pydantic_espresso 0.0.1__tar.gz

pydantic_espresso-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Edward Linscott
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pydantic_espresso-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pydantic_espresso
+Version: 0.0.1
+Summary: Pydantic models for Quantum ESPRESSO
+Keywords: snekpack,cookiecutter
+Author: Edward Linscott
+Author-email: Edward Linscott <edwardlinscott@gmail.com>
+License-File: LICENSE
+Classifier: Development Status :: 1 - Planning
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: tox
+Classifier: Framework :: Sphinx
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Typing :: Typed
+Requires-Dist: pydantic
+Requires-Dist: packaging
+Requires-Dist: click ; extra == 'dev'
+Requires-Dist: python-gitlab ; extra == 'dev'
+Requires-Dist: defusedxml>=0.7.1 ; extra == 'dev'
+Maintainer: Edward Linscott
+Maintainer-email: Edward Linscott <edwardlinscott@gmail.com>
+Requires-Python: >=3.10
+Project-URL: Bug Tracker, https://github.com/elinscott/pydantic-espresso/issues
+Project-URL: Homepage, https://github.com/elinscott/pydantic-espresso
+Project-URL: Repository, https://github.com/elinscott/pydantic-espresso.git
+Project-URL: Documentation, https://pydantic_espresso.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/elinscott
+Provides-Extra: dev
+Description-Content-Type: text/markdown
+
+<!--
+<p align="center">
+  <img src="https://github.com/elinscott/pydantic-espresso/raw/main/docs/source/logo.png" height="150">
+</p>
+-->
+
+<h1 align="center">
+  pydantic-espresso
+</h1>
+
+<p align="center">
+    <a href="https://github.com/elinscott/pydantic-espresso/actions/workflows/tests.yml">
+        <img alt="Tests" src="https://github.com/elinscott/pydantic-espresso/actions/workflows/tests.yml/badge.svg" /></a>
+    <a href="https://pypi.org/project/pydantic_espresso">
+        <img alt="PyPI" src="https://img.shields.io/pypi/v/pydantic_espresso" /></a>
+    <a href="https://pypi.org/project/pydantic_espresso">
+        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/pydantic_espresso" /></a>
+    <a href="https://github.com/elinscott/pydantic-espresso/blob/main/LICENSE">
+        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/pydantic_espresso" /></a>
+    <a href='https://pydantic_espresso.readthedocs.io/en/latest/?badge=latest'>
+        <img src='https://readthedocs.org/projects/pydantic_espresso/badge/?version=latest' alt='Documentation Status' /></a>
+    <a href="https://codecov.io/gh/elinscott/pydantic-espresso/branch/main">
+        <img src="https://codecov.io/gh/elinscott/pydantic-espresso/branch/main/graph/badge.svg" alt="Codecov status" /></a>  
+    <a href="https://github.com/cthoyt/cookiecutter-python-package">
+        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
+    <a href="https://github.com/astral-sh/ruff">
+        <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
+    <a href="https://github.com/elinscott/pydantic-espresso/blob/main/.github/CODE_OF_CONDUCT.md">
+        <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
+    <!-- uncomment if you archive on zenodo
+    <a href="https://zenodo.org/badge/latestdoi/XXXXXX">
+        <img src="https://zenodo.org/badge/XXXXXX.svg" alt="DOI"></a>
+    -->
+</p>
+
+Pydantic models for `Quantum ESPRESSO`.
+
+The models are auto-generated from the `INPUT_*.def` files shipped with
+Quantum ESPRESSO. Supported QE versions are 7.6 and newer (the schema for
+older releases lacks the structured `<units>`, `<dimensionality>`, and
+`<default kind="...">` metadata that the generator depends on).
+
+## 💪 Getting Started
+
+```python
+from pydantic_espresso.models.pw.develop import PWInput
+
+inp = PWInput(
+    system={"ibrav": 0, "nat": 1, "ntyp": 1, "ecutwfc": 30.0},
+    cell_parameters={"unit": "alat", "vectors": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]},
+    atomic_positions={
+        "unit": "alat",
+        "positions": [{"species": "H", "position": [0.0, 0.0, 0.0]}],
+    },
+    k_points={"kind": "gamma"},
+)
+
+# Pydantic enforces both the QE input schema and the field constraints:
+inp.system.ibrav = -1          # ValidationError: invalid Bravais lattice index
+inp.system.nbnd = "a"          # ValidationError: not an int
+inp.control.calculation = "bands"   # OK
+```
+
+Each numeric field carries its physical units and dimensionality as
+`Quantity` metadata, threaded into both the pydantic field info and the
+JSON schema:
+
+```python
+from pydantic_espresso.models.pw.develop import SystemNamelist
+from pydantic_espresso.quantity import quantity_for
+
+q = quantity_for(SystemNamelist.model_fields["ecutwfc"])
+# Quantity(units='Ry', dimensionality='energy')
+
+PWInput.model_json_schema()["$defs"]["SystemNamelist"]["properties"]["ecutwfc"]
+# {'type': 'number', 'units': 'Ry', 'dimensionality': 'energy', ...}
+```
+
+QE namelist branches with mutually-exclusive layouts (e.g. PP's `PLOT`
+namelist discriminated on `iflag`) are exposed as pydantic discriminated
+unions, so the right variant is picked automatically from the input data.
