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build(jupyter): bump the uv-deps group across 1 directory with 11 updates - #187

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Bumps the uv-deps group with 11 updates in the /apps/cogstack-jupyter-hub directory:

Package From To
cogstack-es[os] 0.2.0 0.3.0
virtualenv 21.13.0 21.14.13
py7zr 1.1.3 1.1.4
isort 9.0.1 9.0.2
simplejson 4.1.2 4.2.0
nltk 3.10.3 3.10.4
pymssql 2.4.2 2.4.5
mysql-connector-python 26.7.0 26.10.0
jsonpickle 4.1.2 4.1.4
neo4j 6.3.1 6.4.1
ruff 0.16.9 0.17.2

Updates cogstack-es[os] from 0.2.0 to 0.3.0

Release notes

Sourced from cogstack-es[os]'s releases.

MedCAT den v0.3.0

Minor release.

Most notably difference is the addition of additional API to the den.

What's Changed

Full Changelog: CogStack/cogstack-nlp@medcat-den/v0.2.1...medcat-den/v0.3.0

cogstack-es/v0.3.0

Minor release to allow better data streaming.

What's Changed

Full Changelog: CogStack/cogstack-nlp@cogstack-es/v0.2.0...cogstack-es/v0.3.0

Commits
  • 09cb9ebCogStack/MedCAT2#46
  • 9e83d31CogStack/MedCAT2#62
  • 3b71d2cCogStack/MedCAT2#64
  • ecfc507 Fix test regarding installed dependencies - use lower case dep names (CogStac...
  • cf5cfb1CogStack/MedCAT2#60
  • d3d8a5eCogStack/MedCAT2#59
  • 31cfc78CogStack/MedCAT2#58
  • 62ad0e1CogStack/MedCAT2#57
  • 5967e99CogStack/MedCAT2#56
  • 9f28e8d Avoid resetting subnames upon model load - it is unnecessary (CogStack/MedCAT...
  • Additional commits viewable in compare view

Updates virtualenv from 21.13.0 to 21.14.13

Release notes

Sourced from virtualenv's releases.

21.14.13

Security

  • Stop bash running commands from --prompt or an environment name containing $(...), backticks or a backslash after shopt -s promptvars, set -o posix, or in a child shell that inherits an exported PS1 (GHSA-cx6f-vjhg-g3cc); reported by @​rozzkml. zsh now draws the prompt from psvar[9], which is never parsed as shell syntax. (#3466) by @​gaborbernat.
  • Write the .venv redirect and the wheel RECORD with exclusive create, so a link planted after the existence check cannot redirect the write. On POSIX, replace a read-only .venv redirect that points at a virtualenv. (#3466) by @​gaborbernat.

🐍 PyPI release

📜 Full Changelog

21.14.12

Packaging

  • Upgrade the embedded setuptools wheel from 84.0.0 to 84.2.1 and the embedded pip wheel from 26.2.1 to 26.2.2. (#3452)

New Contributors

🐍 PyPI release

📜 Full Changelog

21.14.11

Bug fixes

  • Search all directories supplied by repeated --extra-search-dir options instead of keeping only the last group. (#3440) by @​repzakske.
  • On Windows, the app data is now migrated into the nested cache directory instead of the migration failing with a warning on every run. (#3441) by @​gaborbernat and @​XXXXXQ-0206.

🐍 PyPI release

📜 Full Changelog

21.14.10

Bug fixes

  • Always copy seed packages when app-data is temporary, including when symlink seeding is enabled through an environment variable or configuration file. Seeded packages remain available after temporary cache cleanup. (#3437) by @​gaborbernat.

🐍 PyPI release

📜 Full Changelog

... (truncated)

Changelog

Sourced from virtualenv's changelog.

################# Release History #################

.. towncrier-draft-entries:: [UNRELEASED DRAFT]

.. towncrier release notes start

.. _release-21-15-1:

21.15.1 (2026-10-28)

.. _release-21-15-1-fixed:

Fixed

  • Keep the name of a seeded console_scripts entry that contains digits but does not end in a version, such as python3-config or 2to3, instead of truncating it at the first digit; python3-config overwrote the environment's python executable (:pr:3451) by :user:JingHao-Leon and :user:gaborbernat.
  • Copy the content of a symlinked directory when a tree is copied into an environment, instead of dropping it (:pr:3454) by :user:JingHao-Leon and :user:gaborbernat.
  • Count each -v, -q, -p and --try-first-with option once instead of once per internal parsing pass, so Session.verbosity is 3 rather than 9 for a single -v (:pr:3457) by :user:darrenhuai and :user:gaborbernat.
  • Copy the seed packages instead of failing when VIRTUALENV_SYMLINK_APP_DATA or symlink_app_data in the config file turns on symlink seeding on a host that cannot create symlinks, such as Windows without the symlink privilege (:pr:3465) by :user:darrenhuai and :user:gaborbernat.
  • Run the interpreter that collects the target debug information (-vv output and Creator.debug) without PYTHONPATH and with the environment passed to cli_run, so the reported sys.path no longer lists the caller's PYTHONPATH entries (:pr:3474) by :user:RaphaelFakhri and :user:gaborbernat.

.. _release-21-15-0:

21.15.0 (2026-10-27)

.. _release-21-15-0-added:

Added

  • Bundle dependencies for Python 3.15 in the standalone zipapp and stop bundling Python 3.8, which is outside the package's supported range (:pr:3458) by :user:gaborbernat.

.. _release-21-15-0-packaging:

... (truncated)

Commits
  • 6accbd5 release 21.14.13
  • 3598e20 🐛 fix(bash): escape the prompt for every PS1 state (#3466)
  • f6512a5 release 21.14.12
  • b535726 [pre-commit.ci] pre-commit autoupdate (#3455)
  • 7e32366 Fix broken pip and code review links in the docs (#3460)
  • 632e56f Upgrade embedded pip/setuptools/wheel and CI test tools (#3452)
  • a8bd1a9 chore(deps): bump certifi from 2026.7.22 to 2026.10.19 in /tasks (#3462)
  • c82323b chore(deps): bump uv from 0.13.0 to 0.13.4 in /tasks (#3461)
  • 863ae6c chore(deps): bump the runtime-dependencies group with 3 updates (#3456)
  • 79537b3 👷 ci: pin App token action v3.3.0 (#3449)
  • Additional commits viewable in compare view

Updates py7zr from 1.1.3 to 1.1.4

Release notes

Sourced from py7zr's releases.

Fix multiple Vulnerbilities and bugs

Changelog

Sourced from py7zr's changelog.

v1.1.4_

Security

  • Fix arbitrary file write above the extraction directory via a symlink chain (incomplete fix of CVE-2026-23879, GHSA-jwx8-hv8g-gjjq).
    • canonical_path() cancelled .. lexically before any symlink was resolved, so link/.. was treated as the directory holding link instead of the parent of its target. A chain of symlink members extracted from the same archive could therefore redirect a later write an archive-chosen number of levels above the extraction directory, while the member name still reduced to something apparently inside it.
    • Containment is now decided on the real path: symlink components are followed first and .. is normalized only afterwards. This also covers symlink targets, which may legitimately contain .. and so cannot be rejected by name.
    • Archive member names containing a .. component are now rejected outright.
  • Fix memory exhaustion when opening a crafted archive header (GHSA-6pr6-cqpq-x889).
  • Fix extraction hang on a crafted COPY stream (GHSA-v999-q5cj-95jg).

Users are encouraged to upgrade. Details will be published in the corresponding security advisories.

Fixed

  • Raise PasswordRequired when an archive is opened in write or append mode with a crypto filter (e.g. FILTER_CRYPTO_AES256_SHA256) but no password, instead of failing later with an AttributeError. The check also covers direct use of SevenZipCompressor. (#723, #739)
  • Limit concurrent extraction workers for non-solid archives to os.cpu_count(), instead of starting one thread or process per folder. When the limit is reached, the oldest task is joined before a new one starts. (#630, #740)
  • Fix AttributeError in archiveinfo() for archives with no compressed content, such as an empty archive or one containing only empty files or directories. _get_method_names(), _is_solid() and archiveinfo() now handle header.main_streams being None. (#665, #741)
  • Fix intermittent false negatives in the relative-path check on Windows. Path.resolve() may or may not return the extended-length prefix (\\?\), and when only one of the compared paths had it, the relative_to check always failed. The prefix is now stripped before comparison. (#714, #743)
  • Fix io.UnsupportedOperation in extract() and extractall() when a WriterFactory returns a non-seekable handle, such as one from zipfile.ZipFile.open. The unnecessary seek(0) after decompression is removed, and MemIO.close() now rewinds only

... (truncated)

Commits
  • c717d21 Release version 1.1.4 to fix multiple vulnerabilities and bugs
  • c51e4f6 Merge commit from fork
  • f4204fa Merge commit from fork
  • 5c78459 Merge commit from fork
  • 23610d1 fix: raise Bad7zFile when decompression makes no progress
  • f3e4862 fix: enhance path sanitization and symlink resolution to prevent directory tr...
  • e41864c docs: update SECURITY.rst with threat model, hardening measures, and regressi...
  • 8ff8a30 docs: add guidelines for writing and organizing security regression tests
  • 0a3c81e tests: add malformed header tests into test_badheaders.py and enhance coverage
  • 3e37932 feat: add boundary checks for truncated reads in read_byte, read_uint64, ...
  • Additional commits viewable in compare view

Updates isort from 9.0.1 to 9.0.2

Release notes

Sourced from isort's releases.

9.0.2

🪲 Fixes

Other changes

Full Changelog: PyCQA/isort@9.0.1...9.0.2

Commits
  • 9f90561 Core developers revision
  • 4371472 Fix a "security" issue
  • e74b4ba Do some formatting and setting updates
  • 539abb1 Bump the uv group with 15 updates
  • 0482160 Fully type check tests and modernize code
  • bbda474 Bump pypa/cibuildwheel from 4.2.0 to 4.2.1 in the github-actions group
  • 1fd0701 Agent Host changes for agents/dependabot-monthly-updates-uv
  • 6911091 Always split on parsed.line_separator
  • 3808b70 Keep CRLF regression cases beside existing check-mode tests
  • 3202ce8 Preserve CRLF blank lines during float-to-top preprocessing
  • Additional commits viewable in compare view

Updates simplejson from 4.1.2 to 4.2.0

Release notes

Sourced from simplejson's releases.

v4.2.0

What's Changed

New Contributors

Full Changelog: simplejson/simplejson@v4.1.2...v4.2.0

Changelog

Sourced from simplejson's changelog.

Version 4.2.0 released 2026-10-02

  • Start building wheels for Python 3.15 and drop Python 3.8 support via upgrade to cibuildwheel v4.2.0 simplejson/simplejson#385
  • Build and test riscv64 Linux wheels on native RISE runners simplejson/simplejson#389
  • The C scanner now reports the same error message as the pure Python decoder for an invalid first key in an object simplejson/simplejson#388
  • int_as_string_bitcount now supports thresholds of 64 bits and above (including 128-bit integers) in both the C and pure Python encoders; the C encoder previously rejected them simplejson/simplejson#387
  • Circular references introduced through for_json() or _asdict() now raise ValueError("Circular reference detected") instead of recursing without bound simplejson/simplejson#390
  • CI now tests Python 3.15 (including free-threaded 3.15t), PyPy 3.12, CPython 3.14.8 debug builds, and uses current GitHub Actions and cibuildwheel v4.2.1 simplejson/simplejson#386

Version 4.1.2 released 2026-08-26

Version 4.1.1 released 2026-04-24

  • The build_wheels_py27 CI job now also builds Python 2.7 wheels for Windows AMD64 and Windows x86, joining the existing Py2.7 manylinux1 / manylinux2010 x86_64 wheels. This unblocks offline / --no-index installs on Py2.7-on-Windows (the original reporter's case), which previously had no matching binary wheel on PyPI, fell through to the sdist, and failed on the PEP 517 isolated-build step complaining that setuptools>=42 was not in the wheelhouse. simplejson/simplejson#377

Version 4.1.0 released 2026-04-22

  • The C extension now accelerates encoding when indent= is set.

