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Merge pull request #3 from ElliottKasoar/add-uv
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Change poetry to uv
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@ElliottKasoar
ElliottKasoar authored Nov 27, 2024
2 parents b603535 + e8a11ba commit 674604f
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121 changes: 60 additions & 61 deletions .github/workflows/ci.yml
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Expand Up @@ -12,34 +12,37 @@ jobs:
python-version: ['3.9','3.10','3.11','3.12']

steps:
- uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install poetry
run: pipx install poetry

- name: Install python dependencies
run: |
poetry env use ${{ matrix.python-version }}
poetry install --with dev --extras all
- name: Run test suite
env:
# show timings of tests
PYTEST_ADDOPTS: "--durations=0"
run: poetry run pytest --run-extra-mlips --cov janus_core --cov-append .

- name: Report coverage to Coveralls
uses: coverallsapp/github-action@v2
with:
parallel: true
flag-name: run-${{ matrix.python-version }}
file: coverage.xml
base-path: janus_core
- uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install uv
uses: astral-sh/setup-uv@v3
with:
version: "0.5.4"

- name: Set up Python ${{ matrix.python-version }}
run: uv python install ${{ matrix.python-version }}

- name: Install dependencies
run: uv sync --all-extras

- name: Run test suite
env:
# show timings of tests
PYTEST_ADDOPTS: "--durations=0"
run: uv run pytest --run-extra-mlips --cov janus_core --cov-append .

- name: Report coverage to Coveralls
uses: coverallsapp/github-action@v2
with:
parallel: true
flag-name: run-${{ matrix.python-version }}
file: coverage.xml
base-path: janus_core

coverage:
needs: tests
Expand All @@ -54,50 +57,46 @@ jobs:
runs-on: ubuntu-latest
timeout-minutes: 15
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v4

- name: Check all sources documented
run: |
diff -y --suppress-common-lines \
<(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
<(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
- name: Check all sources documented
run: |
diff -y --suppress-common-lines \
<(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
<(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
- name: Set up Python 3.11
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install uv
uses: astral-sh/setup-uv@v3
with:
version: "0.5.4"

- name: Install poetry
run: pipx install poetry
- name: Set up Python 3.11
run: uv python install 3.11

- name: Install python dependencies
run: |
poetry env use 3.11
poetry install --with docs
- name: Install dependencies
run: uv sync

- name: Build docs
run: cd docs && poetry run make
- name: Build docs
run: cd docs && uv run make html

pre-commit:
runs-on: ubuntu-latest
timeout-minutes: 15
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v4

- name: Set up Python 3.11
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Install uv
uses: astral-sh/setup-uv@v3
with:
version: "0.5.4"

- name: Install poetry
run: pipx install poetry
- name: Set up Python 3.11
run: uv python install 3.11

- name: Install python dependencies
run: |
poetry env use 3.11
poetry install --with pre-commit,docs,dev --extras "chgnet m3gnet"
- name: Install dependencies
run: uv sync

- name: Run pre-commit
run: |
poetry run pre-commit install
poetry run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
- name: Run pre-commit
run: |
uv run pre-commit install
uv run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
27 changes: 10 additions & 17 deletions .github/workflows/docs.yml
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Expand Up @@ -27,23 +27,16 @@ jobs:
steps:
- uses: actions/checkout@v4

- name: Install poetry
run: |
apt update
apt upgrade -y
apt install -y pipx
pipx install poetry
- name: add deps
run: |
apt install -y python3-dev build-essential
- name: sphinx
run: |
export PATH="$HOME/.local/bin:$PATH"
poetry install --with docs
cd docs
poetry run make html
- name: Install uv
uses: astral-sh/setup-uv@v3
with:
verson: "0.5.4"

- name: Install dependencies
run: uv sync

- name: Build docs
run: cd docs && uv run make html

- name: upload
uses: actions/upload-pages-artifact@v3
Expand Down
155 changes: 86 additions & 69 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,90 +1,100 @@
[tool.poetry]
[project]
name = "janus-core"
version = "0.6.6"
description = "Tools for machine learnt interatomic potentials"
authors = [
"Elliott Kasoar",
"Federica Zanca",
"Harvey Devereux",
"Patrick Austin",
"David Mason",
"Jacob Wilkins",
"Alin M. Elena",
{ name = "Elliott Kasoar" },
{ name = "Federica Zanca" },
{ name = "Harvey Devereux "},
{ name = "Patrick Austin" },
{ name = "David Mason" },
{ name = "Jacob Wilkins" },
{ name = "Alin M. Elena" },
]
readme = "README.md"
packages = [{include = "janus_core"}]
requires-python = "<3.13,>=3.9"
classifiers = [
"Programming Language :: Python",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Development Status :: 3 - Alpha",
]
readme = "README.md"

dependencies = [
"ase<4.0,>=3.23",
"codecarbon<3.0.0,>=2.5.0",
"mace-torch==0.3.8",
"numpy<2.0.0,>=1.26.4",
"phonopy<3.0.0,>=2.23.1",
"pyyaml<7.0.0,>=6.0.1",
"rich<14.0.0,>=13.9.1",
"seekpath<2.0.0,>=1.9.7",
"spglib<3.0.0,>=2.3.0",
"torch<=2.2,>=2.1",
"torch-dftd==0.4.0",
"typer<1.0.0,>=0.12.5",
"typer-config<2.0.0,>=1.4.0",
]

[project.optional-dependencies]
alignn = [
"alignn == 2024.5.27",]

chgnet = [
"chgnet == 0.3.8",]

m3gnet = [
"matgl == 1.1.3",
"dgl == 2.1.0",
"torchdata == 0.7.1",]

sevennet = [
"sevenn == 0.10.0",
"torch-geometric == 2.6.1",]

all = [
"janus-core[alignn]",
"janus-core[chgnet]",
"janus-core[m3gnet]",
"janus-core[sevennet]",
]

[project.scripts]
janus = "janus_core.cli.janus:app"

[project.urls]
repository = "https://github.com/stfc/janus-core/"
documentation = "https://stfc.github.io/janus-core/"

[tool.poetry.scripts]
janus = "janus_core.cli.janus:app"
[dependency-groups]
dev = [
"coverage[toml]<8.0.0,>=7.4.1",
"pgtest<2.0.0,>=1.3.2",
"pytest<9.0,>=8.0",
"pytest-cov<5.0.0,>=4.1.0",
"tox<5.0.0,>=4.12.1",
"wheel<1.0,>=0.42",
]

[tool.poetry.dependencies]
ase = "^3.23"
codecarbon = "^2.5.0"
mace-torch = "0.3.8"
numpy = "^1.26.4"
phonopy = "^2.23.1"
python = "^3.9"
pyyaml = "^6.0.1"
rich = "^13.9.1"
seekpath = "^1.9.7"
spglib = "^2.3.0"
torch = ">= 2.1, <= 2.2" # Range required for dgl
torch-dftd = "0.4.0"
typer = "^0.12.5"
typer-config = "^1.4.0"

alignn = { version = "2024.5.27", optional = true }
chgnet = {version = "0.3.8", optional = true}
dgl = { version = "2.1.0", optional = true } # Pin due to matgl installation issues
matgl = { version = "1.1.3", optional = true}
sevenn = { version = "0.10.0", optional = true }
torchdata = {version = "0.7.1", optional = true} # Pin due to dgl issue
torch_geometric = { version = "^2.5.3", optional = true }

[tool.poetry.extras]
all = ["alignn", "chgnet", "matgl", "dgl", "torchdata", "sevenn", "torch_geometric"]
alignn = ["alignn"]
chgnet = ["chgnet"]
m3gnet = ["matgl", "dgl", "torchdata"]
sevennet = ["sevenn", "torch_geometric"]

[tool.poetry.group.dev.dependencies]
coverage = {extras = ["toml"], version = "^7.4.1"}
pgtest = "^1.3.2"
pytest = "^8.0"
pytest-cov = "^4.1.0"
tox = "^4.12.1"
wheel = "^0.42"

[tool.poetry.group.pre-commit]
optional = true
[tool.poetry.group.pre-commit.dependencies]
pre-commit = "^3.6.0"
ruff = "^0.7.4"

[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
furo = "^2024.1.29"
markupsafe = "<2.1"
numpydoc = "^1.6.0"
sphinx = "^7.2.6"
sphinxcontrib-contentui = "^0.2.5"
sphinxcontrib-details-directive = "^0.1"
sphinx-copybutton = "^0.5.2"
docs = [
"furo<2025.0.0,>=2024.1.29",
"markupsafe<2.1",
"numpydoc<2.0.0,>=1.6.0",
"sphinx<8.0.0,>=7.2.6",
"sphinxcontrib-contentui<1.0.0,>=0.2.5",
"sphinxcontrib-details-directive<1.0,>=0.1",
"sphinx-copybutton<1.0.0,>=0.5.2",
]

pre-commit = [
"pre-commit<4.0.0,>=3.6.0",
"ruff<1.0.0,>=0.7.4",
]

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
requires = ["pdm-backend"]
build-backend = "pdm.backend"

[tool.pytest.ini_options]
# Configuration for [pytest](https://docs.pytest.org)
Expand Down Expand Up @@ -149,3 +159,10 @@ exclude = [
".__weakref__$",
".__repr__$",
]

[tool.uv]
default-groups = [
"dev",
"docs",
"pre-commit",
]

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