From ad5b9ded219d0e1a2200170f4a41749447f63ccf Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Jan 2026 09:04:23 +0000 Subject: [PATCH] Bump the pip group across 1 directory with 37 updates Bumps the pip group with 37 updates in the /src directory: | Package | From | To | | --- | --- | --- | | [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.13.3` | `4.14.3` | | [biopython](https://github.com/biopython/biopython) | `1.85` | `1.86` | | [bokeh](https://github.com/bokeh/bokeh) | `3.6.2` | `3.8.1` | | [certifi](https://github.com/certifi/python-certifi) | `2025.1.31` | `2025.11.12` | | [cryptography](https://github.com/pyca/cryptography) | `44.0.1` | `46.0.3` | | [idna](https://github.com/kjd/idna) | `3.10` | `3.11` | | [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.23.0` | `4.25.1` | | [markdown](https://github.com/Python-Markdown/markdown) | `3.7` | `3.10` | | [markupsafe](https://github.com/pallets/markupsafe) | `3.0.2` | `3.0.3` | | [networkx](https://github.com/networkx/networkx) | `3.4.2` | `3.6.1` | | [numpy](https://github.com/numpy/numpy) | `2.2.3` | `2.4.0` | | [pillow](https://github.com/python-pillow/Pillow) | `11.1.0` | `12.0.0` | | [plotly](https://github.com/plotly/plotly.py) | `5.24.1` | `6.5.0` | | [pycurl](https://github.com/pycurl/pycurl) | `7.45.4` | `7.45.7` | | [pygments](https://github.com/pygments/pygments) | `2.19.1` | `2.19.2` | | [pyopenssl](https://github.com/pyca/pyopenssl) | `25.0.0` | `25.3.0` | | [rsa](https://github.com/sybrenstuvel/python-rsa) | `4.9` | `4.9.1` | | [scipy](https://github.com/scipy/scipy) | `1.15.2` | `1.16.3` | | [setuptools](https://github.com/pypa/setuptools) | `75.8.2` | `80.9.0` | | [sympy](https://github.com/sympy/sympy) | `1.13.3` | `1.14.0` | | [wordcloud](https://github.com/amueller/word_cloud) | `1.9.4` | `1.9.5` | | [ipython](https://github.com/ipython/ipython) | `8.33.0` | `9.8.0` | | [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.5` | `8.1.8` | | [jinja2](https://github.com/pallets/jinja) | `3.1.5` | `3.1.6` | | [pandas](https://github.com/pandas-dev/pandas) | `2.2.3` | `2.3.3` | | [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.11.1` | `4.15.5` | | [pyyaml](https://github.com/yaml/pyyaml) | `6.0.2` | `6.0.3` | | [requests](https://github.com/psf/requests) | `2.32.3` | `2.32.5` | | [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.6.1` | `1.8.0` | | [statsmodels](https://github.com/statsmodels/statsmodels) | `0.14.4` | `0.14.6` | | [tornado](https://github.com/tornadoweb/tornado) | `6.4.2` | `6.5.4` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.6.12` | `7.13.1` | | [pytest](https://github.com/pytest-dev/pytest) | `8.3.4` | `9.0.2` | | [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `6.0.0` | `7.0.0` | | [pytest-recording](https://github.com/kiwicom/pytest-recording) | `0.13.2` | `0.13.4` | | [ruff](https://github.com/astral-sh/ruff) | `0.9.9` | `0.14.10` | | [vcrpy](https://github.com/kevin1024/vcrpy) | `7.0.0` | `8.1.0` | Updates `beautifulsoup4` from 4.13.3 to 4.14.3 Updates `biopython` from 1.85 to 1.86 - [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst) - [Commits](https://github.com/biopython/biopython/commits) Updates `bokeh` from 3.6.2 to 3.8.1 - [Changelog](https://github.com/bokeh/bokeh/blob/3.8.1/docs/CHANGELOG) - [Commits](https://github.com/bokeh/bokeh/compare/3.6.2...3.8.1) Updates `certifi` from 2025.1.31 to 2025.11.12 - [Commits](https://github.com/certifi/python-certifi/compare/2025.01.31...2025.11.12) Updates `cryptography` from 44.0.1 to 46.0.3 - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pyca/cryptography/compare/44.0.1...46.0.3) Updates `idna` from 3.10 to 3.11 - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](https://github.com/kjd/idna/compare/v3.10...v3.11) Updates `jsonschema` from 4.23.0 to 4.25.1 - [Release notes](https://github.com/python-jsonschema/jsonschema/releases) - [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst) - [Commits](https://github.com/python-jsonschema/jsonschema/compare/v4.23.0...v4.25.1) Updates `markdown` from 3.7 to 3.10 - [Release notes](https://github.com/Python-Markdown/markdown/releases) - [Changelog](https://github.com/Python-Markdown/markdown/blob/master/docs/changelog.md) - [Commits](https://github.com/Python-Markdown/markdown/compare/3.7...3.10.0) Updates `markupsafe` from 3.0.2 to 3.0.3 - [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/3.0.2...3.0.3) Updates `networkx` from 3.4.2 to 3.6.1 - [Release notes](https://github.com/networkx/networkx/releases) - [Commits](https://github.com/networkx/networkx/compare/networkx-3.4.2...networkx-3.6.1) Updates `numpy` from 2.2.3 to 2.4.0 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.2.3...v2.4.0) Updates `pillow` from 11.1.0 to 12.0.0 - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](https://github.com/python-pillow/Pillow/compare/11.1.0...12.0.0) Updates `plotly` from 5.24.1 to 6.5.0 - [Release notes](https://github.com/plotly/plotly.py/releases) - [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md) - [Commits](https://github.com/plotly/plotly.py/compare/v5.24.1...v6.5.0) Updates `pycurl` from 7.45.4 to 7.45.7 - [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog) - [Commits](https://github.com/pycurl/pycurl/commits) Updates `pygments` from 2.19.1 to 2.19.2 - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](https://github.com/pygments/pygments/compare/2.19.1...2.19.2) Updates `pyopenssl` from 25.0.0 to 25.3.0 - [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pyca/pyopenssl/compare/25.0.0...25.3.0) Updates `rsa` from 4.9 to 4.9.1 - [Changelog](https://github.com/sybrenstuvel/python-rsa/blob/main/CHANGELOG.md) - [Commits](https://github.com/sybrenstuvel/python-rsa/commits) Updates `scipy` from 1.15.2 to 1.16.3 - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.15.2...v1.16.3) Updates `setuptools` from 75.8.2 to 80.9.0 - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](https://github.com/pypa/setuptools/compare/v75.8.2...v80.9.0) Updates `sympy` from 1.13.3 to 1.14.0 - [Release notes](https://github.com/sympy/sympy/releases) - [Commits](https://github.com/sympy/sympy/compare/sympy-1.13.3...sympy-1.14.0) Updates `wordcloud` from 1.9.4 to 1.9.5 - [Release notes](https://github.com/amueller/word_cloud/releases) - [Changelog](https://github.com/amueller/word_cloud/blob/main/doc/changelog.rst) - [Commits](https://github.com/amueller/word_cloud/compare/1.9.4...1.9.5) Updates `ipython` from 8.33.0 to 9.8.0 - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](https://github.com/ipython/ipython/compare/8.33.0...9.8.0) Updates `ipywidgets` from 8.1.5 to 8.1.8 - [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases) - [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.5...8.1.8) Updates `jinja2` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.5...3.1.6) Updates `pandas` from 2.2.3 to 2.3.3 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.2.3...v2.3.3) Updates `pymongo` from 4.11.1 to 4.15.5 - [Release notes](https://github.com/mongodb/mongo-python-driver/releases) - [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst) - [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.11.1...4.15.5) Updates `pyyaml` from 6.0.2 to 6.0.3 - [Release notes](https://github.com/yaml/pyyaml/releases) - [Changelog](https://github.com/yaml/pyyaml/blob/6.0.3/CHANGES) - [Commits](https://github.com/yaml/pyyaml/compare/6.0.2...6.0.3) Updates `requests` from 2.32.3 to 2.32.5 - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](https://github.com/psf/requests/compare/v2.32.3...v2.32.5) Updates `scikit-learn` from 1.6.1 to 1.8.0 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.6.1...1.8.0) Updates `statsmodels` from 0.14.4 to 0.14.6 - [Release notes](https://github.com/statsmodels/statsmodels/releases) - [Changelog](https://github.com/statsmodels/statsmodels/blob/main/CHANGES.md) - [Commits](https://github.com/statsmodels/statsmodels/compare/v0.14.4...v0.14.6) Updates `tornado` from 6.4.2 to 6.5.4 - [Changelog](https://github.com/tornadoweb/tornado/blob/v6.5.4/docs/releases.rst) - [Commits](https://github.com/tornadoweb/tornado/compare/v6.4.2...v6.5.4) Updates `coverage` from 7.6.12 to 7.13.1 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.6.12...7.13.1) Updates `pytest` from 8.3.4 to 9.0.2 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/8.3.4...9.0.2) Updates `pytest-cov` from 6.0.0 to 7.0.0 - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v6.0.0...v7.0.0) Updates `pytest-recording` from 0.13.2 to 0.13.4 - [Release notes](https://github.com/kiwicom/pytest-recording/releases) - [Changelog](https://github.com/kiwicom/pytest-recording/blob/master/docs/changelog.rst) - [Commits](https://github.com/kiwicom/pytest-recording/compare/v0.13.2...v0.13.4) Updates `ruff` from 0.9.9 to 0.14.10 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.9.9...0.14.10) Updates `vcrpy` from 7.0.0 to 8.1.0 - [Release notes](https://github.com/kevin1024/vcrpy/releases) - [Changelog](https://github.com/kevin1024/vcrpy/blob/master/docs/changelog.rst) - [Commits](https://github.com/kevin1024/vcrpy/compare/v7.0.0...v8.1.0) --- updated-dependencies: - dependency-name: beautifulsoup4 dependency-version: 4.14.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: biopython dependency-version: '1.86' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: bokeh dependency-version: 3.8.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: certifi dependency-version: 2025.11.12 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: cryptography dependency-version: 46.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip - dependency-name: idna dependency-version: '3.11' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: jsonschema dependency-version: 4.25.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: markdown dependency-version: '3.10' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: markupsafe dependency-version: 3.