... (truncated)

Commits
  • 0ace7d1 Prep for v4.2.0 - Update CHANGES and build matrix (#386)
  • c3edf28 ci: build and test riscv64 wheels (#389)
  • 41f8017 Check circular references introduced by custom JSON methods (#390)
  • 48e7c3b Support large integer stringification thresholds in both encoders (#387)
  • 50cadb6 Use the first-key error message in the C scanner (#388)
  • fbc057f Start building CPython 3.15 wheels (#385)
  • See full diff in compare view

Updates nltk from 3.10.3 to 3.10.4

Release notes

Sourced from nltk's releases.

v3.10.4

Version 3.10.4 2026-10-20

This release routes every file path, archive, download, URL fetch and external program through one sandbox that keeps reads and writes inside the trusted data directories, refuses path traversal, symlink escapes and decompression bombs, blocks requests to internal network addresses, and runs Java and other third-party tools only from trusted absolute locations with validated options and input. Pickled models now load through a restricted unpickler, XML and JSON parsing are hardened, and regular expressions, recursion and slow algorithms in the tokenizers, parsers, stemmers and corpus readers are bounded against denial-of-service input. Text that NLTK writes to the terminal, to CSV files, to the WordNet browser and to third-party tool input is sanitized against injection.

Security changes you may notice

Every refusal below raises with a message that starts with "Security Violation" and names the check, so a failure is easy to search for (PR #3877).

  • Data directories (nltk.pathsec, nltk.data): corpora, models and every other resource are read and written only inside the directories listed in nltk.data.path. A path that leaves a data root, a symlink that points out of one, and a NUL byte or encoded traversal in a resource name are refused. A data root, or a directory on the way to a resource, that another account can write to is skipped with a warning naming the directory and the remedy. Keep private data in a private directory and add it to nltk.data.path; /tmp is not a data root. Model save and load methods (perceptron, maxent, named-entity chunker, Weka, crf, hunpos, Stanford) accept destinations inside a data root only (PR #3797, #3753, #3850, #3761, #3755, #3759, #3760, #3763, #3806, #3807, #3808, #3809, #3813, #3814, #3815, #3848, #3851, #3852, #3853, #3863, #3871, #3888, #3945, #3961, #3969, #3981)
  • Downloader: downloaded package archives stay private to the installing account (0600). An install another account must read is extracted: a download made as root or outside the installing account's home extracts on its own, and nltk.download(..., extract=True) / python -m nltk.downloader --extract (or --no-extract) decide explicitly. This also unpacks the packages the index leaves zipped (wordnet, omw-1.4 ...); the extracted files are readable by every account and are found before the archive. find() names an archive it cannot read and says how to extract it instead of reporting it "not found". The downloader installs only into directories no other account can write to, treats an archive another account owns or can write to as stale and downloads it afresh, extracts only from an archive no other account could have changed since its checksum was verified, bounds the size of what it fetches, and refuses index entries and archive members that would write outside the package directory (PR #3929, #3804, #3850, #3778)
  • Pickles: nltk.data.load(..., format="pickle") reconstructs plain data only; a pickle that names any class or function is refused. Model loaders that need classes use an explicit allowlist of audited globals, so a gadget such as os.system can never be reconstructed from a model file. chat80 shelve values load the same way (PR #3794, #3754, #3757, #3802, #3817, #3823, #3824)
  • XML, JSON and YAML: nltk.xmlsec refuses any document that declares an entity or references an external one (billion-laughs, external-entity and DTD attacks) and bounds the tree depth, and every corpus XML view, the downloader index, Toolbox and internals parse through it. JSON resources load with a depth and size bound; YAML (the markdown corpus front matter and nltk.data.load(..., format="yaml")) loads through a bounded safe loader. Oversized or too deeply nested input raises ValueError naming the limit (PR #3754, #3805, #3828, #3933, #3972, #3974)
  • Regular expressions (nltk.redos): every regular expression NLTK compiles, including one you pass to RegexpTokenizer, RegexpStemmer, RegexpParser, re_show, TokenSearcher.findall, tgrep, nltk.help tag-set lookups and the concordance and nemo GUIs, now goes through nltk.redos on the regex engine. A pattern longer than 100,000 characters, nested more than 100 deep, with more than 1,000 capturing groups or an excessive repetition product is refused with nltk.redos.error, a subclass of re.error; a match that runs longer than nltk.redos.DEFAULT_TIMEOUT (5 seconds) raises TimeoutError instead of hanging. Patterns keep re syntax; match objects are the regex engine's (PR #3825, #3829, #3830, #3831, #3832, #3833, #3834, #3835, #3836, #3837, #3838, #3839, #3840, #3841, #3842, #3843, #3844, #3845, #3846, #3796, #3801, #3906, #3907, #3908, #3910)
  • Regular expressions made linear: the leading-run and re-anchoring patterns that a timeout cannot catch were rewritten or bounded in the word, Treebank, blankline, TextTiling, toktok and syllable tokenizers, the readline of corpus streams, the CoNLL SRL, TIMIT, senseval, pl196x, NKJP, Alpino, YCOE, IEER, ACE, VerbNet, reviews and Lin readers, relextract, the valuation parser, the CCG lexicon parser, dependency grammars and chomsky_normal_form, each verified on the real corpus (PR #3947, #3934, #3932, #3938, #3935, #3933, #3869, #3944, #3911, #3909, #3953, #3895)
  • Size, depth and time bounds: trees deeper than nltk.tree.MAX_TREE_DEPTH (500), WordNet and other relation walks deeper than nltk.util.MAX_RECURSION_DEPTH (500), tgrep deeper than 50, Toolbox deeper than 500, dependency graphs deeper than 200, are refused with ValueError naming the limit rather than exhausting the stack, and the stemmers, distance metrics, skipgrams, parsers and grammar transforms run in linear or bounded time with identical output for legitimate input. chart_parse stops after nltk.parse.chart.DEFAULT_MAX_TIME (5 seconds of wall-clock, needed only for feature grammars; max_time=None disables it). Tree.repr no longer recurses, so a deep accepted tree prints (PR #3827, #3885, #3895, #3767, #3784, #3917, #3958, #3960, #3977)
  • External tools and Java: a tool binary is resolved from an absolute path or a trusted search path only, never from the current directory; the binary, its directory and the model and data files handed to it must not be writable by another account (symlinked and multi-call executables such as a packaged Graphviz dot are supported). java() accepts a main class as the first argument only (no -jar, @​argfile or .java source file), validates its options against an allowlist, and loads jars only from a data root unless NLTK_ALLOW_UNSAFE_JARS=1 opts out with a warning. CoreNLP server options are allowlisted. Stanford, Malt, Senna, hunpos, Prover9, megam, TADM, Weka and crf wrappers validate their paths and the text they pipe to the tool against line and argument injection (PR #3772, #3771, #3975, #3743, #3782, #3788, #3768, #3798, #3887, #3858, #3950, #3951, #3812, #3816, #3868, #3894, #3941, #3850, #3925)
  • Network: the downloader, nltk.data.load of a URL and the CHILDES reader fetch through pathsec.urlopen, which refuses addresses that are not globally routable (loopback, private, link-local and multicast, including tunnelled and obfuscated forms), pins the validated address for the connection, allows file:// with a local authority only, and refuses a proxied fetch unless NLTK_ALLOW_PROXIED_URLOPEN=1 (or nltk.pathsec.ALLOW_PROXIED_FETCH = True) asserts the proxy is trusted. The CoreNLP client talks to its local server with requests and is not affected (PR #3847, #3810, #3750, #3850)
  • Terminal, CSV, DOT and HTML output: every print in the library goes through nltk.termsec.safe_print, which renders control characters, escape sequences and unbalanced bidi overrides from corpus text as visible \xNN escapes instead of letting them reach the terminal. The CSV files the twitter and sentiment helpers write neutralise formula-leading and control-sequence cells, AlignedSent DOT labels are escaped, the WordNet browser escapes corpus text, and nltk.data.load's verbose output no longer prints the full resource URL (PR #3914, #3915, #3937, #3946, #3931, #3930, #3856, #3902)
  • Corpus stores and encodings: the PanLex Lite and chat80 sqlite stores open read-only on a pinned descriptor with their schema screened and a statement step budget, chat80 shelves are read by a key manifest, Toolbox SFM markers are sanitised, and a resource encoding that is not a text codec (bz2_codec and friends) is refused (PR #3961, #3964, #3959, #3888, #3800, #3962)
  • Package contents: the wheel no longer ships nltk.test.unit (the attack harnesses, advisory probes and their fixtures), so pip install nltk is about half the size and import nltk.test.unit works from a source checkout or the sdist only. The doctests under nltk.test still ship (PR #3954)

