Update deps

Author: moshi4

requirements-dev.lock

@@ -12,18 +12,14 @@
 -e file:.
 asttokens==2.4.1
     # via stack-data
-astunparse==1.6.3
-    # via griffe
 attrs==24.2.0
     # via jsonschema
     # via referencing
 babel==2.16.0
     # via mkdocs-material
-backcall==0.2.0
-    # via ipython
 beautifulsoup4==4.12.3
     # via nbconvert
-biopython==1.83
+biopython==1.84
     # via pymsaviz
 black==24.8.0
 bleach==6.1.0
@@ -43,7 +39,7 @@ colorama==0.4.6
     # via mkdocs-material
 comm==0.2.2
     # via ipykernel
-contourpy==1.1.1
+contourpy==1.3.0
     # via matplotlib
 coverage==7.6.1
     # via pytest-cov
@@ -58,6 +54,7 @@ defusedxml==0.7.1
 distlib==0.3.8
     # via virtualenv
 exceptiongroup==1.2.2
+    # via ipython
     # via pytest
 executing==2.1.0
     # via stack-data
@@ -69,7 +66,7 @@ fonttools==4.53.1
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-griffe==1.2.0
+griffe==1.3.0
     # via mkdocstrings-python
 identify==2.6.0
     # via pre-commit
@@ -82,15 +79,13 @@ importlib-metadata==8.4.0
     # via mkdocs-get-deps
     # via mkdocstrings
     # via nbconvert
-importlib-resources==6.4.4
-    # via jsonschema
-    # via jsonschema-specifications
+importlib-resources==6.4.5
     # via matplotlib
 iniconfig==2.0.0
     # via pytest
 ipykernel==6.29.5
     # via mkdocs-jupyter
-ipython==8.12.3
+ipython==8.18.1
     # via ipykernel
 jedi==0.19.1
     # via ipython
@@ -133,12 +128,12 @@ markupsafe==2.1.5
     # via mkdocs-autorefs
     # via mkdocstrings
     # via nbconvert
-matplotlib==3.7.5
+matplotlib==3.9.2
     # via pymsaviz
 matplotlib-inline==0.1.7
     # via ipykernel
     # via ipython
-mdit-py-plugins==0.4.1
+mdit-py-plugins==0.4.2
     # via jupytext
 mdurl==0.1.2
     # via markdown-it-py
@@ -157,7 +152,7 @@ mkdocs-autorefs==1.2.0
     # via mkdocstrings-python
 mkdocs-get-deps==0.2.0
     # via mkdocs
-mkdocs-jupyter==0.24.8
+mkdocs-jupyter==0.25.0
 mkdocs-material==9.5.34
     # via mkdocs-jupyter
 mkdocs-material-extensions==1.3.1
@@ -180,7 +175,7 @@ nest-asyncio==1.6.0
     # via ipykernel
 nodeenv==1.9.1
     # via pre-commit
-numpy==1.24.4
+numpy==2.0.2
     # via biopython
     # via contourpy
     # via matplotlib
@@ -203,21 +198,17 @@ pathspec==0.12.1
     # via mkdocs
 pexpect==4.9.0
     # via ipython
-pickleshare==0.7.5
-    # via ipython
 pillow==10.4.0
     # via matplotlib
-pkgutil-resolve-name==1.3.10
-    # via jsonschema
-platformdirs==4.3.1
+platformdirs==4.3.2
     # via black
     # via jupyter-core
     # via mkdocs-get-deps
     # via mkdocstrings
     # via virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==3.5.0
+pre-commit==3.8.0
 prompt-toolkit==3.0.47
     # via ipython
 psutil==6.0.0
@@ -236,15 +227,13 @@ pymdown-extensions==10.9
     # via mkdocstrings
 pyparsing==3.1.4
     # via matplotlib
-pytest==8.3.2
+pytest==8.3.3
     # via pytest-cov
 pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
     # via ghp-import
     # via jupyter-client
     # via matplotlib
-pytz==2024.1
-    # via babel
 pyyaml==6.0.2
     # via jupytext
     # via mkdocs
@@ -270,7 +259,6 @@ rpds-py==0.20.0
 ruff==0.6.4
 six==1.16.0
     # via asttokens
-    # via astunparse
     # via bleach
     # via python-dateutil
 soupsieve==2.6
@@ -305,15 +293,13 @@ urllib3==2.2.2
     # via requests
 virtualenv==20.26.4
     # via pre-commit
-watchdog==4.0.2
+watchdog==5.0.2
     # via mkdocs
 wcwidth==0.2.13
     # via prompt-toolkit
 webencodings==0.5.1
     # via bleach
     # via tinycss2
-wheel==0.44.0
-    # via astunparse
 zipp==3.20.1
     # via importlib-metadata
     # via importlib-resources

requirements.lock

@@ -10,21 +10,21 @@
 #   universal: false
 
 -e file:.
-biopython==1.83
+biopython==1.84
     # via pymsaviz
-contourpy==1.1.1
+contourpy==1.3.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
 fonttools==4.53.1
     # via matplotlib
-importlib-resources==6.4.4
+importlib-resources==6.4.5
     # via matplotlib
 kiwisolver==1.4.7
     # via matplotlib
-matplotlib==3.7.5
+matplotlib==3.9.2
     # via pymsaviz
-numpy==1.24.4
+numpy==2.0.2
     # via biopython
     # via contourpy
     # via matplotlib