From 6714f739f318dae29affa8df75839b2cdc92add8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Oct 2026 03:37:37 +0000 Subject: [PATCH] deps: bump the python group across 1 directory with 8 updates Bumps the python group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [werkzeug](https://github.com/pallets/werkzeug) | `3.1.8` | `3.1.9` | | [markupsafe](https://github.com/pallets/markupsafe) | `3.0.3` | `3.0.4` | | [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.18.2` | `4.18.3` | | [pycparser](https://github.com/eliben/pycparser) | `3.0` | `3.1` | | [openai](https://github.com/openai/openai-python) | `3.19.2` | `3.26.1` | | [openai-agents](https://github.com/openai/openai-agents-python) | `0.22.3` | `0.23.1` | | [pytz](https://github.com/stub42/pytz) | `2026.4` | `2026.5` | | [wrapt](https://github.com/GrahamDumpleton/wrapt) | `2.4.1` | `2.5.0` | Updates `werkzeug` from 3.1.8 to 3.1.9 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/werkzeug/compare/3.1.8...3.1.9) Updates `markupsafe` from 3.0.3 to 3.0.4 - [Release notes](https://github.com/pallets/markupsafe/releases) - [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/markupsafe/compare/3.0.3...3.0.4) Updates `pymongo` from 4.18.2 to 4.18.3 - [Release notes](https://github.com/mongodb/mongo-python-driver/releases) - [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.18.3/doc/changelog.rst) - [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.18.2...4.18.3) Updates `pycparser` from 3.0 to 3.1 - [Release notes](https://github.com/eliben/pycparser/releases) - [Commits](https://github.com/eliben/pycparser/compare/release_v3.00...release_v3.01) Updates `openai` from 3.19.2 to 3.26.1 - [Release notes](https://github.com/openai/openai-python/releases) - [Changelog](https://github.com/openai/openai-python/blob/main/CHANGELOG.md) - [Commits](https://github.com/openai/openai-python/compare/v3.19.2...v3.26.1) Updates `openai-agents` from 0.22.3 to 0.23.1 - [Release notes](https://github.com/openai/openai-agents-python/releases) - [Changelog](https://github.com/openai/openai-agents-python/blob/main/CHANGELOG.md) - [Commits](https://github.com/openai/openai-agents-python/compare/v0.22.3...v0.23.1) Updates `pytz` from 2026.4 to 2026.5 - [Release notes](https://github.com/stub42/pytz/releases) - [Commits](https://github.com/stub42/pytz/compare/release_2026.4...release_2026.5) Updates `wrapt` from 2.4.1 to 2.5.0 - [Release notes](https://github.com/GrahamDumpleton/wrapt/releases) - [Changelog](https://github.com/GrahamDumpleton/wrapt/blob/develop/docs/changes.rst) - [Commits](https://github.com/GrahamDumpleton/wrapt/compare/2.4.1...2.5.0) --- updated-dependencies: - dependency-name: werkzeug dependency-version: 3.1.9 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: markupsafe dependency-version: 3.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: pymongo dependency-version: 4.18.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: pycparser dependency-version: '3.1' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python - dependency-name: openai dependency-version: 3.26.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python - dependency-name: openai-agents dependency-version: 0.23.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python - dependency-name: pytz dependency-version: '2026.5' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python - dependency-name: wrapt dependency-version: 2.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python ... Signed-off-by: dependabot[bot] --- requirements.txt | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/requirements.txt b/requirements.txt index 8be5864d..2ae818ad 100644 --- a/requirements.txt +++ b/requirements.txt @@ -50,9 +50,9 @@ # blinker is new here: Flask 2.3 made signals unconditional, so it is a hard # dependency rather than the optional extra it used to be. Flask==3.1.3 -Werkzeug==3.1.8 +Werkzeug==3.1.9 Jinja2==3.1.6 -MarkupSafe==3.0.3 +MarkupSafe==3.0.4 itsdangerous==2.2.0 click==8.5.0 blinker==1.9.0 @@ -67,7 +67,7 @@ uWSGI==2.0.31 # pymongo 4 is required, not optional: the deployment runs MongoDB 7, and # pymongo 3.11 speaks wire-protocol opcodes MongoDB removed in 5.1. See # src/tests/test_pymongo4_compat.py. -pymongo==4.18.2 +pymongo==4.18.3 # --- Scientific stack --- numpy==2.4.6 @@ -101,7 +101,7 @@ cssselect2==0.10.1 webencodings==0.6.1 defusedxml==0.7.1 cffi==2.1.1 -pycparser==3.0 +pycparser==3.1 # --- HTTP --- # requests is imported by AdminTools/DBManager.py and scripts/downloadReactome.py @@ -132,8 +132,8 @@ requests==2.34.2 chardet==5.2.0 # --- AI interpretation pipeline (src/classes/AIInterpret/) --- -openai==3.19.2 -openai-agents==0.22.3 +openai==3.26.1 +openai-agents==0.23.1 # Imported directly by AIInterpret/agent.py (Timeout for the SDK client, # HTTPError while iterating a completion stream -- openai wraps only the # initial request, so a mid-stream failure arrives as a raw transport error). @@ -172,7 +172,7 @@ setuptools<85 APScheduler==3.11.3 psutil==7.2.2 python-dateutil==2.9.0.post0 -pytz==2026.4 +pytz==2026.5 # Moves as a pair with APScheduler: 3.11.3 requires tzlocal>=3.0, and tzlocal 3 # returns a zoneinfo where 2.x returned a pytz tzinfo. Safe here because the # tree never calls .localize() or get_localzone() itself -- it hands APScheduler @@ -184,5 +184,5 @@ six==1.17.0 # dead weight that only stayed invisible because the modules reaching it are # not on the request path. statsmodels 0.15.0 also pulls formulaic, which # imports wrapt directly. -wrapt==2.4.1 +wrapt==2.5.0 scriptinep3==0.3.1