Wrong behavior of --only-group and --extra #15676
Description
Summary
I have a pretty standard pyproject.toml file:
[project]
name = "project-name"
version = "1.0.0"
description = ""
authors = [{ name = "ML team" }]
readme = "README.md"
requires-python = ">=3.12,<3.13"
dependencies = []
# select a CPU or GPU variant of PyTorch
pytorch_variant = {train_model = "pytorch-gpu", inference = "pytorch-cpu"}
[dependency-groups]
dev = [
"jupyter",
"pre-commit",
"ruff"
]
training = [
"accelerate==1.*",
"boto3==1.*",
"pillow==11.*",
"pydantic-settings==2.*",
"scikit-learn==1.7.*",
"tqdm",
"transformers==4.56.*",
]
jenkins = [
"boto3==1.*",
"pyyaml",
"sagemaker==2.*"
]
inference = [
"fastapi==0.116.*",
"opentelemetry-api==1.36.*",
"opentelemetry-exporter-otlp==1.36.*",
"opentelemetry-instrumentation-fastapi",
"opentelemetry-sdk==1.36.*",
"pandas==2.*",
"pillow==11.*",
"pydantic-settings==2.*",
"scikit-learn==1.7.*",
"sentry-sdk[fastapi]==2.*",
"transformers==4.56.*",
"uvicorn==0.35.*",
]
[project.optional-dependencies]
pytorch-cpu = ["torch==2.8.0"]
pytorch-gpu = ["torch==2.8.0"]
[tool.uv]
conflicts = [
[
{ extra = "pytorch-cpu" },
{ extra = "pytorch-gpu" }
]
]
[tool.uv.sources]
torch = [
{ index = "pytorch-cpu", extra = "pytorch-cpu" },
{ index = "pytorch-gpu", extra = "pytorch-gpu" }
]
[[tool.uv.index]]
name = "pytorch-cpu"
url = "https://download.pytorch.org/whl/cpu"
explicit = true
[[tool.uv.index]]
name = "pytorch-gpu"
url = "https://download.pytorch.org/whl/cu126" # sync with PyTorch version
explicit = true
When I run uv sync --only-group inference --extra pytorch-cpu, my environment does not contain PyTorch at all, and extra is ignored. Result of uv pip list is:
annotated-types 0.7.0
anyio 4.10.0
asgiref 3.9.1
certifi 2025.8.3
charset-normalizer 3.4.3
click 8.2.1
fastapi 0.116.1
filelock 3.19.1
fsspec 2025.9.0
googleapis-common-protos 1.70.0
grpcio 1.74.0
h11 0.16.0
hf-xet 1.1.9
huggingface-hub 0.34.4
idna 3.10
importlib-metadata 6.11.0
joblib 1.5.2
numpy 1.26.4
opentelemetry-api 1.36.0
opentelemetry-exporter-otlp 1.36.0
opentelemetry-exporter-otlp-proto-common 1.36.0
opentelemetry-exporter-otlp-proto-grpc 1.36.0
opentelemetry-exporter-otlp-proto-http 1.36.0
opentelemetry-instrumentation 0.57b0
opentelemetry-instrumentation-asgi 0.57b0
opentelemetry-instrumentation-fastapi 0.57b0
opentelemetry-proto 1.36.0
opentelemetry-sdk 1.36.0
opentelemetry-semantic-conventions 0.57b0
opentelemetry-util-http 0.57b0
packaging 24.2
pandas 2.3.2
pillow 11.3.0
protobuf 6.31.1
pydantic 2.11.7
pydantic-core 2.33.2
pydantic-settings 2.10.1
python-dateutil 2.9.0.post0
python-dotenv 1.1.1
pytz 2025.2
pyyaml 6.0.2
regex 2025.9.1
requests 2.32.5
safetensors 0.6.2
scikit-learn 1.7.1
scipy 1.16.1
sentry-sdk 2.36.0
six 1.17.0
sniffio 1.3.1
starlette 0.47.3
threadpoolctl 3.6.0
tokenizers 0.22.0
tqdm 4.67.1
transformers 4.56.0
typing-extensions 4.15.0
typing-inspection 0.4.1
tzdata 2025.2
urllib3 2.5.0
uvicorn 0.35.0
wrapt 1.17.3
zipp 3.23.0
Meanwhile, uv sync --no-default-groups --group inference --extra pytorch-cpu is behaving properly:
annotated-types 0.7.0
anyio 4.10.0
asgiref 3.9.1
certifi 2025.8.3
charset-normalizer 3.4.3
click 8.2.1
fastapi 0.116.1
filelock 3.19.1
fsspec 2025.9.0
googleapis-common-protos 1.70.0
grpcio 1.74.0
h11 0.16.0
hf-xet 1.1.9
huggingface-hub 0.34.4
idna 3.10
importlib-metadata 6.11.0
jinja2 3.1.6
joblib 1.5.2
markupsafe 3.0.2
mpmath 1.3.0
networkx 3.5
numpy 1.26.4
opentelemetry-api 1.36.0
opentelemetry-exporter-otlp 1.36.0
opentelemetry-exporter-otlp-proto-common 1.36.0
opentelemetry-exporter-otlp-proto-grpc 1.36.0
opentelemetry-exporter-otlp-proto-http 1.36.0
opentelemetry-instrumentation 0.57b0
opentelemetry-instrumentation-asgi 0.57b0
opentelemetry-instrumentation-fastapi 0.57b0
opentelemetry-proto 1.36.0
opentelemetry-sdk 1.36.0
opentelemetry-semantic-conventions 0.57b0
opentelemetry-util-http 0.57b0
packaging 24.2
pandas 2.3.2
pillow 11.3.0
protobuf 6.31.1
pydantic 2.11.7
pydantic-core 2.33.2
pydantic-settings 2.10.1
python-dateutil 2.9.0.post0
python-dotenv 1.1.1
pytz 2025.2
pyyaml 6.0.2
regex 2025.9.1
requests 2.32.5
safetensors 0.6.2
scikit-learn 1.7.1
scipy 1.16.1
sentry-sdk 2.36.0
setuptools 80.9.0
six 1.17.0
sniffio 1.3.1
starlette 0.47.3
sympy 1.14.0
threadpoolctl 3.6.0
tokenizers 0.22.0
torch 2.8.0+cpu
tqdm 4.67.1
transformers 4.56.0
typing-extensions 4.15.0
typing-inspection 0.4.1
tzdata 2025.2
urllib3 2.5.0
uvicorn 0.35.0
wrapt 1.17.3
zipp 3.23.0
This is a bug, because when I explicitly specify an extra, it should override the --only-group. Those are two different things anyway (dependency groups vs optional dependencies).
Platform
Ubuntu 25.04
Version
0.8.15
Python version
3.12.11