmark to fix exponential parser event growth and duplicate diagnostics after empty wikilink labels (RUSTSEC-2026-0414), and upgrade Tokio to address its I/O safety advisory (RUSTSEC-2026-0386). Release publication now requires a fresh dependency security audit, including during recovery runs.

• MD087 recognizes inline suppression of heading-capitalization diagnostics, avoiding false unused-disable warnings (#973).

• MD022 enforces configured spacing below headings before lists and code fences, including when MD031 or MD032 is disabled. Overlapping spacing fixes insert the required blank lines only once (#971).

• MD067 can safely reorder complete footnote definitions to match their first references. Reordering is atomic, preserves surrounding content and directive scope, and leaves ambiguous Markdown or MDX cases report-only (#969).

• MD013 recognizes additional common abbreviations and titles, including numeric references with formatted numbers, while preserving sentence boundaries after ambiguous units and labels. Sentence-spacing checks share this behavior (#966).

• MD013 preserves meaningful indentation inside multiline code spans following a bare list marker when reflowing text.

• security: patch parser dependencies and gate release publication (41d60e1)

• ci: install only the tools required by parity checks (ce014aa)

• MD013: preserve code-span indentation after bare list markers (9cf648f)

0.3.1 - 2026-10-27

Added

• rumdl check-assets reports assets unreferenced in complete Markdown source scans, with explicit include/keep globs and text or versioned JSON output. Literal filename mentions are kept separately; incomplete scans emit no findings.
• MD022 lines-above-mode = "exact" removes surplus blank lines above headings while preserving comments and the existing minimum-spacing default (#838).
• Opt-in code-block tool version verification against uv.lock, declared pyproject.toml constraints, or pre-commit/prek hook revisions for Ruff, Black, djLint and SQLFluff. Supports automatic source selection and one configurable policy for mismatched or unresolved versions.
• MD013 link-text-punctuation = "trailing" optionally recognizes sentence endings in link text and image alt text while keeping each construct intact. When enabled, semantic reflow also preserves detected sentence boundaries when merging short lines.
• MD063 style = "consistent" infers heading capitalization per document while respecting ignored words, proper names, level filters, and inline disables.
• Independent code blocks can share the existing worker pool when error policies permit parallel execution, preserving tool order and applying formatted replacements together from their original source ranges.
• MD013 break-words adds project-specific or localized words to the semantic reflow defaults, with case-insensitive Unicode matching.

... (truncated)

Commits

• 1e0f1d1 chore: refresh release preparation for v0.3.2
• 41d60e1 fix(security): patch parser dependencies and gate release publication
• ce014aa fix(ci): install only the tools required by parity checks
• 9cf648f fix(MD013): preserve code-span indentation after bare list markers
• 0422ba6 chore: refresh release preparation for v0.3.2
• 5ac78e0 chore: bump version to v0.3.2
• 62791bf fix: harden heading spacing, footnote ordering, and abbreviations
• 0e8d8b8 fix: preserve suppression accounting across lint paths
• 9b8161e chore: refresh release preparation for v0.3.1
• 56cffdb chore: bump version to v0.3.1
• Additional commits viewable in compare view

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