+
+### Readable error reports
+
+Construction raises a standard `pydantic.ValidationError`. Pass the caught
+error to `pydantic_espresso.errors.explain` for a grouped, recursive summary
+that names each missing input together with its type, units, and help text:
+
+```python
+from pydantic import ValidationError
+from pydantic_espresso.errors import explain
+from pydantic_espresso.models.pw.develop import PWInput
+
+try:
+    inp = PWInput(
+        system={"ibrav": 0, "ecutwfc": 30.0},                     # missing nat, ntyp
+        cell_parameters={"vectors": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]},  # missing 'unit'
+        k_points={"kind": "automatic"},                           # missing grid
+        # atomic_positions omitted entirely
+    )
+except ValidationError as exc:
+    print(explain(exc, PWInput))
+```
+
+```text
+PWInput is missing required inputs:
+  system:
+      - nat (int): number of atoms in the unit cell (ALL atoms, except if space_group is set, in
+        which case, INEQUIVALENT atoms)
+      - ntyp (int): number of types of atoms in the unit cell
+  atomic_positions: required — choose 'unit': ['alat', 'bohr', 'angstrom', 'crystal', 'crystal_sg']
+  k_points [kind='automatic']:
+      - grid (tuple[int, int, int]): Monkhorst-Pack mesh dimensions (nk1, nk2, nk3): number of
+        k-points along each reciprocal-lattice direction of the uniform grid.
+  cell_parameters: missing discriminator 'unit' (one of ['alat', 'bohr', 'angstrom'])
+```
+
+### Command Line Interface
+
+The `pydantic_espresso` command line tool ships with the package but requires
+the optional `dev` extra (which pulls in `click`, `python-gitlab`, and
+`defusedxml`). Install it with `pip install pydantic_espresso[dev]` or
+`uv pip install "pydantic_espresso[dev]"`.
+
+It can be used from the console with the `--help` flag to show all subcommands:
+
+```console
+$ pydantic_espresso --help
+```
+
+The JSON schema for `pw.x` can be generated with the command
+
+```console
+$ pydantic_espresso schema pw
+```
+
+## 🚀 Installation
+
+<!-- Uncomment this section after your first ``tox -e finish``
+The most recent release can be installed from
+[PyPI](https://pypi.org/project/pydantic_espresso/) with uv:
+
+```console
+$ uv pip install pydantic_espresso
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install pydantic_espresso
+```
+-->
+
+The most recent code and data can be installed directly from GitHub with uv:
+
+```console
+$ uv pip install git+https://github.com/elinscott/pydantic-espresso.git
+```
+
+or with pip:
+
+```console
+$ python3 -m pip install git+https://github.com/elinscott/pydantic-espresso.git
+```
+
+## 👐 Contributing
+
+Contributions, whether filing an issue, making a pull request, or forking, are
+appreciated. See
+[CONTRIBUTING.md](https://github.com/elinscott/pydantic-espresso/blob/master/.github/CONTRIBUTING.md)
+for more information on getting involved.
+
+## 👋 Attribution
+
+### ⚖️ License
+
+The code in this package is licensed under the MIT License.
+
+<!--
+### 📖 Citation
+
+Citation goes here!
+-->
+
+<!--
+### 🎁 Support
+
+This project has been supported by the following organizations (in alphabetical order):
+
+- [Biopragmatics Lab](https://biopragmatics.github.io)
+
+-->
+
+<!--
+### 💰 Funding
+
+This project has been supported by the following grants:
+
+| Funding Body  | Program                                                      | Grant Number |
+|---------------|--------------------------------------------------------------|--------------|
+| Funder        | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ       |
+-->
+
+### 🍪 Cookiecutter
+
+This package was created with
+[@audreyfeldroy](https://github.com/audreyfeldroy)'s
+[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using
+[@cthoyt](https://github.com/cthoyt)'s
+[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
+template.
+
+## 🛠️ For Developers
+
+<details>
+  <summary>See developer instructions</summary>
+
+The final section of the README is for if you want to get involved by making a
+code contribution.
+
+### Development Installation
+
+To install in development mode, use the following:
+
+```console
+$ git clone git+https://github.com/elinscott/pydantic-espresso.git
+$ cd pydantic-espresso
+$ uv pip install -e .
