Update all Python dependencies to latest versions

Notable updates: cryptography 46.0.7 (fixes 3 Dependabot alerts),
cffi 2.0.0, Flask-Limiter 4.1.1, gunicorn 25.3.0, pytest 9.0.3,
SQLAlchemy 2.0.49, IPython 8.39.0, pylint 4.0.5, mypy 1.20.1.

Author: Nils Bars

ref-docker-base/pyproject.toml

@@ -5,29 +5,29 @@ description = "Docker base image dependencies for REF"
 requires-python = ">=3.10"
 dependencies = [
     "backcall==0.2.0",
-    "blinker==1.7.0",
-    "cerberus==1.3.7",
-    "chardet==5.2.0",
+    "blinker==1.9.0",
+    "cerberus==1.3.8",
+    "chardet==7.4.3",
     "distro==1.9.0",
-    "importlib-resources==6.5.2",
-    "ipython==8.31.0",
+    "importlib-resources==7.1.0",
+    "ipython==8.39.0",
     "itsdangerous==2.2.0",
-    "lazy-object-proxy==1.10.0",
-    "matplotlib==3.10.0",
-    "mypy==1.14.1",
-    "oauthlib==3.2.2",
-    "opencv-python==4.11.0.86",
+    "lazy-object-proxy==1.12.0",
+    "matplotlib==3.10.8",
+    "mypy==1.20.1",
+    "oauthlib==3.3.1",
+    "opencv-python==4.13.0.92",
     "pathlib2==2.3.7.post1",
     "pickleshare==0.7.5",
-    "pwntools==4.14.0",
-    "pyjwt==2.7.0",
-    "pylint==3.3.4",
-    "pyyaml==6.0.1",
-    "requests-unixsocket==0.3.0",
-    "tomli==2.2.1",
-    "tqdm==4.67.1",
-    "wrapt==1.17.2",
-    "zipp==3.21.0",
+    "pwntools==4.15.0",
+    "pyjwt==2.12.1",
+    "pylint==4.0.5",
+    "pyyaml==6.0.3",
+    "requests-unixsocket==0.4.1",
+    "tomli==2.4.1",
+    "tqdm==4.67.3",
+    "wrapt==2.1.2",
+    "zipp==3.23.1",
 ]
 
 [tool.uv]