Security test and CI infrastructure

Other changes

  • Added RTL language syntactic tree visualization support (PR #3472)
  • Fix #3394: Ensure punkt_tab is downloaded when punkt is requested (PR #3505)
  • Show README.md as the PyPI long description (PR #3746)
  • Add stopwords.words("english-extended") (PR #3747)
  • Krippendorff's alpha: treat placeholder labels as missing data (#2865, #2732) (PR #3752)
  • Fix shared defaults in chat80 Concept (PR #3773)
  • Fix Java wrappers decoding str output from java() (universal_newlines) (PR #3777)
  • Prevent IndexError in Hungarian stemmer on empty string (PR #3785)
  • Isolate MTE tag filters per view (PR #3792)
  • Fix newline in ellipsis tokens in TweetTokenizer (PR #3819)
  • Isolate default WordNet reference relations (PR #3872)
  • Fix resolution paths that cancel distinct literals (PR #3878)
  • Fix UTF-8 text preprocessing in NKJP corpus reader (PR #3879)
  • Remove shadowed FeatStruct._walk stub and preserve its docstring (PR #3893)
  • Count all increasing pairs in RIBES kendall_tau (PR #3900)
  • Fix the TweetTokenizer ZWJ emoji pattern capturing adjacent whitespace (PR #3913)
  • Surface the CoreNLP server's reason for a non-2xx answer (PR #3942)
  • Omit unaligned (NULL target) pairs from Alignment strings, so IBM model output prints (PR #3967)
  • Fix DependencyGraph cycle detection, which returned False on every parsed graph (PR #3978)
  • Show, range and draw an alignment with an unaligned pair on every surface (PR #3987)

Thanks to the following contributors to 3.10.4: Zhewen Tan, Yanhaoxi, Yazan Balawneh (Cystack.ps),

... (truncated)

Changelog

Sourced from nltk's changelog.

Version 3.10.4 2026-10-20

This release routes every file path, archive, download, URL fetch and external program through one sandbox that keeps reads and writes inside the trusted data directories, refuses path traversal, symlink escapes and decompression bombs, blocks requests to internal network addresses, and runs Java and other third-party tools only from trusted absolute locations with validated options and input. Pickled models now load through a restricted unpickler, XML and JSON parsing are hardened, and regular expressions, recursion and slow algorithms in the tokenizers, parsers, stemmers and corpus readers are bounded against denial-of-service input. Text that NLTK writes to the terminal, to CSV files, to the WordNet browser and to third-party tool input is sanitized against injection.

Security changes you may notice

Every refusal below raises with a message that starts with "Security Violation" and names the check, so a failure is easy to search for (PR #3877).

  • Data directories (nltk.pathsec, nltk.data): corpora, models and every other resource are read and written only inside the directories listed in nltk.data.path. A path that leaves a data root, a symlink that points out of one, and a NUL byte or encoded traversal in a resource name are refused. A data root, or a directory on the way to a resource, that another account can write to is skipped with a warning naming the directory and the remedy. Keep private data in a private directory and add it to nltk.data.path; /tmp is not a data root. Model save and load methods (perceptron, maxent, named-entity chunker, Weka, crf, hunpos, Stanford) accept destinations inside a data root only (PR #3797, #3753, #3850, #3761, #3755, #3759, #3760, #3763, #3806, #3807, #3808, #3809, #3813, #3814, #3815, #3848, #3851, #3852, #3853, #3863, #3871, #3888, #3945, #3961, #3969, #3981)
  • Downloader: downloaded package archives stay private to the installing account (0600). An install another account must read is extracted: a download made as root or outside the installing account's home extracts on its own, and nltk.download(..., extract=True) / python -m nltk.downloader --extract (or --no-extract) decide explicitly. This also unpacks the packages the index leaves zipped (wordnet, omw-1.4 ...); the extracted files are readable by every account and are found before the archive. find() names an archive it cannot read and says how to extract it instead of reporting it "not found". The downloader installs only into directories no other account can write to, treats an archive another account owns or can write to as stale and downloads it afresh, extracts only from an archive no other account could have changed since its checksum was verified, bounds the size of what it fetches, and refuses index entries and archive members that would write outside the package directory (PR #3929, #3804, #3850, #3778)
  • Pickles: nltk.data.load(..., format="pickle") reconstructs plain data only; a pickle that names any class or function is refused. Model loaders that need classes use an explicit allowlist of audited globals, so a gadget such as os.system can never be reconstructed from a model file. chat80 shelve values load the same way (PR #3794, #3754, #3757, #3802, #3817, #3823, #3824)
  • XML, JSON and YAML: nltk.xmlsec refuses any document that declares an entity or references an external one (billion-laughs, external-entity and DTD attacks) and bounds the tree depth, and every corpus XML view, the downloader index, Toolbox and internals parse through it. JSON resources load with a depth and size bound; YAML (the markdown corpus front matter and nltk.data.load(..., format="yaml")) loads through a bounded safe loader. Oversized or too deeply nested input raises ValueError naming the limit (PR #3754, #3805,

@dependabot
build(jupyter): bump the uv-deps group across 1 directory with 11 upd…
617a8e0 
…ates

Bumps the uv-deps group with 11 updates in the /apps/cogstack-jupyter-hub directory:

| Package | From | To |
| --- | --- | --- |
| [cogstack-es[os]](https://github.com/CogStack/cogstack-nlp) | `0.2.0` | `0.3.0` |
| [virtualenv](https://github.com/pypa/virtualenv) | `21.13.0` | `21.14.13` |
| [py7zr](https://github.com/miurahr/py7zr) | `1.1.3` | `1.1.4` |
| [isort](https://github.com/PyCQA/isort) | `9.0.1` | `9.0.2` |
| [simplejson](https://github.com/simplejson/simplejson) | `4.1.2` | `4.2.0` |
| [nltk](https://github.com/nltk/nltk) | `3.10.3` | `3.10.4` |
| [pymssql](https://github.com/pymssql/pymssql) | `2.4.2` | `2.4.5` |
| [mysql-connector-python](https://github.com/mysql/mysql-connector-python) | `26.7.0` | `26.10.0` |
| [jsonpickle](https://github.com/jsonpickle/jsonpickle) | `4.1.2` | `4.1.4` |
| [neo4j](https://github.com/neo4j/neo4j-python-driver) | `6.3.1` | `6.4.1` |
| [ruff](https://github.com/astral-sh/ruff) | `0.16.9` | `0.17.2` |