+```
+
+Alternatively, install using pip:
+
+```console
+$ python3 -m pip install -e .
+```
+
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
+### 🥼 Testing
+
+After cloning the repository and installing `tox` with
+`uv tool install tox --with tox-uv` or
+`python3 -m pip install tox tox-uv`, the unit tests in the `tests/` folder
+can be run reproducibly with:
+
+```console
+$ tox -e py
+```
+
+Additionally, these tests are automatically re-run with each commit in a
+[GitHub Action](https://github.com/elinscott/pydantic-espresso/actions?query=workflow%3ATests).
+
+### 📖 Building the Documentation
+
+The documentation can be built locally using the following:
+
+```console
+$ git clone git+https://github.com/elinscott/pydantic-espresso.git
+$ cd pydantic-espresso
+$ tox -e docs
+$ open docs/build/html/index.html
+```
+
+The documentation automatically installs the package as well as the `docs` extra
+specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like
+`texext` can be added there. Additionally, they need to be added to the
+`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
+
+The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
+[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The
+[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration
+you'll need. You can also set up continuous integration on GitHub to check not
+only that Sphinx can build the documentation in an isolated environment (i.e.,
+with `tox -e docs-test`) but also that
+[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
+
+#### Configuring ReadTheDocs
+
+1. Log in to ReadTheDocs with your GitHub account to install the integration at
+   https://readthedocs.org/accounts/login/?next=/dashboard/
+2. Import your project by navigating to https://readthedocs.org/dashboard/import
+   then clicking the plus icon next to your repository
+3. You can rename the repository on the next screen using a more stylized name
+   (i.e., with spaces and capital letters)
+4. Click next, and you're good to go!
+
+### 📦 Making a Release
+
+#### Configuring Zenodo
+
+[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
+to each release of your package.
+
+1. Log in to Zenodo via GitHub with this link:
+   https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
+   that lists all of your organizations and asks you to approve installing the
+   Zenodo app on GitHub. Click "grant" next to any organizations you want to
+   enable the integration for, then click the big green "approve" button. This
+   step only needs to be done once.
+2. Navigate to https://zenodo.org/account/settings/github/, which lists all of
+   your GitHub repositories (both in your username and any organizations you
+   enabled). Click the on/off toggle for any relevant repositories. When you
+   make a new repository, you'll have to come back to this
+
+After these steps, you're ready to go! After you make "release" on GitHub (steps
+for this are below), you can navigate to
+https://zenodo.org/account/settings/github/repository/elinscott/pydantic-espresso
+to see the DOI for the release and link to the Zenodo record for it.
+
+#### Registering with the Python Package Index (PyPI)
+
+You only have to do the following steps once.
+
+1. Register for an account on the
+   [Python Package Index (PyPI)](https://pypi.org/account/register)
+2. Navigate to https://pypi.org/manage/account and make sure you have verified
+   your email address. A verification email might not have been sent by default,
+   so you might have to click the "options" dropdown next to your address to get
+   to the "re-send verification email" button
+3. 2-Factor authentication is required for PyPI since the end of 2023 (see this
+   [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).
+   This means you have to first issue account recovery codes, then set up
+   2-factor authentication
+4. Issue an API token from https://pypi.org/manage/account/token
+
+#### Configuring your machine's connection to PyPI
+
+You have to do the following steps once per machine.
+
+```console
+$ uv tool install keyring
+$ keyring set https://upload.pypi.org/legacy/ __token__
+$ keyring set https://test.pypi.org/legacy/ __token__
+```
+
+Note that this deprecates previous workflows using `.pypirc`.
+
+#### Uploading to PyPI
+
+After installing the package in development mode and installing
+`tox` with `uv tool install tox --with tox-uv` or
+`python3 -m pip install tox tox-uv`, run the following from the console:
+
+```console
+$ tox -e finish
+```
+
+This script does the following:
+
+1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to
+   switch the version number in the `pyproject.toml`, `CITATION.cff`,
+   `src/pydantic_espresso/version.py`, and
+   [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
+2. Packages the code in both a tar archive and a wheel using
+   [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
+3. Uploads to PyPI using
+   [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).
+4. Push to GitHub. You'll need to make a release going with the commit where the
+   version was bumped.
+5. Bump the version to the next patch. If you made big changes and want to bump
+   the version by minor, you can use `tox -e bumpversion -- minor` after.
+
+#### Releasing on GitHub
+
+1. Navigate to
+   https://github.com/elinscott/pydantic-espresso/releases/new
+   to draft a new release
+2. Click the "Choose a Tag" dropdown and select the tag corresponding to the
+   release you just made
+3. Click the "Generate Release Notes" button to get a quick outline of recent
+   changes. Modify the title and description as you see fit
+4. Click the big green "Publish Release" button
+
+This will trigger Zenodo to assign a DOI to your release as well.
+
+</details>