Automated dependency upgrades (#437)

* update dependencies for ubuntu-latest/py3.11

* update dependencies for ubuntu-latest/py3.12

---------

Co-authored-by: github-actions <[email protected]>

Author: tschaume

requirements/ubuntu-latest_py3.11.txt

@@ -2,11 +2,8 @@
 # This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
-#    pip-compile --output-file=requirements/ubuntu-latest_py3.12.txt pyproject.toml
+#    pip-compile --output-file=requirements/ubuntu-latest_py3.11.txt pyproject.toml
 #
---extra-index-url https://pypi.ngc.nvidia.com
---trusted-host pypi.ngc.nvidia.com
-
 aiofiles==22.1.0
     # via ypy-websocket
 aioitertools==0.12.0
@@ -17,8 +14,6 @@ annotated-types==0.7.0
     # via pydantic
 anyio==4.9.0
     # via jupyter-server
-appnope==0.1.4
-    # via ipykernel
 argon2-cffi==25.1.0
     # via
     #   jupyter-server
@@ -46,15 +41,15 @@ bleach[css]==6.2.0
     # via nbconvert
 blinker==1.9.0
     # via flask
-boto3==1.38.32
+boto3==1.39.14
     # via maggma
-botocore==1.38.32
+botocore==1.39.14
     # via
     #   boto3
     #   s3transfer
 cachelib==0.13.0
     # via flask-caching
-certifi==2025.4.26
+certifi==2025.7.14
     # via requests
 cffi==1.17.1
     # via
@@ -65,21 +60,21 @@ charset-normalizer==3.4.2
     # via requests
 click==8.2.1
     # via flask
-comm==0.2.2
+comm==0.2.3
     # via ipykernel
-contourpy==1.3.2
+contourpy==1.3.3
     # via matplotlib
-cryptography==45.0.3
+cryptography==45.0.5
     # via paramiko
 crystaltoolkit-extension==0.6.0
     # via crystal_toolkit (pyproject.toml)
 cycler==0.12.1
     # via matplotlib
-dash==3.0.4
+dash==3.1.1
     # via crystal_toolkit (pyproject.toml)
 dash-mp-components==0.4.47
     # via crystal_toolkit (pyproject.toml)
-debugpy==1.8.14
+debugpy==1.8.15
     # via ipykernel
 decorator==5.2.1
     # via ipython
@@ -89,21 +84,21 @@ dnspython==2.7.0
     # via
     #   maggma
     #   pymongo
-emmet-core==0.84.7rc4
+emmet-core==0.84.9rc0
     # via mp-api
 entrypoints==0.4
     # via jupyter-client
 executing==2.2.0
     # via stack-data
 fastjsonschema==2.21.1
     # via nbformat
-flask==3.0.3
+flask==3.1.1
     # via
     #   dash
     #   flask-caching
 flask-caching==2.3.1
     # via crystal_toolkit (pyproject.toml)
-fonttools==4.58.2
+fonttools==4.59.0
     # via matplotlib
 fqdn==1.5.1
     # via jsonschema
@@ -122,7 +117,7 @@ ipykernel==6.29.5
     # via
     #   nbclassic
     #   notebook
-ipython==9.3.0
+ipython==9.4.0
     # via
     #   ipykernel
     #   jupyterlab
@@ -160,7 +155,7 @@ jsonlines==4.0.0
     # via maggma
 jsonpointer==3.0.0
     # via jsonschema
-jsonschema[format-nongpl]==4.24.0
+jsonschema[format-nongpl]==4.25.0
     # via
     #   jupyter-events
     #   jupyterlab-server
@@ -212,14 +207,17 @@ jupyterlab-server==2.27.3
     # via jupyterlab
 kiwisolver==1.4.8
     # via matplotlib
-latexcodec==3.0.0
+lark==1.2.2
+    # via rfc3987-syntax
+latexcodec==3.0.1
     # via pybtex
 lazy-loader==0.4
     # via scikit-image
 maggma==0.71.5
     # via mp-api
 markupsafe==3.0.2
     # via
+    #   flask
     #   jinja2
     #   nbconvert
     #   werkzeug
@@ -239,15 +237,15 @@ monty==2025.3.3
     #   maggma
     #   mp-api
     #   pymatgen
-mp-api==0.45.5
+mp-api==0.45.7
     # via crystal_toolkit (pyproject.toml)
 mpmath==1.3.0
     # via sympy
-msgpack==1.1.0
+msgpack==1.1.1
     # via
     #   maggma
     #   mp-api
-narwhals==1.41.1
+narwhals==2.0.0
     # via plotly
 nbclassic==1.3.1
     # via
@@ -280,7 +278,7 @@ notebook==6.5.7
     # via jupyterlab
 notebook-shim==0.2.4
     # via nbclassic
-numpy==2.2.6
+numpy==2.3.2
     # via
     #   contourpy
     #   imageio
@@ -295,7 +293,7 @@ numpy==2.2.6
     #   shapely
     #   spglib
     #   tifffile
-orjson==3.10.18
+orjson==3.11.1
     # via
     #   maggma
     #   pymatgen
@@ -316,7 +314,7 @@ packaging==25.0
     #   scikit-image
 palettable==3.3.3
     # via pymatgen
-pandas==2.3.0
+pandas==2.3.1
     # via
     #   maggma
