diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index f49c7032..b29b439e 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -15,11 +15,11 @@ dependencies: - structuretoolkit =0.0.39 - seekpath =2.2.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - jupyter-book =1.0.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 - pyiron_vasp =0.2.19 - hatchling =1.28.0 - hatch-vcs =0.5.0 diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 33d79574..d8172f47 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -2,9 +2,9 @@ channels: - conda-forge dependencies: - lammps =2024.08.29=*openmpi* -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - iprpy-data =2023.07.25 - dynaphopy =1.18.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 4dd14386..06d648aa 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,8 +5,8 @@ dependencies: - papermill - gpaw =25.7.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - dynaphopy =1.18.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index e6b9585a..0ca1aee3 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -6,7 +6,7 @@ dependencies: - lxml =6.0.2 - mendeleev =1.1.0 - numpy =2.3.5 -- pandas =2.3.3 +- pandas =3.0.0 - phonopy =2.47.1 - requests =2.32.5 - scipy =1.16.3 diff --git a/binder/environment.yml b/binder/environment.yml index 6438e092..1fc8a7d1 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -10,12 +10,12 @@ dependencies: - seekpath =2.2.0 - gpaw =25.7.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - dynaphopy =1.18.0 - tqdm =4.67.1 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 - pyiron_vasp =0.2.19 - hatchling =1.28.0 - hatch-vcs =0.5.0 diff --git a/pyproject.toml b/pyproject.toml index c0fef190..af0c7b82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,20 +49,20 @@ gpaw = [ lammps = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", - "pandas==2.3.3", - "pyiron_lammps==0.5.3", + "pandas==3.0.0", + "pyiron_lammps==0.5.4", ] lammps_phonons = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", - "pandas==2.3.3", + "pandas==3.0.0", "dynaphopy==1.18.0", - "pyiron_lammps==0.5.3", + "pyiron_lammps==0.5.4", ] experimental = [ "lxml==6.0.2", "mendeleev==1.1.0", - "pandas==2.3.3", + "pandas==3.0.0", "requests==2.32.5", ] sphinxdft = [ diff --git a/src/atomistics/referencedata/wikipedia.py b/src/atomistics/referencedata/wikipedia.py index 5a74bd23..9498bc1f 100644 --- a/src/atomistics/referencedata/wikipedia.py +++ b/src/atomistics/referencedata/wikipedia.py @@ -1,3 +1,5 @@ +from io import StringIO + import pandas import requests @@ -33,7 +35,7 @@ def get_elastic_properties(chemical_symbol: str) -> dict: "https://en.wikipedia.org/wiki/Elastic_properties_of_the_elements_(data_page)", headers={"User-Agent": "atomistics package"}, ) - df_lst = pandas.read_html(response.text) + df_lst = pandas.read_html(StringIO(response.text)) property_dict = {} for i, p in enumerate(property_lst): df_tmp = df_lst[i] diff --git a/src/atomistics/referencedata/wolframalpha.py b/src/atomistics/referencedata/wolframalpha.py index 9abe941c..864a7a0b 100644 --- a/src/atomistics/referencedata/wolframalpha.py +++ b/src/atomistics/referencedata/wolframalpha.py @@ -1,4 +1,5 @@ import os +from io import StringIO from typing import Callable, Optional, Union import numpy as np @@ -17,7 +18,7 @@ def _get_content_from_url(url: str) -> pandas.DataFrame: Returns: pandas.DataFrame: The content retrieved from the URL as a pandas DataFrame. """ - content = pandas.read_html(requests.get(url).text) + content = pandas.read_html(StringIO(requests.get(url).text)) if len(content[8]) > 1: return content[8] else: