Automated dependency upgrades (#1052)

Author: tsmathis

requirements/requirements-ubuntu-latest_py3.11.txt

@@ -10,9 +10,9 @@ bibtexparser==1.4.3
     # via pymatgen
 blake3==1.0.8
     # via emmet-core
-boto3==1.42.30
+boto3==1.42.33
     # via mp-api (pyproject.toml)
-botocore==1.42.30
+botocore==1.42.33
     # via
     #   boto3
     #   s3transfer
@@ -24,13 +24,13 @@ contourpy==1.3.3
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-emmet-core==0.87.0.dev4
+emmet-core==0.86.3rc1
     # via mp-api (pyproject.toml)
 fonttools==4.61.1
     # via matplotlib
 idna==3.11
     # via requests
-jmespath==1.0.1
+jmespath==1.1.0
     # via
     #   boto3
     #   botocore
@@ -49,8 +49,6 @@ monty==2025.3.3
     #   pymatgen
 mpmath==1.3.0
     # via sympy
-msgpack==1.1.2
-    # via mp-api (pyproject.toml)
 narwhals==2.15.0
     # via plotly
 networkx==3.6.1
@@ -69,13 +67,13 @@ orjson==3.11.5
     # via
     #   mp-api (pyproject.toml)
     #   pymatgen
-packaging==25.0
+packaging==26.0
     # via
     #   matplotlib
     #   plotly
 palettable==3.3.3
     # via pymatgen
-pandas==2.3.3
+pandas==3.0.0
     # via pymatgen
 pillow==12.1.0
     # via matplotlib
@@ -101,7 +99,7 @@ pymatgen==2025.10.7
     #   pymatgen-io-validation
 pymatgen-io-validation==0.1.2
     # via emmet-core
-pyparsing==3.3.1
+pyparsing==3.3.2
     # via
     #   bibtexparser
     #   matplotlib
@@ -112,8 +110,6 @@ python-dateutil==2.9.0.post0
     #   pandas
 python-dotenv==1.2.1
     # via pydantic-settings
-pytz==2025.2
-    # via pandas
 pyyaml==6.0.3
     # via pybtex
 requests==2.32.5
@@ -127,12 +123,10 @@ ruamel-yaml==0.19.1
     #   pymatgen
 s3transfer==0.16.0
     # via boto3
-scipy==1.16.3
+scipy==1.17.0
     # via pymatgen
 six==1.17.0
     # via python-dateutil
-smart-open==7.5.0
-    # via mp-api (pyproject.toml)
 spglib==2.7.0
     # via pymatgen
 sympy==1.14.0
@@ -154,13 +148,9 @@ typing-inspection==0.4.2
     # via
     #   pydantic
     #   pydantic-settings
-tzdata==2025.3
-    # via pandas
-uncertainties==3.2.4
+uncertainties==3.2.3
     # via pymatgen
 urllib3==2.6.3
     # via
     #   botocore
     #   requests
-wrapt==2.0.1
-    # via smart-open

requirements/requirements-ubuntu-latest_py3.11_extras.txt

@@ -41,11 +41,9 @@ blake3==1.0.8
     # via emmet-core
 boltons==25.0.0
     # via mpcontribs-client
-boto3==1.42.30
-    # via
-    #   mp-api
-    #   mp-api (pyproject.toml)
-botocore==1.42.30
+boto3==1.42.33
+    # via mp-api (pyproject.toml)
+botocore==1.42.33
     # via
     #   boto3
     #   s3transfer
@@ -108,10 +106,8 @@ docutils==0.22.4
     #   sphinx
 email-validator==2.3.0
     # via pydantic
-emmet-core[all]==0.87.0.dev4
-    # via
-    #   mp-api
-    #   mp-api (pyproject.toml)
+emmet-core[all]==0.86.3rc1
+    # via mp-api (pyproject.toml)
 exceptiongroup==1.3.1
     # via fastmcp
 execnet==2.1.2
@@ -120,7 +116,7 @@ executing==2.2.1
     # via stack-data
 fakeredis[lua]==2.33.0
     # via pydocket
-fastmcp==2.14.3
+fastmcp==2.14.4
     # via mp-api (pyproject.toml)
 filelock==3.20.3
     # via virtualenv
@@ -193,7 +189,7 @@ jeepney==0.9.0
     #   secretstorage
 jinja2==3.1.6
     # via sphinx
-jmespath==1.0.1
+jmespath==1.1.0
     # via
     #   boto3
     #   botocore
@@ -207,7 +203,9 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
+    # via
+    #   bravado-core
+    #   fastmcp
 jsonschema[format-nongpl]==4.26.0
     # via
     #   bravado-core
@@ -235,9 +233,10 @@ markdown-it-py==4.0.0
     # via rich
 markupsafe==3.0.3
     # via jinja2
-matminer==0.9.3
+matminer==0.10.0
     # via
     #   emmet-core
+    #   mp-api (pyproject.toml)
     #   robocrys
 matplotlib==3.10.8
     # via
@@ -259,7 +258,6 @@ monty==2025.3.3
     #   custodian
     #   emmet-core
     #   matminer
-    #   mp-api
     #   mp-api (pyproject.toml)
     #   pymatgen
     #   robocrys
@@ -268,8 +266,6 @@ more-itertools==10.8.0
     #   inflect
     #   jaraco-classes
     #   jaraco-functools
-mp-api[mcp]==0.45.15
-    # via mp-api (pyproject.toml)
 mp-pyrho==0.5.1
     # via pymatgen-analysis-defects
 mpcontribs-client==5.10.4
@@ -280,8 +276,6 @@ msgpack==1.1.2
     # via
     #   bravado
     #   bravado-core
-    #   mp-api
-    #   mp-api (pyproject.toml)
 mypy==1.19.1
     # via mp-api (pyproject.toml)
 mypy-extensions==1.1.0
@@ -341,11 +335,11 @@ opentelemetry-semantic-conventions==0.60b1
     #   opentelemetry-sdk
 orjson==3.11.5
     # via
-    #   mp-api
     #   mp-api (pyproject.toml)
     #   pymatgen
-packaging==25.0
+packaging==26.0
     # via
+    #   fastmcp
     #   lazy-loader
     #   matplotlib
     #   opentelemetry-instrumentation
@@ -413,7 +407,7 @@ py-key-value-aio[disk,keyring,memory,redis]==0.3.0
     #   pydocket
 py-key-value-shared==0.3.0
     # via py-key-value-aio
-pyarrow==22.0.0
+pyarrow==23.0.0
     # via emmet-core
 pybtex==0.25.1
     # via
@@ -423,7 +417,7 @@ pycodestyle==2.14.0
     # via
     #   flake8
     #   mp-api (pyproject.toml)
-pycparser==2.23
+pycparser==3.0
     # via cffi
 pydantic[email]==2.12.5
     # via
@@ -459,7 +453,6 @@ pymatgen==2025.10.7
     # via
     #   emmet-core
     #   matminer
-    #   mp-api
     #   mp-api (pyproject.toml)
     #   mp-pyrho
     #   mpcontribs-client
@@ -480,7 +473,7 @@ pymongo==4.16.0
     # via
     #   matminer
     #   mpcontribs-client
-pyparsing==3.3.1
+pyparsing==3.3.2
     # via
     #   bibtexparser
     #   matplotlib
@@ -545,7 +538,6 @@ requests==2.32.5
     #   bravado-core
     #   jsonschema-path
     #   matminer
-    #   mp-api
     #   mp-api (pyproject.toml)
     #   pymatgen
     #   pymatgen-io-validation
@@ -568,7 +560,7 @@ rich==14.2.0
     #   typer
 rich-rst==1.3.2
     # via cyclopts
-robocrys==0.2.12
+robocrys==0.2.13
     # via emmet-core
 roman-numerals==4.1.0
     # via sphinx
@@ -587,9 +579,10 @@ scikit-image==0.26.0
     # via pymatgen-analysis-defects
 scikit-learn==1.8.0
     # via matminer
-scipy==1.16.3
+scipy==1.17.0
     # via
     #   ase
+    #   matminer
     #   pymatgen
     #   robocrys
     #   scikit-image
@@ -598,7 +591,7 @@ seaborn==0.13.2
     # via pymatgen-analysis-diffusion
 secretstorage==3.5.0
     # via keyring
-seekpath==2.1.0
+seekpath==2.2.0
     # via emmet-core
 semantic-version==2.10.0
     # via mpcontribs-client
@@ -617,10 +610,6 @@ six==1.17.0
     #   flatten-dict
     #   python-dateutil
     #   rfc3339-validator
-smart-open==7.5.0
-    # via
-    #   mp-api
-    #   mp-api (pyproject.toml)
 snowballstemmer==3.0.1
     # via sphinx
 sortedcontainers==2.4.0
@@ -644,11 +633,11 @@ sphinxcontrib-qthelp==2.0.0
     # via sphinx
 sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
-sse-starlette==3.1.2
+sse-starlette==3.2.0
     # via mcp
 stack-data==0.6.3
     # via ipython
-starlette==0.51.0
+starlette==0.52.1
     # via
     #   mcp
     #   sse-starlette
@@ -694,7 +683,6 @@ typing-extensions==4.15.0
     #   flexparser
     #   ipython
     #   mcp
-    #   mp-api
     #   mp-api (pyproject.toml)
     #   mypy
     #   opentelemetry-api
@@ -724,7 +712,7 @@ tzdata==2025.3
     #   pandas
 ujson==5.11.0
     # via mpcontribs-client
-uncertainties==3.2.4
+uncertainties==3.2.3
     # via pymatgen
 uri-template==1.3.0
     # via jsonschema
@@ -739,15 +727,13 @@ uvicorn==0.40.0
     #   mcp
 virtualenv==20.36.1
     # via pre-commit
-wcwidth==0.2.14
+wcwidth==0.3.1
     # via prompt-toolkit
 webcolors==25.10.0
     # via jsonschema
 websockets==16.0
     # via fastmcp
 wrapt==1.17.3
-    # via
-    #   opentelemetry-instrumentation
-    #   smart-open
+    # via opentelemetry-instrumentation
 zipp==3.23.0
     # via importlib-metadata