Bump the pip group in /src with 20 updates

Bumps the pip group in /src with 20 updates:

| Package | From | To |
| --- | --- | --- |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.2` | `7.6.9` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.3` | `8.3.4` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `5.0.0` | `6.0.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.6.9` | `0.8.3` |
| [bokeh](https://github.com/bokeh/bokeh) | `3.6.0` | `3.6.2` |
| [certifi](https://github.com/certifi/python-certifi) | `2024.8.30` | `2024.12.14` |
| [cryptography](https://github.com/pyca/cryptography) | `43.0.1` | `44.0.0` |
| [markupsafe](https://github.com/pallets/markupsafe) | `3.0.1` | `3.0.2` |
| [networkx](https://github.com/networkx/networkx) | `3.4` | `3.4.2` |
| [numpy](https://github.com/numpy/numpy) | `2.1.2` | `2.2.0` |
| [pillow](https://github.com/python-pillow/Pillow) | `10.4.0` | `11.0.0` |
| [pycurl](https://github.com/pycurl/pycurl) | `7.45.3` | `7.45.4` |
| [pyopenssl](https://github.com/pyca/pyopenssl) | `24.2.1` | `24.3.0` |
| python-daemon | `3.0.1` | `3.1.2` |
| [setuptools](https://github.com/pypa/setuptools) | `75.1.0` | `75.6.0` |
| [six](https://github.com/benjaminp/six) | `1.16.0` | `1.17.0` |
| [wordcloud](https://github.com/amueller/word_cloud) | `1.9.3` | `1.9.4` |
| [ipython](https://github.com/ipython/ipython) | `8.28.2` | `8.30.0` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.5.2` | `1.6.0` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.4.1` | `6.4.2` |


Updates `coverage` from 7.6.2 to 7.6.9
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.6.2...7.6.9)

Updates `pytest` from 8.3.3 to 8.3.4
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.3...8.3.4)

Updates `pytest-cov` from 5.0.0 to 6.0.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v5.0.0...v6.0.0)

Updates `ruff` from 0.6.9 to 0.8.3
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.6.9...0.8.3)

Updates `bokeh` from 3.6.0 to 3.6.2
- [Changelog](https://github.com/bokeh/bokeh/blob/3.6.2/docs/CHANGELOG)
- [Commits](bokeh/bokeh@3.6.0...3.6.2)

Updates `certifi` from 2024.8.30 to 2024.12.14
- [Commits](certifi/python-certifi@2024.08.30...2024.12.14)

Updates `cryptography` from 43.0.1 to 44.0.0
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@43.0.1...44.0.0)

Updates `markupsafe` from 3.0.1 to 3.0.2
- [Release notes](https://github.com/pallets/markupsafe/releases)
- [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst)
- [Commits](pallets/markupsafe@3.0.1...3.0.2)

Updates `networkx` from 3.4 to 3.4.2
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.4...networkx-3.4.2)

Updates `numpy` from 2.1.2 to 2.2.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.1.2...v2.2.0)

Updates `pillow` from 10.4.0 to 11.0.0
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.4.0...11.0.0)

Updates `pycurl` from 7.45.3 to 7.45.4
- [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog)
- [Commits](https://github.com/pycurl/pycurl/commits)

Updates `pyopenssl` from 24.2.1 to 24.3.0
- [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst)
- [Commits](pyca/pyopenssl@24.2.1...24.3.0)

Updates `python-daemon` from 3.0.1 to 3.1.2

Updates `setuptools` from 75.1.0 to 75.6.0
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v75.1.0...v75.6.0)

Updates `six` from 1.16.0 to 1.17.0
- [Changelog](https://github.com/benjaminp/six/blob/main/CHANGES)
- [Commits](benjaminp/six@1.16.0...1.17.0)

Updates `wordcloud` from 1.9.3 to 1.9.4
- [Release notes](https://github.com/amueller/word_cloud/releases)
- [Changelog](https://github.com/amueller/word_cloud/blob/main/doc/changelog.rst)
- [Commits](amueller/word_cloud@1.9.3...1.9.4)

Updates `ipython` from 8.28.2 to 8.30.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/commits/8.30.0)

Updates `scikit-learn` from 1.5.2 to 1.6.0
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.5.2...1.6.0)

Updates `tornado` from 6.4.1 to 6.4.2
- [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.4.1...v6.4.2)

---
updated-dependencies:
- dependency-name: coverage
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pytest-cov
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: bokeh
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: certifi
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: cryptography
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: markupsafe
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: networkx
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pillow
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: pycurl
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pyopenssl
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: python-daemon
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: setuptools
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: six
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: wordcloud
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: tornado
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <[email protected]>

src/requirements-dev.txt

@@ -1,7 +1,7 @@
-coverage==7.6.2
-pytest==8.3.3
-pytest-cov==5.0.0
+coverage==7.6.9
+pytest==8.3.4
+pytest-cov==6.0.0
 pytest-recording==0.13.2
 requests-mock==1.12.1
-ruff==0.6.9
+ruff==0.8.3
 vcrpy==6.0.2

src/requirements.txt

@@ -1,44 +1,44 @@
 appdirs==1.4.4
 beautifulsoup4==4.12.3
 biopython==1.84
-bokeh==3.6.0
-certifi==2024.8.30
+bokeh==3.6.2
+certifi==2024.12.14
 chardet==5.2.0
 chart_studio==1.1.0
-cryptography==43.0.1
+cryptography==44.0.0
 decorator==5.1.1
 ete3==3.1.3
 html5lib==1.1
 idna==3.10
 jsonschema==4.23.0
 markdown==3.7
-markupsafe==3.0.1
+markupsafe==3.0.2
 ndg-httpsclient==0.5.1
-networkx==3.4
-numpy==2.1.2
+networkx==3.4.2
+numpy==2.2.0
 pexpect==4.9.0
 pickleshare==0.7.5
-pillow==10.4.0
+pillow==11.0.0
 plotly==5.24.1
 pyasn1==0.6.1
-pycurl==7.45.3
+pycurl==7.45.4
 pygments==2.18.0
-pyopenssl==24.2.1
-python-daemon==3.0.1
+pyopenssl==24.3.0
+python-daemon==3.1.2
 python-dateutil==2.9.0.post0
 qgrid==1.3.1
 rsa==4.9
 scipy==1.14.1
 seaborn==0.13.2
-setuptools==75.1.0
-six==1.16.0
+setuptools==75.6.0
+six==1.17.0
 sympy==1.13.3
 terminado==0.18.1
-wordcloud==1.9.3
+wordcloud==1.9.4
 
 # Narrative/Jupyter requirements
 clustergrammer2==0.18.0
-ipython==8.28.2
+ipython==8.30.0
 ipywidgets==8.1.5
 jinja2==3.1.4
 # N.b. notebook version must stay under 7
@@ -47,6 +47,6 @@ pandas==2.2.3
 pymongo==4.10.1
 pyyaml==6.0.2
 requests==2.32.3
-scikit-learn==1.5.2
+scikit-learn==1.6.0
 statsmodels==0.14.4
-tornado==6.4.1
+tornado==6.4.2