update dependencies for ubuntu-latest/py3.9

Author: github-actions

requirements/ubuntu-latest_py3.9.txt

@@ -5,15 +5,18 @@
 #    pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.9.txt
 #
 aflow==0.0.11
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 alabaster==0.7.16
     # via sphinx
 ase==3.23.0
     # via
     #   aflow
     #   dscribe
-    #   matminer (setup.py)
-astroid==3.3.3
+    #   matminer
+    #   matminer (pyproject.toml)
+astroid==3.3.5
     # via pylint
 attrs==24.2.0
     # via
@@ -23,58 +26,69 @@ babel==2.16.0
     # via sphinx
 beautifulsoup4==4.12.3
     # via aflow
-black==24.8.0
-    # via matminer (setup.py)
+black==24.10.0
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 certifi==2024.8.30
     # via requests
 cffi==1.17.1
     # via cryptography
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 citrination-client==6.5.1
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 click==8.1.7
     # via black
 contourpy==1.3.0
     # via matplotlib
-coverage[toml]==7.6.1
+coverage[toml]==7.6.4
     # via
     #   coveralls
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   pytest-cov
 coveralls==4.0.1
-    # via matminer (setup.py)
-cryptography==43.0.1
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
+cryptography==43.0.3
     # via
     #   globus-sdk
     #   pyjwt
 cycler==0.12.1
     # via matplotlib
-dill==0.3.8
+dill==0.3.9
     # via pylint
-dnspython==2.6.1
+dnspython==2.7.0
     # via pymongo
 docopt==0.6.2
     # via coveralls
 docutils==0.21.2
     # via sphinx
 dscribe==2.1.1
-    # via matminer (setup.py)
+    # via matminer (pyproject.toml)
 exceptiongroup==1.2.2
     # via pytest
 fair-research-login==0.3.1
     # via mdf-toolbox
 flake8==7.1.1
-    # via matminer (setup.py)
-fonttools==4.53.1
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
+fonttools==4.54.1
     # via matplotlib
-globus-sdk==3.45.0
+globus-sdk==3.46.0
     # via
     #   fair-research-login
     #   mdf-forge
     #   mdf-toolbox
 httplib2==0.22.0
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 idna==3.10
     # via requests
 imagesize==1.4.1
@@ -94,26 +108,31 @@ jinja2==3.1.4
     #   aflow
     #   sphinx
 jmespath==1.0.1
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 joblib==1.4.2
     # via
     #   dscribe
     #   pymatgen
     #   scikit-learn
 jsonschema==4.23.0
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   mdf-toolbox
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
 kiwisolver==1.4.7
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
 llvmlite==0.43.0
     # via numba
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
+matminer[aflow,citrine,describe,dev,mdfforge,mpds] @ file:///home/runner/work/matminer/matminer
+    # via file:///home/runner/work/matminer/matminer
 matplotlib==3.9.2
     # via
     #   ase
@@ -123,12 +142,15 @@ mccabe==0.7.0
     #   flake8
     #   pylint
 mdf-forge==0.8.0
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 mdf-toolbox==0.7.1
     # via mdf-forge
 monty==2024.7.30
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   pymatgen
 mpmath==1.3.0
     # via sympy
@@ -138,13 +160,14 @@ networkx==3.2.1
     # via pymatgen
 numba==0.60.0
     # via sparse
-numpy==1.26.4
+numpy==2.0.2
     # via
     #   aflow
     #   ase
     #   contourpy
     #   dscribe
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   matplotlib
     #   numba
     #   pandas
@@ -165,11 +188,12 @@ palettable==3.3.3
     # via pymatgen
 pandas==2.2.3
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   pymatgen
 pathspec==0.12.1
     # via black
-pillow==10.4.0
+pillow==11.0.0
     # via matplotlib
 platformdirs==4.3.6
     # via
@@ -191,27 +215,38 @@ pygments==2.18.0
     # via sphinx
 pyjwt[crypto]==2.9.0
     # via globus-sdk
-pylint==3.3.0
-    # via matminer (setup.py)
+pylint==3.3.1
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 pymatgen==2024.8.9
-    # via matminer (setup.py)
-pymongo==4.9.1
-    # via matminer (setup.py)
-pyparsing==3.1.4
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
+pymongo==4.10.1
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
+pyparsing==3.2.0
     # via
     #   httplib2
     #   matplotlib
 pypif==2.1.2
     # via citrination-client
 pytest==8.3.3
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   pytest-cov
     #   pytest-timeout
 pytest-cov==5.0.0
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 pytest-timeout==2.3.1
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
     #   matplotlib
@@ -231,7 +266,8 @@ requests==2.32.3
     #   citrination-client
     #   coveralls
     #   globus-sdk
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   mdf-forge
     #   mdf-toolbox
     #   pymatgen
@@ -242,12 +278,13 @@ rpds-py==0.20.0
     #   referencing
 ruamel-yaml==0.18.6
     # via pymatgen
-ruamel-yaml-clib==0.2.8
+ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
 scikit-learn==1.5.2
     # via
     #   dscribe
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
 scipy==1.13.1
     # via
     #   ase
@@ -271,7 +308,9 @@ sparse==0.15.4
 spglib==2.5.0
     # via pymatgen
 sphinx==7.4.7
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 sphinxcontrib-applehelp==2.0.0
     # via sphinx
 sphinxcontrib-devhelp==2.0.0
@@ -286,17 +325,18 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 sympy==1.13.3
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   pymatgen
 tabulate==0.9.0
     # via pymatgen
 tenacity==9.0.0
     # via plotly
-termcolor==2.4.0
+termcolor==2.5.0
     # via aflow
 threadpoolctl==3.5.0
     # via scikit-learn
-tomli==2.0.1
+tomli==2.0.2
     # via
     #   black
     #   coverage
@@ -307,7 +347,8 @@ tomlkit==0.13.2
     # via pylint
 tqdm==4.66.5
     # via
-    #   matminer (setup.py)
+    #   matminer
+    #   matminer (pyproject.toml)
     #   mdf-forge
     #   pymatgen
 typing-extensions==4.12.2
@@ -317,10 +358,12 @@ typing-extensions==4.12.2
     #   globus-sdk
     #   pylint
     #   spglib
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
 ujson==5.10.0
-    # via matminer (setup.py)
+    # via
+    #   matminer
+    #   matminer (pyproject.toml)
 uncertainties==3.2.2
     # via pymatgen
 urllib3==2.2.3