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: networkx dependency-version: 3.6.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: numpy dependency-version: 2.4.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: pillow dependency-version: 12.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip - dependency-name: plotly dependency-version: 6.5.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip - dependency-name: pycurl dependency-version: 7.45.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: pygments dependency-version: 2.19.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: pyopenssl dependency-version: 25.3.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: rsa dependency-version: 4.9.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: scipy dependency-version: 1.16.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: setuptools dependency-version: 80.9.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip - dependency-name: sympy dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: wordcloud dependency-version: 1.9.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: ipython dependency-version: 9.8.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip - dependency-name: ipywidgets dependency-version: 8.1.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: jinja2 dependency-version: 3.1.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: pandas dependency-version: 2.3.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: pymongo dependency-version: 4.15.5 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: pyyaml dependency-version: 6.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: requests dependency-version: 2.32.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: scikit-learn dependency-version: 1.8.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: statsmodels dependency-version: 0.14.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip - dependency-name: tornado dependency-version: 6.5.4 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip - dependency-name: coverage dependency-version: 7.13.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: pip - dependency-name: pytest dependency-version: 9.0.2 dependency-type: direct:development update-type: version-update:semver-major dependency-group: pip - dependency-name: pytest-cov dependency-version: 7.0.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: pip - dependency-name: pytest-recording dependency-version: 0.13.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: pip - dependency-name: ruff dependency-version: 0.14.10 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: pip - dependency-name: vcrpy dependency-version: 8.1.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: pip ... Signed-off-by: dependabot[bot] --- src/requirements-dev.txt | 12 ++++---- src/requirements.txt | 62 ++++++++++++++++++++-------------------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/src/requirements-dev.txt b/src/requirements-dev.txt index eaf0f3a922..6f97019530 100644 --- a/src/requirements-dev.txt +++ b/src/requirements-dev.txt @@ -1,7 +1,7 @@ -coverage==7.6.12 -pytest==8.3.4 -pytest-cov==6.0.0 -pytest-recording==0.13.2 +coverage==7.13.1 +pytest==9.0.2 +pytest-cov==7.0.0 +pytest-recording==0.13.4 requests-mock==1.12.1 -ruff==0.9.9 -vcrpy==7.0.0 +ruff==0.14.10 +vcrpy==8.1.0 diff --git a/src/requirements.txt b/src/requirements.txt index f57d4fbb42..340d5335e9 100644 --- a/src/requirements.txt +++ b/src/requirements.txt @@ -1,52 +1,52 @@ appdirs==1.4.4 -beautifulsoup4==4.13.3 -biopython==1.85 -bokeh==3.6.2 -certifi==2025.1.31 +beautifulsoup4==4.14.3 +biopython==1.86 +bokeh==3.8.1 +certifi==2025.11.12 chardet==5.2.0 chart_studio==1.1.0 -cryptography==44.0.1 +cryptography==46.0.3 decorator==5.2.1 ete3==3.1.3 html5lib==1.1 -idna==3.10 -jsonschema==4.23.0 -markdown==3.7 -markupsafe==3.0.2 +idna==3.11 +jsonschema==4.25.1 +markdown==3.10 +markupsafe==3.0.3 ndg-httpsclient==0.5.1 -networkx==3.4.2 -numpy==2.2.3 +networkx==3.6.1 +numpy==2.4.0 pexpect==4.9.0 pickleshare==0.7.5 -pillow==11.1.0 -plotly==5.24.1 +pillow==12.0.0 +plotly==6.5.0 pyasn1==0.6.1 -pycurl==7.45.4 -pygments==2.19.1 -pyopenssl==25.0.0 +pycurl==7.45.7 +pygments==2.19.2 +pyopenssl==25.3.0 python-daemon==3.1.2 python-dateutil==2.9.0.post0 qgrid==1.3.1 -rsa==4.9 -scipy==1.15.2 +rsa==4.9.1 +scipy==1.16.3 seaborn==0.13.2 -setuptools==75.8.2 +setuptools==80.9.0 six==1.17.0 -sympy==1.13.3 +sympy==1.14.0 terminado==0.18.1 -wordcloud==1.9.4 +wordcloud==1.9.5 # Narrative/Jupyter requirements clustergrammer2==0.18.0 -ipython==8.33.0 -ipywidgets==8.1.5 -jinja2==3.1.5 +ipython==9.8.0 +ipywidgets==8.1.8 +jinja2==3.1.6 # N.b. notebook version must stay under 7 notebook==6.5.7 -pandas==2.2.3 -pymongo==4.11.1 -pyyaml==6.0.2 -requests==2.32.3 -scikit-learn==1.6.1 -statsmodels==0.14.4 -tornado==6.4.2 +pandas==2.3.3 +pymongo==4.15.5 +pyyaml==6.0.3 +requests==2.32.5 +scikit-learn==1.8.0 +statsmodels==0.14.6 +tornado==6.5.4