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Dependency updates #41

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Dependency updates #41

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3b4145c
added black notebook formatting
wolearyc Oct 11, 2024
27dde49
made file_format case insensitive
wolearyc Oct 11, 2024
4ef7244
added automatic file_format determination based on filename
wolearyc Oct 11, 2024
7143e21
removed basics
wolearyc Dec 14, 2024
cdf1624
dropped support for python 3.10
wolearyc Dec 14, 2024
e39e25a
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Oct 28, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/python-package.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
python-version: ["3.10", "3.11", "3.12"]
python-version: ["3.11", "3.12", "3.13"]
uv-arg: ["--resolution=lowest", ""]

runs-on: ${{ matrix.os }}
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7 changes: 4 additions & 3 deletions .pre-commit-config.yaml
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Expand Up @@ -5,7 +5,7 @@ ci:
exclude: EPS_OUTCAR
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
rev: v5.0.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
Expand All @@ -16,9 +16,10 @@ repos:
- id: debug-statements
- id: requirements-txt-fixer
- repo: https://github.com/psf/black
rev: 24.8.0
rev: 24.10.0
hooks:
- id: black
- id: black-jupyter
- repo: local
hooks:
- id: pylint
Expand All @@ -32,7 +33,7 @@ repos:
"-rn", # Only display messages
]
- repo: https://github.com/pre-commit/mirrors-mypy
rev: 'v1.11.2' # Use the sha / tag you want to point at
rev: 'v1.13.0' # Use the sha / tag you want to point at
hooks:
- id: mypy
args: [--strict]
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -4,7 +4,7 @@
</div>

-------
![PyPI - Version](https://img.shields.io/pypi/v/ramannoodle?color=dark%20green) [![python](https://img.shields.io/badge/python-3.10|3.11|3.12-3776AB.svg?style=flat&logo=python&logoColor=white)](https://www.python.org) ![Tests](docs/tests-badge.svg) ![Coverage](docs/coverage-badge.svg) [![Documentation Status](https://readthedocs.org/projects/ramannoodle/badge/?version=latest)](https://ramannoodle.readthedocs.io/en/latest/?badge=latest) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit)
![PyPI - Version](https://img.shields.io/pypi/v/ramannoodle?color=dark%20green) [![python](https://img.shields.io/badge/python-3.11|3.12|3.13-3776AB.svg?style=flat&logo=python&logoColor=white)](https://www.python.org) ![Tests](docs/tests-badge.svg) ![Coverage](docs/coverage-badge.svg) [![Documentation Status](https://readthedocs.org/projects/ramannoodle/badge/?version=latest)](https://ramannoodle.readthedocs.io/en/latest/?badge=latest) [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit)

## About

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6 changes: 3 additions & 3 deletions deps/pymatgen_requirements.txt
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@@ -1,15 +1,15 @@
matplotlib >= 3.7.0 # min recommended
mpmath >= 1.2.0
pandas >= 2.0.0 # min recommended
pillow >= 8.3.2;python_version=='3.10' and sys_platform=='darwin' # working
pillow >= 8.3.2;python_version=='3.10' and sys_platform=='win32' # working
pillow >= 8.3.2;python_version=='3.10' and sys_platform=='linux' # min recommended
pillow >= 8.3.2;python_version=='3.11' and sys_platform=='darwin' # min recommended
pillow >= 10.0.0;python_version=='3.11' and sys_platform=='win32' # working
pillow >= 8.3.2;python_version=='3.11' and sys_platform=='linux' # min recommended
pillow >= 10.1.0;python_version=='3.12' and sys_platform=='darwin' # working
pillow >= 10.1.0;python_version=='3.12' and sys_platform=='win32' # working
pillow >= 10.1.0;python_version=='3.12' and sys_platform=='linux' # min recommended
pillow >= 10.1.0;python_version=='3.13' and sys_platform=='darwin' # working
pillow >= 10.1.0;python_version=='3.13' and sys_platform=='win32' # working
pillow >= 10.1.0;python_version=='3.13' and sys_platform=='linux' # min recommended
pymatgen >= 2024.8.9 # min working
pyparsing >= 3.0.0 # min working
ruamel-yaml >= 0.17.2
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4 changes: 2 additions & 2 deletions deps/requirements.txt
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@@ -1,12 +1,12 @@
# numpy, scipy recommendations: https://scientific-python.org/specs/spec-0000/