     #   pymatgen
@@ -328,14 +326,14 @@ parso==0.8.4
     # via jedi
 pexpect==4.9.0
     # via ipython
-pillow==11.2.1
+pillow==11.3.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
 platformdirs==4.3.8
     # via jupyter-core
-plotly==6.1.2
+plotly==6.2.0
     # via
     #   dash
     #   pymatgen
@@ -353,30 +351,30 @@ ptyprocess==0.7.0
     #   terminado
 pure-eval==0.2.3
     # via stack-data
-pybtex==0.24.0
+pybtex==0.25.1
     # via emmet-core
 pycparser==2.22
     # via cffi
-pydantic==2.11.5
+pydantic==2.11.7
     # via
     #   emmet-core
     #   maggma
     #   pydantic-settings
 pydantic-core==2.33.2
     # via pydantic
-pydantic-settings==2.9.1
+pydantic-settings==2.10.1
     # via
     #   crystal_toolkit (pyproject.toml)
     #   emmet-core
     #   maggma
 pydash==8.0.5
     # via maggma
-pygments==2.19.1
+pygments==2.19.2
     # via
     #   ipython
     #   ipython-pygments-lexers
     #   nbconvert
-pymatgen==2025.5.28
+pymatgen==2025.6.14
     # via
     #   crystal_toolkit (pyproject.toml)
     #   emmet-core
@@ -397,7 +395,7 @@ python-dateutil==2.9.0.post0
     #   maggma
     #   matplotlib
     #   pandas
-python-dotenv==1.1.0
+python-dotenv==1.1.1
     # via pydantic-settings
 python-json-logger==3.3.0
     # via jupyter-events
@@ -409,7 +407,7 @@ pyyaml==6.0.2
     # via
     #   jupyter-events
     #   pybtex
-pyzmq==26.4.0
+pyzmq==27.0.0
     # via
     #   ipykernel
     #   jupyter-client
@@ -421,13 +419,13 @@ referencing==0.36.2
     #   jsonschema
     #   jsonschema-specifications
     #   jupyter-events
-requests==2.32.3
+requests==2.32.4
     # via
     #   dash
     #   jupyterlab-server
     #   mp-api
     #   pymatgen
-retrying==1.3.4
+retrying==1.4.1
     # via dash
 rfc3339-validator==0.1.4
     # via
@@ -437,24 +435,26 @@ rfc3986-validator==0.1.1
     # via
     #   jsonschema
     #   jupyter-events
-rpds-py==0.25.1
+rfc3987-syntax==1.1.0
+    # via jsonschema
+rpds-py==0.26.0
     # via
     #   jsonschema
     #   referencing
-ruamel-yaml==0.18.13
+ruamel-yaml==0.18.14
     # via
     #   maggma
     #   monty
     #   pymatgen
 ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
-s3transfer==0.13.0
+s3transfer==0.13.1
     # via boto3
 scikit-image==0.25.2
     # via crystal_toolkit (pyproject.toml)
-scikit-learn==1.7.0
+scikit-learn==1.7.1
     # via crystal_toolkit (pyproject.toml)
-scipy==1.15.3
+scipy==1.16.1
     # via
     #   pymatgen
     #   scikit-image
@@ -469,11 +469,9 @@ shapely==2.1.1
     # via crystal_toolkit (pyproject.toml)
 six==1.17.0
     # via
-    #   pybtex
     #   python-dateutil
-    #   retrying
     #   rfc3339-validator
-smart-open==7.1.0
+smart-open==7.3.0.post1
     # via mp-api
 sniffio==1.3.1
     # via anyio
@@ -496,7 +494,7 @@ terminado==0.18.1
     #   notebook
 threadpoolctl==3.6.0
     # via scikit-learn
-tifffile==2025.6.1
+tifffile==2025.6.11
     # via scikit-image
 tinycss2==1.4.0
     # via bleach
@@ -514,7 +512,6 @@ tqdm==4.67.1
     #   pymatgen
 traitlets==5.14.3
     # via
-    #   comm
     #   ipykernel
     #   ipython
     #   jupyter-client
@@ -526,9 +523,9 @@ traitlets==5.14.3
     #   nbconvert
     #   nbformat
     #   notebook
-types-python-dateutil==2.9.0.20250516
+types-python-dateutil==2.9.0.20250708
     # via arrow
-typing-extensions==4.14.0
+typing-extensions==4.14.1
     # via
     #   aiosqlite
     #   anyio
@@ -553,7 +550,7 @@ uncertainties==3.2.3
     # via pymatgen
 uri-template==1.3.0
     # via jsonschema
-urllib3==2.4.0
+urllib3==2.5.0
     # via
     #   botocore
     #   requests
@@ -569,7 +566,7 @@ webencodings==0.5.1
     #   tinycss2
 websocket-client==1.8.0
     # via jupyter-server
-werkzeug==3.0.6
+werkzeug==3.1.3
     # via
     #   dash
     #   flask
@@ -581,7 +578,7 @@ y-py==0.6.2
     #   ypy-websocket
 ypy-websocket==0.8.4
     # via jupyter-server-ydoc
-zipp==3.22.0
+zipp==3.23.0
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file: