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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
share/python-wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
MANIFEST | ||
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# PyInstaller | ||
# Usually these files are written by a python script from a template | ||
# before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
*.manifest | ||
*.spec | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.nox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
*.py,cover | ||
.hypothesis/ | ||
.pytest_cache/ | ||
cover/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
db.sqlite3 | ||
db.sqlite3-journal | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
.pybuilder/ | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# IPython | ||
profile_default/ | ||
ipython_config.py | ||
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# pyenv | ||
# For a library or package, you might want to ignore these files since the code is | ||
# intended to run in multiple environments; otherwise, check them in: | ||
# .python-version | ||
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# pipenv | ||
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
# However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
# having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
# install all needed dependencies. | ||
#Pipfile.lock | ||
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# poetry | ||
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. | ||
# This is especially recommended for binary packages to ensure reproducibility, and is more | ||
# commonly ignored for libraries. | ||
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control | ||
#poetry.lock | ||
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# pdm | ||
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. | ||
#pdm.lock | ||
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it | ||
# in version control. | ||
# https://pdm.fming.dev/#use-with-ide | ||
.pdm.toml | ||
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm | ||
__pypackages__/ | ||
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# Celery stuff | ||
celerybeat-schedule | ||
celerybeat.pid | ||
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# SageMath parsed files | ||
*.sage.py | ||
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# Environments | ||
.env | ||
.venv | ||
env/ | ||
venv/ | ||
ENV/ | ||
env.bak/ | ||
venv.bak/ | ||
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
.dmypy.json | ||
dmypy.json | ||
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# Pyre type checker | ||
.pyre/ | ||
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# pytype static type analyzer | ||
.pytype/ | ||
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# Cython debug symbols | ||
cython_debug/ | ||
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# PyCharm | ||
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can | ||
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore | ||
# and can be added to the global gitignore or merged into this file. For a more nuclear | ||
# option (not recommended) you can uncomment the following to ignore the entire idea folder. | ||
#.idea/ | ||
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# Models | ||
*.pt |
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# .readthedocs.yml | ||
# Read the Docs configuration file | ||
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details | ||
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# Required | ||
version: 2 | ||
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# Set the OS, Python version and other tools you might need | ||
build: | ||
os: ubuntu-22.04 | ||
tools: | ||
python: "3.11" | ||
rust: "1.70" | ||
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# Build documentation in the docs/ directory with Sphinx | ||
sphinx: | ||
configuration: docs/src/conf.py | ||
fail_on_warning: true | ||
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# Declare the Python requirements required to build the docs. | ||
# Additionally, a custom environment variable | ||
# PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu | ||
# is declared in the project’s dashboard | ||
python: | ||
install: | ||
- method: pip | ||
path: . | ||
- requirements: docs/requirements.txt |
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BSD 3-Clause License | ||
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Copyright (c) 2023, Laboratory of Computational Science and Modeling | ||
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Redistribution and use in source and binary forms, with or without | ||
modification, are permitted provided that the following conditions are met: | ||
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1. Redistributions of source code must retain the above copyright notice, this | ||
list of conditions and the following disclaimer. | ||
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2. Redistributions in binary form must reproduce the above copyright notice, | ||
this list of conditions and the following disclaimer in the documentation | ||
and/or other materials provided with the distribution. | ||
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3. Neither the name of the copyright holder nor the names of its | ||
contributors may be used to endorse or promote products derived from | ||
this software without specific prior written permission. | ||
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE | ||
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | ||
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | ||
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | ||
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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graft src | ||
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include LICENSE | ||
include README.md | ||
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prune docs | ||
prune tests | ||
prune .github | ||
prune .tox | ||
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exclude .gitignore | ||
exclude tox.ini | ||
exclude .readthedocs.yml | ||
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global-exclude *.py[cod] __pycache__/* *.so *.dylib |
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metatensor-models | ||
----------------- | ||
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This is a repository for models using metatensor, in one shape or another. The only | ||
requirement is for these models to be able to take metatensor objects as inputs and | ||
outputs. The models do not need to live entirely in this repository: in the most extreme | ||
case, this repository can simply contain a wrapper to an external model. |
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furo | ||
sphinx >= 7 | ||
sphinx-toggleprompt | ||
tomli |
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import os | ||
import sys | ||
from datetime import datetime | ||
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import tomli # Replace by tomllib from std library once docs are build with Python 3.11 | ||
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import metatensor.models | ||
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ROOT = os.path.abspath(os.path.join("..", "..")) | ||
sys.path.insert(0, ROOT) | ||
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# -- Project information ----------------------------------------------------- | ||
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# The master toctree document. | ||
master_doc = "index" | ||
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with open(os.path.join(ROOT, "pyproject.toml"), "rb") as fp: | ||
project_dict = tomli.load(fp)["project"] | ||
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project = project_dict["name"] | ||
author = ", ".join(a["name"] for a in project_dict["authors"]) | ||
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copyright = f"{datetime.now().date().year}, {author}" | ||
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# The full version, including alpha/beta/rc tags | ||
release = metatensor.models.__version__ | ||
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# -- General configuration --------------------------------------------------- | ||
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# Add any Sphinx extension module names here, as strings. They can be | ||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom | ||
# ones. | ||
extensions = [ | ||
"sphinx.ext.viewcode", | ||
"sphinx.ext.autodoc", | ||
"sphinx.ext.intersphinx", | ||
"sphinx_toggleprompt", | ||
] | ||
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python_use_unqualified_type_names = True | ||
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autoclass_content = "both" | ||
autodoc_member_order = "bysource" | ||
autodoc_typehints = "both" | ||
autodoc_typehints_format = "short" | ||
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intersphinx_mapping = { | ||
"ase": ("https://wiki.fysik.dtu.dk/ase/", None), | ||
"python": ("https://docs.python.org/3", None), | ||
"torch": ("https://pytorch.org/docs/stable/", None), | ||
"metatensor": ("https://lab-cosmo.github.io/metatensor/latest/", None), | ||
"rascaline": ("https://luthaf.fr/rascaline/latest/", None), | ||
} | ||
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# -- Options for HTML output ------------------------------------------------- | ||
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# The theme to use for HTML and HTML Help pages. See the documentation for | ||
# a list of builtin themes. | ||
# | ||
html_theme = "furo" | ||
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html_theme_options = { | ||
"footer_icons": [ | ||
{ | ||
"name": "GitHub", | ||
"url": project_dict["urls"]["repository"], | ||
"html": "", | ||
"class": "fa-brands fa-github fa-2x", | ||
}, | ||
], | ||
} | ||
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# font-awesome logos (used in the footer) | ||
html_css_files = [ | ||
"https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/fontawesome.min.css", | ||
"https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/solid.min.css", | ||
"https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css", | ||
] |
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Adding new models | ||
================= | ||
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To be done. |
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Developer documentation | ||
======================= | ||
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This is a collection of documentation for developers of the metatensor-models package. | ||
It includes documentation on how to add a new model, as well as the API of the utils | ||
module. | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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adding-models | ||
utils/index |
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Dataset | ||
####### | ||
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.. automodule:: metatensor.models.utils.data.dataset | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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Utility API | ||
=========== | ||
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This is the API for the ``utils`` module of ``metatensor-models``. | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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dataset | ||
readers/index | ||
model-io |
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Model IO | ||
######## | ||
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.. automodule:: metatensor.models.utils.model_io | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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Structure and Target data Readers | ||
================================= | ||
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The main entry point for reading structure and target information are the two reader | ||
functions | ||
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.. automodule:: metatensor.models.utils.data.readers | ||
:members: | ||
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Based on the provided filename they chose which child reader they use. For details on | ||
these refer to their documentation | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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structure | ||
target |
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