Merge pull request #1 from stfc/setup-repo

Add initial repo contents

.gitignore

@@ -0,0 +1,17 @@
+*.lock
+*.pyc
+*.swo
+*.swp
+~*
+*~
+.project
+*.egg*
+.DS_Store
+.coverage
+.pytest_cache
+.vscode
+build/
+dist/
+pip-wheel-metadata/
+__pycache__/
+.tox/

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# Install pre-commit hooks via:
+# pre-commit install
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+    - id: check-json
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.0
+  hooks:
+  - id: pyupgrade
+    args: ["--py310-plus"]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
+  hooks:
+    - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 24.1.1
+  hooks:
+    - id: black
+
+- repo: local
+  hooks:
+  - id: pylint
+    language: system
+    types: [file, python]
+    name: pylint
+    description: "This hook runs the pylint static code analyzer"
+    exclude: &exclude_files >
+      (?x)^(
+          docs/.*|
+      )$
+    entry: pylint

README.md

@@ -0,0 +1,48 @@
+[![Build Status][ci-badge]][ci-link]
+[![Coverage Status][cov-badge]][cov-link]
+[![Docs status][docs-badge]][docs-link]
+[![PyPI version][pypi-badge]][pypi-link]
+[![License][license-badge]][license-link]
+
+# janus-core
+
+Tools for machine learnt interatomic potentials
+
+## Development
+
+1. Install [poetry](https://python-poetry.org/docs/#installation)
+2. (Optional) Create a virtual environment
+3. Install `janus-core` with dependencies:
+
+```shell
+git clone https://github.com/stfc/janus-core
+cd janus-core
+pip install --upgrade pip
+poetry install --with pre-commit,dev,docs  # install extra dependencies
+pre-commit install  # install pre-commit hooks
+pytest -v  # discover and run all tests
+```
+
+## License
+
+[BSD 3-Clause License](LICENSE)
+
+## Funding
+
+Contributors to this project were funded by
+
+[![PSDI](docs/source/images/psdi-100.webp)](https://www.psdi.ac.uk/)
+[![ALC](docs/source/images/alc-100.webp)](https://adalovelacecentre.ac.uk/)
+[![CoSeC](docs/source/images/cosec-100.webp)](https://www.scd.stfc.ac.uk/Pages/CoSeC.aspx)
+
+
+[ci-badge]: https://github.com/stfc/janus-core/workflows/ci/badge.svg
+[ci-link]: https://github.com/stfc/janus-core/actions
+[cov-badge]: https://coveralls.io/repos/github/stfc/janus-core/badge.svg?branch=main
+[cov-link]: https://coveralls.io/github/stfc/janus-core?branch=main
+[docs-badge]: https://github.com/stfc/janus-core/actions/workflows/pages/pages-build-deployment/badge.svg
+[docs-link]: https://stfc.github.io/janus-core/
+[pypi-badge]: https://badge.fury.io/py/janus-core.svg
+[pypi-link]: https://badge.fury.io/py/janus-core
+[license-badge]: https://img.shields.io/badge/License-BSD_3--Clause-blue.svg
+[license-link]: https://opensource.org/licenses/BSD-3-Clause

janus_core/__init__.py

@@ -0,0 +1,8 @@
+"""
+janus_core
+
+Tools for machine learnt interatomic potentials
+"""
+
+__version__ = "0.1.0a0"
+

pyproject.toml

@@ -0,0 +1,73 @@
+[tool.poetry]
+name = "janus-core"
+version = "0.1.0a0"
+description = "Tools for machine learnt interatomic potentials"
+authors = [
+    "Elliott Kasoar",
+    "Federica Zanca",
+    "Patrick Austin",
+    "David Mason",
+    "Jacob Wilkins",
+    "Alin M. Elena",
+]
+license = "LICENSE"
+readme = "README.md"
+packages = [{include = "janus_core"}]
+classifiers = [
+    "Programming Language :: Python",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD 3-Clause License",
+    "Natural Language :: English",
+    "Development Status :: 3 - Alpha",
+]
+repository = "https://github.com/stfc/janus-core/"
+documentation = "https://stfc.github.io/janus-core/"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+ase = "^3.22.1"
+
+[tool.poetry.group.dev.dependencies]
+coverage = {extras = ["toml"], version = "^7.4.1"}
+pgtest = "^1.3.2"
+pytest = "^8.0"
+pytest-cov = "^4.1.0"
+wheel = "^0.42"
+
+[tool.poetry.group.pre-commit]
+optional = true
+[tool.poetry.group.pre-commit.dependencies]
+black = "^24.1.1"
+pre-commit = "^3.6.0"
+pylint = "^2.15.10"
+
+[tool.poetry.group.docs]
+optional = true
+[tool.poetry.group.docs.dependencies]
+furo = "^2024.1.29"
+markupsafe = "<2.1"
+sphinx = "^7.2.6"
+sphinxcontrib-contentui = "^0.2.5"
+sphinxcontrib-details-directive = "^0.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pylint.format]
+max-line-length = 125
+
+[tool.pytest.ini_options]
+# Configuration for [pytest](https://docs.pytest.org)
+python_files = "test_*.py"
+
+[tool.coverage.run]
+# Configuration of [coverage.py](https://coverage.readthedocs.io)
+# reporting which lines of your plugin are covered by tests
+source=["janus_core"]
+
+[tool.isort]
+# Configuration of [isort](https://isort.readthedocs.io)
+line_length = 120
+force_sort_within_sections = true
+sections = ['FUTURE', 'STDLIB', 'THIRDPARTY', 'FIRSTPARTY', 'LOCALFOLDER']

tests/__init__.py

@@ -0,0 +1,8 @@
+""" Tests for janus_core.
+
+Includes example test (test.py).
+"""
+
+import os
+
+TEST_DIR = os.path.dirname(os.path.realpath(__file__))

tests/test_example.py

@@ -0,0 +1,8 @@
+"""Example test."""
+
+def test_example():
+    """
+    Example test.
+    """
+    assert 1 == 1
+