Updates `cogstack-es[os]` from 0.2.0 to 0.3.0
- [Release notes](https://github.com/CogStack/cogstack-nlp/releases)
- [Commits](CogStack/cogstack-nlp@MedCAT2/v0.2.0...MedCAT2/v0.3.0)

Updates `virtualenv` from 21.13.0 to 21.14.13
- [Release notes](https://github.com/pypa/virtualenv/releases)
- [Changelog](https://github.com/pypa/virtualenv/blob/main/docs/changelog.rst)
- [Commits](pypa/virtualenv@21.13.0...21.14.13)

Updates `py7zr` from 1.1.3 to 1.1.4
- [Release notes](https://github.com/miurahr/py7zr/releases)
- [Changelog](https://github.com/miurahr/py7zr/blob/master/docs/Changelog.rst)
- [Commits](miurahr/py7zr@v1.1.3...v1.1.4)

Updates `isort` from 9.0.1 to 9.0.2
- [Release notes](https://github.com/PyCQA/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](PyCQA/isort@9.0.1...9.0.2)

Updates `simplejson` from 4.1.2 to 4.2.0
- [Release notes](https://github.com/simplejson/simplejson/releases)
- [Changelog](https://github.com/simplejson/simplejson/blob/main/CHANGES.txt)
- [Commits](simplejson/simplejson@v4.1.2...v4.2.0)

Updates `nltk` from 3.10.3 to 3.10.4
- [Release notes](https://github.com/nltk/nltk/releases)
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](nltk/nltk@v3.10.3...v3.10.4)

Updates `pymssql` from 2.4.2 to 2.4.5
- [Release notes](https://github.com/pymssql/pymssql/releases)
- [Changelog](https://github.com/pymssql/pymssql/blob/master/ChangeLog.rst)
- [Commits](pymssql/pymssql@v2.4.2...v2.4.5)

Updates `mysql-connector-python` from 26.7.0 to 26.10.0
- [Changelog](https://github.com/mysql/mysql-connector-python/blob/trunk/CHANGES.txt)
- [Commits](mysql/mysql-connector-python@26.7.0...26.10.0)

Updates `jsonpickle` from 4.1.2 to 4.1.4
- [Release notes](https://github.com/jsonpickle/jsonpickle/releases)
- [Changelog](https://github.com/jsonpickle/jsonpickle/blob/v4.1.4/CHANGES.rst)
- [Commits](jsonpickle/jsonpickle@v4.1.2...v4.1.4)

Updates `neo4j` from 6.3.1 to 6.4.1
- [Release notes](https://github.com/neo4j/neo4j-python-driver/releases)
- [Changelog](https://github.com/neo4j/neo4j-python-driver/blob/6.x/CHANGELOG.md)
- [Commits](neo4j/neo4j-python-driver@6.3.1...6.4.1)

Updates `ruff` from 0.16.9 to 0.17.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.9...0.17.2)

---
updated-dependencies:
- dependency-name: cogstack-es[os]
  dependency-version: 0.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
- dependency-name: virtualenv
  dependency-version: 21.14.13
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
- dependency-name: py7zr
  dependency-version: 1.1.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv-deps
- dependency-name: isort
  dependency-version: 9.0.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv-deps
- dependency-name: simplejson
  dependency-version: 4.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
- dependency-name: nltk
  dependency-version: 3.10.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv-deps
- dependency-name: pymssql
  dependency-version: 2.4.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv-deps
- dependency-name: mysql-connector-python
  dependency-version: 26.10.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
- dependency-name: jsonpickle
  dependency-version: 4.1.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv-deps
- dependency-name: neo4j
  dependency-version: 6.4.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
- dependency-name: ruff
  dependency-version: 0.17.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv-deps
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Oct 28, 2026
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