Automated dependency upgrades (#1235)

* update dependencies for emmet-api (ubuntu-latest/py3.11)

* update dependencies for emmet-api (ubuntu-latest/py3.12)

* update dependencies for emmet-builders (ubuntu-latest/py3.11)

* update dependencies for emmet-builders (ubuntu-latest/py3.12)

* update dependencies for emmet-core (ubuntu-latest/py3.11)

* update dependencies for emmet-core (ubuntu-latest/py3.12)

---------

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

Author: tschaume

emmet-api/requirements/ubuntu-latest_py3.11.txt

@@ -23,11 +23,11 @@ bcrypt==4.3.0
     # via paramiko
 bibtexparser==1.4.3
     # via pymatgen
-boto3==1.38.21
+boto3==1.38.29
     # via
     #   emmet-api (setup.py)
     #   maggma
-botocore==1.38.21
+botocore==1.38.29
     # via
     #   boto3
     #   s3transfer
@@ -45,14 +45,12 @@ click==8.2.1
     # via uvicorn
 contourpy==1.3.2
     # via matplotlib
-cryptography==45.0.2
+cryptography==45.0.3
     # via paramiko
 cycler==0.12.1
     # via matplotlib
 ddtrace==2.21.8
     # via emmet-api (setup.py)
-deprecated==1.2.18
-    # via opentelemetry-api
 dnspython==2.7.0
     # via
     #   maggma
@@ -65,7 +63,7 @@ fastapi==0.115.12
     # via
     #   emmet-api (setup.py)
     #   maggma
-fonttools==4.58.0
+fonttools==4.58.1
     # via matplotlib
 gunicorn==23.0.0
     # via emmet-api (setup.py)
@@ -77,17 +75,17 @@ idna==3.10
     #   requests
 imageio==2.37.0
     # via scikit-image
-importlib-metadata==8.6.1
+importlib-metadata==8.7.0
     # via opentelemetry-api
 jmespath==1.0.1
     # via
     #   boto3
     #   botocore
-joblib==1.5.0
+joblib==1.5.1
     # via pymatgen
 jsonlines==4.0.0
     # via maggma
-jsonschema==4.23.0
+jsonschema==4.24.0
     # via maggma
 jsonschema-specifications==2025.4.1
     # via jsonschema
@@ -114,9 +112,9 @@ mpmath==1.3.0
     # via sympy
 msgpack==1.1.0
     # via maggma
-narwhals==1.40.0
+narwhals==1.41.0
     # via plotly
-networkx==3.4.2
+networkx==3.5
     # via
     #   pymatgen
     #   scikit-image
@@ -135,10 +133,12 @@ numpy==1.26.4
     #   shapely
     #   spglib
     #   tifffile
-opentelemetry-api==1.33.1
+opentelemetry-api==1.34.0
     # via ddtrace
 orjson==3.10.18
-    # via maggma
+    # via
+    #   maggma
+    #   pymatgen
 packaging==25.0
     # via
     #   gunicorn
@@ -160,15 +160,15 @@ pillow==11.2.1
     #   imageio
     #   matplotlib
     #   scikit-image
-plotly==6.1.1
+plotly==6.1.2
     # via pymatgen
-protobuf==6.31.0
+protobuf==6.31.1
     # via ddtrace
 pybtex==0.24.0
     # via emmet-core
 pycparser==2.22
     # via cffi
-pydantic==2.11.4
+pydantic==2.11.5
     # via
     #   emmet-core
     #   fastapi
@@ -182,7 +182,7 @@ pydantic-settings==2.9.1
     #   maggma
 pydash==8.0.5
     # via maggma
-pymatgen==2025.5.2
+pymatgen==2025.5.28
     # via
     #   emmet-core
     #   mp-pyrho
@@ -226,14 +226,14 @@ rpds-py==0.25.1
     # via
     #   jsonschema
     #   referencing
-ruamel-yaml==0.18.10
+ruamel-yaml==0.18.12
     # via
     #   maggma
     #   monty
     #   pymatgen
 ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
-s3transfer==0.12.0
+s3transfer==0.13.0
     # via boto3
 scikit-image==0.25.2
     # via pymatgen-analysis-defects
@@ -265,18 +265,19 @@ sympy==1.14.0
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
-tifffile==2025.5.21
+tifffile==2025.6.1
     # via scikit-image
 tqdm==4.67.1
     # via
     #   maggma
     #   pymatgen
-typing-extensions==4.13.2
+typing-extensions==4.14.0
     # via
     #   anyio
     #   ddtrace
     #   emmet-core
     #   fastapi
+    #   opentelemetry-api
     #   pydantic
     #   pydantic-core
     #   pydash
@@ -295,15 +296,13 @@ urllib3==2.4.0
     # via
     #   botocore
     #   requests
-uvicorn==0.34.2
+uvicorn==0.34.3
     # via maggma
 wrapt==1.17.2
-    # via
-    #   ddtrace
-    #   deprecated
+    # via ddtrace
 xmltodict==0.14.2
     # via ddtrace
-zipp==3.21.0
+zipp==3.22.0
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file: