diff --git a/matminer/featurizers/base.py b/matminer/featurizers/base.py index 00ac9e3ed..f5c3a3d12 100644 --- a/matminer/featurizers/base.py +++ b/matminer/featurizers/base.py @@ -334,6 +334,8 @@ def featurize_dataframe( # Check names to avoid overwriting the current columns # ConversionFeaturizer have attribute called _overwrite_data which # determines whether an Error is thrown + if not isinstance(labels, list): + labels = labels.tolist() overwrite = getattr(self, "_overwrite_data", False) if not overwrite: for col in df.columns.values: diff --git a/matminer/featurizers/structure/bonding.py b/matminer/featurizers/structure/bonding.py index 39df1fb38..f22a3cdbc 100644 --- a/matminer/featurizers/structure/bonding.py +++ b/matminer/featurizers/structure/bonding.py @@ -356,8 +356,9 @@ def _species_from_bondstr(self, bondstr): species = [] for ss in bondstr.split(self.token): try: - species.append(Specie.from_string(ss)) - except ValueError: + species.append(Specie.from_str(ss)) + # pymatgen deprecated from_string in favour of from_str, if it is missing then fallback to from_dict + except (ValueError, AttributeError): d = {"element": ss, "oxidation_state": 0} species.append(Specie.from_dict(d)) return tuple(species) diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt index fcfc65a5d..8a6c4ac8a 100644 --- a/requirements/ubuntu-latest_py3.10.txt +++ b/requirements/ubuntu-latest_py3.10.txt @@ -2,40 +2,40 @@ # This file is autogenerated by pip-compile with Python 3.10 # by the following command: # -# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.10_extras.txt +# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.10.txt # aflow==0.0.11 # via matminer (setup.py) -alabaster==0.7.13 +alabaster==0.7.16 # via sphinx ase==3.22.1 # via # aflow # dscribe # matminer (setup.py) -astroid==2.15.6 +astroid==3.1.0 # via pylint -attrs==23.1.0 +attrs==23.2.0 # via # jsonschema # referencing -babel==2.12.1 +babel==2.14.0 # via sphinx -beautifulsoup4==4.12.2 +beautifulsoup4==4.12.3 # via aflow -black==23.7.0 +black==24.3.0 # via matminer (setup.py) -certifi==2023.7.22 +certifi==2024.2.2 # via requests -cffi==1.15.1 +cffi==1.16.0 # via cryptography -charset-normalizer==3.2.0 +charset-normalizer==3.3.2 # via requests citrination-client==6.5.1 # via matminer (setup.py) click==8.1.7 # via black -contourpy==1.1.0 +contourpy==1.2.0 # via matplotlib coverage[toml]==6.5.0 # via @@ -44,15 +44,15 @@ coverage[toml]==6.5.0 # pytest-cov coveralls==3.3.1 # via matminer (setup.py) -cryptography==41.0.3 +cryptography==42.0.5 # via # globus-sdk # pyjwt -cycler==0.11.0 +cycler==0.12.1 # via matplotlib -dill==0.3.7 +dill==0.3.8 # via pylint -dnspython==2.4.2 +dnspython==2.6.1 # via pymongo docopt==0.6.2 # via coveralls @@ -60,39 +60,32 @@ docutils==0.20.1 # via sphinx dscribe==2.1.0 # via matminer (setup.py) -emmet-core==0.67.5 - # via mp-api -exceptiongroup==1.1.3 +exceptiongroup==1.2.0 # via pytest fair-research-login==0.3.1 # via mdf-toolbox -flake8==6.1.0 +flake8==7.0.0 # via matminer (setup.py) -fonttools==4.42.1 +fonttools==4.50.0 # via matplotlib -future==0.18.3 - # via - # matminer (setup.py) - # uncertainties -globus-nexus-client==0.4.1 - # via mdf-toolbox -globus-sdk==3.28.0 +future==1.0.0 + # via uncertainties +globus-sdk==3.39.0 # via # fair-research-login - # globus-nexus-client # mdf-forge # mdf-toolbox httplib2==0.22.0 # via matminer (setup.py) -idna==3.4 +idna==3.6 # via requests imagesize==1.4.1 # via sphinx iniconfig==2.0.0 # via pytest -isort==5.12.0 +isort==5.13.2 # via pylint -jinja2==3.1.2 +jinja2==3.1.3 # via # aflow # sphinx @@ -103,21 +96,21 @@ joblib==1.3.2 # dscribe # pymatgen # scikit-learn -jsonschema==4.3.0 +jsonschema==4.21.1 # via # matminer (setup.py) # mdf-toolbox +jsonschema-specifications==2023.12.1 + # via jsonschema kiwisolver==1.4.5 # via matplotlib -latexcodec==2.0.1 +latexcodec==3.0.0 # via pybtex -lazy-object-proxy==1.9.0 - # via astroid -llvmlite==0.40.1 +llvmlite==0.42.0 # via numba -markupsafe==2.1.3 +markupsafe==2.1.5 # via jinja2 -matplotlib==3.7.2 +matplotlib==3.8.3 # via # ase # pymatgen @@ -127,27 +120,21 @@ mccabe==0.7.0 # pylint mdf-forge==0.8.0 # via matminer (setup.py) -mdf-toolbox==0.6.0 +mdf-toolbox==0.7.1 # via mdf-forge -monty==2023.9.5 +monty==2024.2.26 # via - # emmet-core # matminer (setup.py) - # mp-api # pymatgen -mp-api==0.35.1 - # via pymatgen mpmath==1.3.0 # via sympy -msgpack==1.0.5 - # via mp-api mypy-extensions==1.0.0 # via black -networkx==3.1 +networkx==3.2.1 # via pymatgen -numba==0.57.1 +numba==0.59.1 # via sparse -numpy==1.24.4 +numpy==1.26.4 # via # aflow # ase @@ -163,7 +150,7 @@ numpy==1.24.4 # scipy # sparse # spglib -packaging==23.1 +packaging==24.0 # via # black # matplotlib @@ -172,78 +159,71 @@ packaging==23.1 # sphinx palettable==3.3.3 # via pymatgen -pandas==2.1.0 +pandas==1.5.3 # via # matminer (setup.py) # pymatgen -pathspec==0.11.2 +pathspec==0.12.1 # via black -pillow==10.0.0 +pillow==10.2.0 # via matplotlib -platformdirs==3.10.0 +platformdirs==4.2.0 # via # black # pylint -plotly==5.16.1 +plotly==5.20.0 # via pymatgen -pluggy==1.3.0 +pluggy==1.4.0 # via pytest pybind11==2.11.1 # via dscribe pybtex==0.24.0 - # via - # emmet-core - # pymatgen -pycodestyle==2.11.0 + # via pymatgen +pycodestyle==2.11.1 # via flake8 pycparser==2.21 # via cffi -pydantic==1.10.12 - # via - # emmet-core - # pymatgen -pyflakes==3.1.0 +pyflakes==3.2.0 # via flake8 -pygments==2.16.1 +pygments==2.17.2 # via sphinx pyjwt[crypto]==2.8.0 # via globus-sdk -pylint==2.17.5 +pylint==3.1.0 # via matminer (setup.py) -pymatgen==2023.9.2 - # via - # emmet-core - # matminer (setup.py) - # mp-api -pymongo==4.5.0 +pymatgen==2024.3.1 + # via matminer (setup.py) +pymongo==4.6.2 # via matminer (setup.py) -pyparsing==3.0.9 +pyparsing==3.1.2 # via # httplib2 # matplotlib pypif==2.1.2 # via citrination-client -pyrsistent==0.19.3 - # via jsonschema -pytest==7.4.1 +pytest==8.1.1 # via # matminer (setup.py) # pytest-cov # pytest-timeout -pytest-cov==4.1.0 +pytest-cov==5.0.0 # via matminer (setup.py) -pytest-timeout==2.1.0 +pytest-timeout==2.3.1 # via matminer (setup.py) -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via # matplotlib # pandas -pytz==2023.3.post1 +pytz==2024.1 # via pandas pyyaml==6.0.1 # via # citrination-client # pybtex +referencing==0.34.0 + # via + # jsonschema + # jsonschema-specifications requests==2.31.0 # via # citrination-client @@ -252,18 +232,21 @@ requests==2.31.0 # matminer (setup.py) # mdf-forge # mdf-toolbox - # mp-api # pymatgen # sphinx -ruamel-yaml==0.17.32 +rpds-py==0.18.0 + # via + # jsonschema + # referencing +ruamel-yaml==0.18.6 # via pymatgen -ruamel-yaml-clib==0.2.7 +ruamel-yaml-clib==0.2.8 # via ruamel-yaml -scikit-learn==1.3.0 +scikit-learn==1.4.1.post1 # via # dscribe # matminer (setup.py) -scipy==1.11.2 +scipy==1.12.0 # via # ase # dscribe @@ -274,7 +257,6 @@ six==1.16.0 # via # aflow # citrination-client - # latexcodec # pybtex # pypif # python-dateutil @@ -282,31 +264,23 @@ snowballstemmer==2.2.0 # via sphinx soupsieve==2.5 # via beautifulsoup4 -sparse==0.14.0 +sparse==0.15.1 # via dscribe -spglib==2.0.2 - # via - # emmet-core - # pymatgen -sphinx==7.2.5 - # via - # matminer (setup.py) - # sphinxcontrib-applehelp - # sphinxcontrib-devhelp - # sphinxcontrib-htmlhelp - # sphinxcontrib-qthelp - # sphinxcontrib-serializinghtml -sphinxcontrib-applehelp==1.0.7 +spglib==2.3.1 + # via pymatgen +sphinx==7.2.6 + # via matminer (setup.py) +sphinxcontrib-applehelp==1.0.8 # via sphinx -sphinxcontrib-devhelp==1.0.5 +sphinxcontrib-devhelp==1.0.6 # via sphinx -sphinxcontrib-htmlhelp==2.0.4 +sphinxcontrib-htmlhelp==2.0.5 # via sphinx sphinxcontrib-jsmath==1.0.1 # via sphinx -sphinxcontrib-qthelp==1.0.6 +sphinxcontrib-qthelp==1.0.7 # via sphinx -sphinxcontrib-serializinghtml==1.1.9 +sphinxcontrib-serializinghtml==1.1.10 # via sphinx sympy==1.12 # via @@ -316,9 +290,9 @@ tabulate==0.9.0 # via pymatgen tenacity==8.2.3 # via plotly -termcolor==2.3.0 +termcolor==2.4.0 # via aflow -threadpoolctl==3.2.0 +threadpoolctl==3.4.0 # via scikit-learn tomli==2.0.1 # via @@ -326,29 +300,20 @@ tomli==2.0.1 # coverage # pylint # pytest -tomlkit==0.12.1 +tomlkit==0.12.4 # via pylint -tqdm==4.66.1 +tqdm==4.66.2 # via # matminer (setup.py) # mdf-forge # pymatgen -typing-extensions==4.7.1 +typing-extensions==4.10.0 # via # astroid - # emmet-core - # mp-api - # pydantic -tzdata==2023.3 - # via pandas -ujson==5.8.0 + # black +ujson==5.9.0 # via matminer (setup.py) uncertainties==3.1.7 # via pymatgen -urllib3==2.0.4 +urllib3==2.2.1 # via requests -wrapt==1.15.0 - # via astroid - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt index fcfc65a5d..26af6a703 100644 --- a/requirements/ubuntu-latest_py3.11.txt +++ b/requirements/ubuntu-latest_py3.11.txt @@ -1,41 +1,41 @@ # -# This file is autogenerated by pip-compile with Python 3.10 +# This file is autogenerated by pip-compile with Python 3.11 # by the following command: # -# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.10_extras.txt +# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.11.txt # aflow==0.0.11 # via matminer (setup.py) -alabaster==0.7.13 +alabaster==0.7.16 # via sphinx ase==3.22.1 # via # aflow # dscribe # matminer (setup.py) -astroid==2.15.6 +astroid==3.1.0 # via pylint -attrs==23.1.0 +attrs==23.2.0 # via # jsonschema # referencing -babel==2.12.1 +babel==2.14.0 # via sphinx -beautifulsoup4==4.12.2 +beautifulsoup4==4.12.3 # via aflow -black==23.7.0 +black==24.3.0 # via matminer (setup.py) -certifi==2023.7.22 +certifi==2024.2.2 # via requests -cffi==1.15.1 +cffi==1.16.0 # via cryptography -charset-normalizer==3.2.0 +charset-normalizer==3.3.2 # via requests citrination-client==6.5.1 # via matminer (setup.py) click==8.1.7 # via black -contourpy==1.1.0 +contourpy==1.2.0 # via matplotlib coverage[toml]==6.5.0 # via @@ -44,15 +44,15 @@ coverage[toml]==6.5.0 # pytest-cov coveralls==3.3.1 # via matminer (setup.py) -cryptography==41.0.3 +cryptography==42.0.5 # via # globus-sdk # pyjwt -cycler==0.11.0 +cycler==0.12.1 # via matplotlib -dill==0.3.7 +dill==0.3.8 # via pylint -dnspython==2.4.2 +dnspython==2.6.1 # via pymongo docopt==0.6.2 # via coveralls @@ -60,39 +60,30 @@ docutils==0.20.1 # via sphinx dscribe==2.1.0 # via matminer (setup.py) -emmet-core==0.67.5 - # via mp-api -exceptiongroup==1.1.3 - # via pytest fair-research-login==0.3.1 # via mdf-toolbox -flake8==6.1.0 +flake8==7.0.0 # via matminer (setup.py) -fonttools==4.42.1 +fonttools==4.50.0 # via matplotlib -future==0.18.3 - # via - # matminer (setup.py) - # uncertainties -globus-nexus-client==0.4.1 - # via mdf-toolbox -globus-sdk==3.28.0 +future==1.0.0 + # via uncertainties +globus-sdk==3.39.0 # via # fair-research-login - # globus-nexus-client # mdf-forge # mdf-toolbox httplib2==0.22.0 # via matminer (setup.py) -idna==3.4 +idna==3.6 # via requests imagesize==1.4.1 # via sphinx iniconfig==2.0.0 # via pytest -isort==5.12.0 +isort==5.13.2 # via pylint -jinja2==3.1.2 +jinja2==3.1.3 # via # aflow # sphinx @@ -103,21 +94,21 @@ joblib==1.3.2 # dscribe # pymatgen # scikit-learn -jsonschema==4.3.0 +jsonschema==4.21.1 # via # matminer (setup.py) # mdf-toolbox +jsonschema-specifications==2023.12.1 + # via jsonschema kiwisolver==1.4.5 # via matplotlib -latexcodec==2.0.1 +latexcodec==3.0.0 # via pybtex -lazy-object-proxy==1.9.0 - # via astroid -llvmlite==0.40.1 +llvmlite==0.42.0 # via numba -markupsafe==2.1.3 +markupsafe==2.1.5 # via jinja2 -matplotlib==3.7.2 +matplotlib==3.8.3 # via # ase # pymatgen @@ -127,27 +118,21 @@ mccabe==0.7.0 # pylint mdf-forge==0.8.0 # via matminer (setup.py) -mdf-toolbox==0.6.0 +mdf-toolbox==0.7.1 # via mdf-forge -monty==2023.9.5 +monty==2024.2.26 # via - # emmet-core # matminer (setup.py) - # mp-api # pymatgen -mp-api==0.35.1 - # via pymatgen mpmath==1.3.0 # via sympy -msgpack==1.0.5 - # via mp-api mypy-extensions==1.0.0 # via black -networkx==3.1 +networkx==3.2.1 # via pymatgen -numba==0.57.1 +numba==0.59.1 # via sparse -numpy==1.24.4 +numpy==1.26.4 # via # aflow # ase @@ -163,7 +148,7 @@ numpy==1.24.4 # scipy # sparse # spglib -packaging==23.1 +packaging==24.0 # via # black # matplotlib @@ -172,78 +157,71 @@ packaging==23.1 # sphinx palettable==3.3.3 # via pymatgen -pandas==2.1.0 +pandas==1.5.3 # via # matminer (setup.py) # pymatgen -pathspec==0.11.2 +pathspec==0.12.1 # via black -pillow==10.0.0 +pillow==10.2.0 # via matplotlib -platformdirs==3.10.0 +platformdirs==4.2.0 # via # black # pylint -plotly==5.16.1 +plotly==5.20.0 # via pymatgen -pluggy==1.3.0 +pluggy==1.4.0 # via pytest pybind11==2.11.1 # via dscribe pybtex==0.24.0 - # via - # emmet-core - # pymatgen -pycodestyle==2.11.0 + # via pymatgen +pycodestyle==2.11.1 # via flake8 pycparser==2.21 # via cffi -pydantic==1.10.12 - # via - # emmet-core - # pymatgen -pyflakes==3.1.0 +pyflakes==3.2.0 # via flake8 -pygments==2.16.1 +pygments==2.17.2 # via sphinx pyjwt[crypto]==2.8.0 # via globus-sdk -pylint==2.17.5 +pylint==3.1.0 # via matminer (setup.py) -pymatgen==2023.9.2 - # via - # emmet-core - # matminer (setup.py) - # mp-api -pymongo==4.5.0 +pymatgen==2024.3.1 + # via matminer (setup.py) +pymongo==4.6.2 # via matminer (setup.py) -pyparsing==3.0.9 +pyparsing==3.1.2 # via # httplib2 # matplotlib pypif==2.1.2 # via citrination-client -pyrsistent==0.19.3 - # via jsonschema -pytest==7.4.1 +pytest==8.1.1 # via # matminer (setup.py) # pytest-cov # pytest-timeout -pytest-cov==4.1.0 +pytest-cov==5.0.0 # via matminer (setup.py) -pytest-timeout==2.1.0 +pytest-timeout==2.3.1 # via matminer (setup.py) -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via # matplotlib # pandas -pytz==2023.3.post1 +pytz==2024.1 # via pandas pyyaml==6.0.1 # via # citrination-client # pybtex +referencing==0.34.0 + # via + # jsonschema + # jsonschema-specifications requests==2.31.0 # via # citrination-client @@ -252,18 +230,21 @@ requests==2.31.0 # matminer (setup.py) # mdf-forge # mdf-toolbox - # mp-api # pymatgen # sphinx -ruamel-yaml==0.17.32 +rpds-py==0.18.0 + # via + # jsonschema + # referencing +ruamel-yaml==0.18.6 # via pymatgen -ruamel-yaml-clib==0.2.7 +ruamel-yaml-clib==0.2.8 # via ruamel-yaml -scikit-learn==1.3.0 +scikit-learn==1.4.1.post1 # via # dscribe # matminer (setup.py) -scipy==1.11.2 +scipy==1.12.0 # via # ase # dscribe @@ -274,7 +255,6 @@ six==1.16.0 # via # aflow # citrination-client - # latexcodec # pybtex # pypif # python-dateutil @@ -282,31 +262,23 @@ snowballstemmer==2.2.0 # via sphinx soupsieve==2.5 # via beautifulsoup4 -sparse==0.14.0 +sparse==0.15.1 # via dscribe -spglib==2.0.2 - # via - # emmet-core - # pymatgen -sphinx==7.2.5 - # via - # matminer (setup.py) - # sphinxcontrib-applehelp - # sphinxcontrib-devhelp - # sphinxcontrib-htmlhelp - # sphinxcontrib-qthelp - # sphinxcontrib-serializinghtml -sphinxcontrib-applehelp==1.0.7 +spglib==2.3.1 + # via pymatgen +sphinx==7.2.6 + # via matminer (setup.py) +sphinxcontrib-applehelp==1.0.8 # via sphinx -sphinxcontrib-devhelp==1.0.5 +sphinxcontrib-devhelp==1.0.6 # via sphinx -sphinxcontrib-htmlhelp==2.0.4 +sphinxcontrib-htmlhelp==2.0.5 # via sphinx sphinxcontrib-jsmath==1.0.1 # via sphinx -sphinxcontrib-qthelp==1.0.6 +sphinxcontrib-qthelp==1.0.7 # via sphinx -sphinxcontrib-serializinghtml==1.1.9 +sphinxcontrib-serializinghtml==1.1.10 # via sphinx sympy==1.12 # via @@ -316,39 +288,20 @@ tabulate==0.9.0 # via pymatgen tenacity==8.2.3 # via plotly -termcolor==2.3.0 +termcolor==2.4.0 # via aflow -threadpoolctl==3.2.0 +threadpoolctl==3.4.0 # via scikit-learn -tomli==2.0.1 - # via - # black - # coverage - # pylint - # pytest -tomlkit==0.12.1 +tomlkit==0.12.4 # via pylint -tqdm==4.66.1 +tqdm==4.66.2 # via # matminer (setup.py) # mdf-forge # pymatgen -typing-extensions==4.7.1 - # via - # astroid - # emmet-core - # mp-api - # pydantic -tzdata==2023.3 - # via pandas -ujson==5.8.0 +ujson==5.9.0 # via matminer (setup.py) uncertainties==3.1.7 # via pymatgen -urllib3==2.0.4 +urllib3==2.2.1 # via requests -wrapt==1.15.0 - # via astroid - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt index 8b2e7c594..8d05b6369 100644 --- a/requirements/ubuntu-latest_py3.9.txt +++ b/requirements/ubuntu-latest_py3.9.txt @@ -2,40 +2,40 @@ # This file is autogenerated by pip-compile with Python 3.9 # by the following command: # -# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.9_extras.txt +# pip-compile --all-extras --output-file=requirements/ubuntu-latest_py3.9.txt # aflow==0.0.11 # via matminer (setup.py) -alabaster==0.7.13 +alabaster==0.7.16 # via sphinx ase==3.22.1 # via # aflow # dscribe # matminer (setup.py) -astroid==2.15.6 +astroid==3.1.0 # via pylint -attrs==23.1.0 +attrs==23.2.0 # via # jsonschema # referencing -babel==2.12.1 +babel==2.14.0 # via sphinx -beautifulsoup4==4.12.2 +beautifulsoup4==4.12.3 # via aflow -black==23.7.0 +black==24.3.0 # via matminer (setup.py) -certifi==2023.7.22 +certifi==2024.2.2 # via requests -cffi==1.15.1 +cffi==1.16.0 # via cryptography -charset-normalizer==3.2.0 +charset-normalizer==3.3.2 # via requests citrination-client==6.5.1 # via matminer (setup.py) click==8.1.7 # via black -contourpy==1.1.0 +contourpy==1.2.0 # via matplotlib coverage[toml]==6.5.0 # via @@ -44,15 +44,15 @@ coverage[toml]==6.5.0 # pytest-cov coveralls==3.3.1 # via matminer (setup.py) -cryptography==41.0.3 +cryptography==42.0.5 # via # globus-sdk # pyjwt -cycler==0.11.0 +cycler==0.12.1 # via matplotlib -dill==0.3.7 +dill==0.3.8 # via pylint -dnspython==2.4.2 +dnspython==2.6.1 # via pymongo docopt==0.6.2 # via coveralls @@ -60,43 +60,36 @@ docutils==0.20.1 # via sphinx dscribe==2.1.0 # via matminer (setup.py) -emmet-core==0.67.5 - # via mp-api -exceptiongroup==1.1.3 +exceptiongroup==1.2.0 # via pytest fair-research-login==0.3.1 # via mdf-toolbox -flake8==6.1.0 +flake8==7.0.0 # via matminer (setup.py) -fonttools==4.42.1 +fonttools==4.50.0 # via matplotlib -future==0.18.3 - # via - # matminer (setup.py) - # uncertainties -globus-nexus-client==0.4.1 - # via mdf-toolbox -globus-sdk==3.28.0 +future==1.0.0 + # via uncertainties +globus-sdk==3.39.0 # via # fair-research-login - # globus-nexus-client # mdf-forge # mdf-toolbox httplib2==0.22.0 # via matminer (setup.py) -idna==3.4 +idna==3.6 # via requests imagesize==1.4.1 # via sphinx -importlib-metadata==6.8.0 +importlib-metadata==7.1.0 # via sphinx -importlib-resources==6.0.1 +importlib-resources==6.4.0 # via matplotlib iniconfig==2.0.0 # via pytest -isort==5.12.0 +isort==5.13.2 # via pylint -jinja2==3.1.2 +jinja2==3.1.3 # via # aflow # sphinx @@ -107,21 +100,21 @@ joblib==1.3.2 # dscribe # pymatgen # scikit-learn -jsonschema==4.3.0 +jsonschema==4.21.1 # via # matminer (setup.py) # mdf-toolbox +jsonschema-specifications==2023.12.1 + # via jsonschema kiwisolver==1.4.5 # via matplotlib -latexcodec==2.0.1 +latexcodec==3.0.0 # via pybtex -lazy-object-proxy==1.9.0 - # via astroid -llvmlite==0.40.1 +llvmlite==0.42.0 # via numba -markupsafe==2.1.3 +markupsafe==2.1.5 # via jinja2 -matplotlib==3.7.2 +matplotlib==3.8.3 # via # ase # pymatgen @@ -131,27 +124,21 @@ mccabe==0.7.0 # pylint mdf-forge==0.8.0 # via matminer (setup.py) -mdf-toolbox==0.6.0 +mdf-toolbox==0.7.1 # via mdf-forge -monty==2023.9.5 +monty==2024.2.26 # via - # emmet-core # matminer (setup.py) - # mp-api # pymatgen -mp-api==0.35.1 - # via pymatgen mpmath==1.3.0 # via sympy -msgpack==1.0.5 - # via mp-api mypy-extensions==1.0.0 # via black -networkx==3.1 +networkx==3.2.1 # via pymatgen -numba==0.57.1 +numba==0.59.1 # via sparse -numpy==1.24.4 +numpy==1.26.4 # via # aflow # ase @@ -167,7 +154,7 @@ numpy==1.24.4 # scipy # sparse # spglib -packaging==23.1 +packaging==24.0 # via # black # matplotlib @@ -176,78 +163,71 @@ packaging==23.1 # sphinx palettable==3.3.3 # via pymatgen -pandas==2.1.0 +pandas==1.5.3 # via # matminer (setup.py) # pymatgen -pathspec==0.11.2 +pathspec==0.12.1 # via black -pillow==10.0.0 +pillow==10.2.0 # via matplotlib -platformdirs==3.10.0 +platformdirs==4.2.0 # via # black # pylint -plotly==5.16.1 +plotly==5.20.0 # via pymatgen -pluggy==1.3.0 +pluggy==1.4.0 # via pytest pybind11==2.11.1 # via dscribe pybtex==0.24.0 - # via - # emmet-core - # pymatgen -pycodestyle==2.11.0 + # via pymatgen +pycodestyle==2.11.1 # via flake8 pycparser==2.21 # via cffi -pydantic==1.10.12 - # via - # emmet-core - # pymatgen -pyflakes==3.1.0 +pyflakes==3.2.0 # via flake8 -pygments==2.16.1 +pygments==2.17.2 # via sphinx pyjwt[crypto]==2.8.0 # via globus-sdk -pylint==2.17.5 +pylint==3.1.0 # via matminer (setup.py) -pymatgen==2023.9.2 - # via - # emmet-core - # matminer (setup.py) - # mp-api -pymongo==4.5.0 +pymatgen==2024.3.1 + # via matminer (setup.py) +pymongo==4.6.2 # via matminer (setup.py) -pyparsing==3.0.9 +pyparsing==3.1.2 # via # httplib2 # matplotlib pypif==2.1.2 # via citrination-client -pyrsistent==0.19.3 - # via jsonschema -pytest==7.4.1 +pytest==8.1.1 # via # matminer (setup.py) # pytest-cov # pytest-timeout -pytest-cov==4.1.0 +pytest-cov==5.0.0 # via matminer (setup.py) -pytest-timeout==2.1.0 +pytest-timeout==2.3.1 # via matminer (setup.py) -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via # matplotlib # pandas -pytz==2023.3.post1 +pytz==2024.1 # via pandas pyyaml==6.0.1 # via # citrination-client # pybtex +referencing==0.34.0 + # via + # jsonschema + # jsonschema-specifications requests==2.31.0 # via # citrination-client @@ -256,18 +236,21 @@ requests==2.31.0 # matminer (setup.py) # mdf-forge # mdf-toolbox - # mp-api # pymatgen # sphinx -ruamel-yaml==0.17.32 +rpds-py==0.18.0 + # via + # jsonschema + # referencing +ruamel-yaml==0.18.6 # via pymatgen -ruamel-yaml-clib==0.2.7 +ruamel-yaml-clib==0.2.8 # via ruamel-yaml -scikit-learn==1.3.0 +scikit-learn==1.4.1.post1 # via # dscribe # matminer (setup.py) -scipy==1.11.2 +scipy==1.12.0 # via # ase # dscribe @@ -278,7 +261,6 @@ six==1.16.0 # via # aflow # citrination-client - # latexcodec # pybtex # pypif # python-dateutil @@ -286,31 +268,23 @@ snowballstemmer==2.2.0 # via sphinx soupsieve==2.5 # via beautifulsoup4 -sparse==0.14.0 +sparse==0.15.1 # via dscribe -spglib==2.0.2 - # via - # emmet-core - # pymatgen -sphinx==7.2.5 - # via - # matminer (setup.py) - # sphinxcontrib-applehelp - # sphinxcontrib-devhelp - # sphinxcontrib-htmlhelp - # sphinxcontrib-qthelp - # sphinxcontrib-serializinghtml -sphinxcontrib-applehelp==1.0.7 +spglib==2.3.1 + # via pymatgen +sphinx==7.2.6 + # via matminer (setup.py) +sphinxcontrib-applehelp==1.0.8 # via sphinx -sphinxcontrib-devhelp==1.0.5 +sphinxcontrib-devhelp==1.0.6 # via sphinx -sphinxcontrib-htmlhelp==2.0.4 +sphinxcontrib-htmlhelp==2.0.5 # via sphinx sphinxcontrib-jsmath==1.0.1 # via sphinx -sphinxcontrib-qthelp==1.0.6 +sphinxcontrib-qthelp==1.0.7 # via sphinx -sphinxcontrib-serializinghtml==1.1.9 +sphinxcontrib-serializinghtml==1.1.10 # via sphinx sympy==1.12 # via @@ -320,9 +294,9 @@ tabulate==0.9.0 # via pymatgen tenacity==8.2.3 # via plotly -termcolor==2.3.0 +termcolor==2.4.0 # via aflow -threadpoolctl==3.2.0 +threadpoolctl==3.4.0 # via scikit-learn tomli==2.0.1 # via @@ -330,36 +304,26 @@ tomli==2.0.1 # coverage # pylint # pytest -tomlkit==0.12.1 +tomlkit==0.12.4 # via pylint -tqdm==4.66.1 +tqdm==4.66.2 # via # matminer (setup.py) # mdf-forge # pymatgen -typing-extensions==4.7.1 +typing-extensions==4.10.0 # via # astroid # black - # emmet-core # globus-sdk - # mp-api - # pydantic # pylint -tzdata==2023.3 - # via pandas -ujson==5.8.0 +ujson==5.9.0 # via matminer (setup.py) uncertainties==3.1.7 # via pymatgen -urllib3==2.0.4 +urllib3==2.2.1 # via requests -wrapt==1.15.0 - # via astroid -zipp==3.16.2 +zipp==3.18.1 # via # importlib-metadata # importlib-resources - -# The following packages are considered to be unsafe in a requirements file: -# setuptools