defusedxml >= 0.6.0 # min working
numpy >= 1.24.0;python_version=='3.10' # min recommended
numpy >= 1.24.0;python_version=='3.11' # min recommended
numpy >= 1.26.0;python_version=='3.12' # min working
scipy >= 1.10.0;python_version=='3.10' # min recommended
numpy >= 1.26.0;python_version=='3.13' # min working
scipy >= 1.10.0;python_version=='3.11' # min recommended
scipy >= 1.11.2;python_version=='3.12' # min working
scipy >= 1.11.2;python_version=='3.13' # min working
spglib >= 1.16.4 # min working
tabulate >= 0.8.8 # min working
tqdm >= 2.0 # min working
11 changes: 6 additions & 5 deletions deps/torch_geometric_requirements.txt
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@@ -1,16 +1,17 @@
aiohttp >= 3.8.0;python_version=='3.10' # min working
aiohttp >= 3.8.3;python_version=='3.11' # min working
aiohttp >= 3.9.0;python_version=='3.12' # min working
aiohttp >= 3.9.0;python_version=='3.13' # min working
dill >= 0.3.4 # min working
frozenlist >= 1.2.0;python_version=='3.10' # min working
frozenlist >= 1.3.3;python_version=='3.11' # min working
frozenlist >= 1.4.1;python_version=='3.12' # min working
fsspec>= 2021.4.0;python_version=='3.10' # min working
frozenlist >= 1.4.1;python_version=='3.13' # min working
jinja2 >= 3.0.2 # min working
pyparsing >= 3.0.0 # min working
scikit-learn >= 1.2.0;python_version=='3.10' # min working
scikit-learn >= 1.2.0;python_version=='3.11' # min working
scikit-learn >= 1.3.0;python_version=='3.11' # min working
scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='darwin' # min working
scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='linux' # min working
scikit-learn >= 1.4.0;python_version=='3.12' and sys_platform=='win32' # min working
scikit-learn >= 1.3.0;python_version=='3.13' and sys_platform=='darwin' # min working
scikit-learn >= 1.3.0;python_version=='3.13' and sys_platform=='linux' # min working
scikit-learn >= 1.4.0;python_version=='3.13' and sys_platform=='win32' # min working
torch_geometric >= 2.3.0 # min working
43 changes: 22 additions & 21 deletions docs/source/conf.py
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@@ -1,4 +1,5 @@
"""Sphinx conf.py."""

# pylint: skip-file
# flake-8: noqa
# cspell: disable
Expand All @@ -13,52 +14,52 @@
import sys
import os

project = 'ramannoodle'
project = "ramannoodle"
copyright = "2023-present, Willis O'Leary"
author = "Willis O'Leary"
release = '0.5.0'
release = "0.5.0"

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.intersphinx',
'sphinx.ext.napoleon',
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.intersphinx",
"sphinx.ext.napoleon",
"sphinx_autodoc_typehints",
'nbsphinx',
'IPython.sphinxext.ipython_console_highlighting',
"nbsphinx",
"IPython.sphinxext.ipython_console_highlighting",
]
autodoc_typehints = 'description'
autodoc_typehints = "description"
nbsphinx_allow_errors = True

intersphinx_mapping = {
'python': ('https://docs.python.org/3/', None),
'numpy': ('http://docs.scipy.org/doc/numpy', None),
'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
'torch': ('https://pytorch.org/docs/stable/', None),
'pymatgen': ('https://pymatgen.org', None),
"python": ("https://docs.python.org/3/", None),
"numpy": ("http://docs.scipy.org/doc/numpy", None),
"scipy": ("http://docs.scipy.org/doc/scipy/reference", None),
"torch": ("https://pytorch.org/docs/stable/", None),
"pymatgen": ("https://pymatgen.org", None),
}

intersphinx_disabled_domains = ['std']
intersphinx_disabled_domains = ["std"]

templates_path = ['_templates']
templates_path = ["_templates"]
exclude_patterns = []

autodoc_member_order = 'groupwise'
autodoc_member_order = "groupwise"

# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = 'furo'
html_title = 'ramannoodle'
html_static_path = ['_static']
html_theme = "furo"
html_title = "ramannoodle"
html_static_path = ["_static"]
html_theme_options = {
"light_logo": "logo.png",
"dark_logo": "logo_dark.png",
"sidebar_hide_name": True,
}
html_extra_path = ["robots.txt"]

sys.path.insert(0, os.path.abspath('../../'))
sys.path.insert(0, os.path.abspath("../../"))
2 changes: 1 addition & 1 deletion docs/source/io.rst
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Expand Up @@ -33,7 +33,7 @@ These generic functions are less flexible than those first mentioned, and theref
model = rn.pmodel.InterpolationModel(...)
model.add_dof_from_files(..., file_format = "outcar")

:meth:`.InterpolationModel.add_dof_from_files` and other methods like it rely on these generic methods, as apparent from the ``file_format`` argument.
:meth:`.InterpolationModel.add_dof_from_files` and other methods like it rely on these generic methods, as apparent from the ``file_format`` argument. When ``file_format=="auto"``, ramannoodle will guess the file format based on the filename. Otherwise, ``file_format`` should be set according to the next section.

.. _Supported formats:

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