lockfile reported as out of date with `--locked` even after running `pixi lock`

[cpcloud]

Checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

Commands I ran and their output:

$ pixi lock && pixi install --locked
Error:   × lock-file not up-to-date with the workspace

pixi.toml/pyproject.toml file that reproduces my issue:

# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: BSD-2-Clause
[workspace]
channels = ["conda-forge"]
platforms = ["linux-64", "linux-aarch64", "win-64"]
preview = ["pixi-build"]

[workspace.build-variants]
python = ["3.10.*", "3.11.*", "3.12.*", "3.13.*", "3.14.*"]

[dependencies]
# source
numba-cuda = { path = "." }

[feature.cu.dependencies]
cuda-nvcc = "*"
cuda-nvcc-impl = "*"
cuda-cuobjdump = "*"
cuda-nvrtc = "*"
libnvjitlink = "*"
cuda-cccl = "*"
libcurand = "*"

[feature.cu-12.system-requirements]
cuda = "12"

[feature.cu-12.dependencies]
cuda-version = "12.*"

[feature.cu-12-0.dependencies]
cuda-version = "12.0.*"

[feature.nvvm.dependencies]
# supported by cuda >=12.2
cuda-nvvm = "*"

[feature.cu-12-2.dependencies]
cuda-version = "12.2.*"

[feature.cu-rt.dependencies]
# supported by cuda >=12.8
cuda-runtime = "*"

[feature.cu-12-8.dependencies]
cuda-version = "12.8.*"

[feature.cu-12-9.dependencies]
cuda-version = "12.9.*"

[feature.cu-13.system-requirements]
cuda = "13"

[feature.cu-13.dependencies]
cuda-version = "13.*"

[feature.cu-13-0.dependencies]
cuda-version = "13.0.*"

[feature.cu-13-1.dependencies]
cuda-version = "13.1.*"

[feature.bench.dependencies]
pytorch = ">=2.8"
pytorch-gpu = ">=2.8"
libtorch = ">=2.8"
cupy = "*"

[feature.test.dependencies]
# for building cuda artifacts for testing
make = "*"
pre-commit = ">=4.3"
psutil = ">=6"
cffi = ">=1"
pytest = ">=8,<9"
pytest-xdist = ">=3.8"
pytest-benchmark = ">=5.1"

[feature.test.pypi-dependencies]
ml_dtypes = "*"
filecheck = "*"

[feature.py310.dependencies]
python = "3.10.*"

[feature.py311.dependencies]
python = "3.11.*"

[feature.py312.dependencies]
python = "3.12.*"

[feature.py313.dependencies]
python = "3.13.*"

[feature.py314.dependencies]
python = "3.14.*"

[feature.docs.dependencies]
make = "*"
psutil = ">=7.1.3"
sphinx = ">=8.2.3"
sphinx-rtd-theme = ">=3.0.2"
numpydoc = ">=1.9.0"

[feature.docs.pypi-dependencies]
nvidia-sphinx-theme = "*"

[environments]
bench-against = { features = ["test"], no-default-feature = true }
# CUDA 12
cu-12-0-py310 = { features = [
    "cu-12-0",
    "test",
    "cu",
    "cu-12",
    "py310",
], solve-group = "cu-12-0-py310" }
cu-12-0-py311 = { features = [
    "cu-12-0",
    "test",
    "cu",
    "cu-12",
    "py311",
], solve-group = "cu-12-0-py311" }
cu-12-2-py311 = { features = [
    "cu-12-2",
    "test",
    "cu",
    "cu-12",
    "nvvm",
    "py311",
], solve-group = "cu-12-2-py311" }
cu-12-8-py310 = { features = [
    "cu-12-8",
    "test",
    "cu",
    "cu-12",
    "cu-rt",
    "nvvm",
    "py310",
], solve-group = "cu-12-8-py310" }
cu-12-8-py311 = { features = [
    "cu-12-8",
    "test",
    "cu",
    "cu-12",
    "cu-rt",
    "nvvm",
    "py311",
], solve-group = "cu-12-8-py311" }
cu-12-8-py312 = { features = [
    "cu-12-8",
    "test",
    "cu",
    "cu-12",
    "cu-rt",
    "nvvm",
    "py312",
], solve-group = "cu-12-8-py312" }
cu-12-8-py313 = { features = [
    "cu-12-8",
    "test",
    "cu",
    "cu-12",
    "cu-rt",
    "nvvm",
    "py313",
], solve-group = "cu-12-8-py313" }
cu-12-9-py312 = { features = [
    "cu-12-9",
    "test",
    "bench",
    "cu",
    "cu-12",
    "cu-rt",
    "nvvm",
    "py312",
], solve-group = "cu-12-9-py312" }
# CUDA 13
cu-13-0-py312 = { features = [
    "cu-13-0",
    "test",
    "cu",
    "cu-13",
    "cu-rt",
    "nvvm",
    "py312",
], solve-group = "cu-13-0-py312" }
cu-13-0-py313 = { features = [
    "cu-13-0",
    "test",
    "cu",
    "cu-13",
    "cu-rt",
    "nvvm",
    "py313",
], solve-group = "cu-13-0-py313" }
cu-13-0-py314 = { features = [
    "cu-13-0",
    "test",
    "cu",
    "cu-13",
    "cu-rt",
    "nvvm",
    "py314",
], solve-group = "cu-13-0-py314" }
cu-13-1-py314 = { features = [
    "cu-13-1",
    "test",
    "cu",
    "cu-13",
    "cu-rt",
    "nvvm",
    "py314",
], solve-group = "cu-13-1-py314" }

docs = { features = ["docs"], solve-group = "docs" }

[target.linux.tasks]
build-tests = { cmd = [
    "make",
    "-j",
    "$(nproc)",
    "-C",
    "$PIXI_PROJECT_ROOT/testing",
] }
clean-tests = { cmd = [
    "make",
    "-j",
    "$(nproc)",
    "-C",
    "$PIXI_PROJECT_ROOT/testing",
    "clean",
] }
bench = { cmd = [
    "pytest",
    "$PIXI_PROJECT_ROOT/testing",
    "--pyargs",
    "numba.cuda.tests.benchmarks",
    "--benchmark-only",
    "--benchmark-enable",
    "--benchmark-autosave",
    "--benchmark-group-by=func",
] }
benchcmp = { cmd = [
    "pytest",
    "$PIXI_PROJECT_ROOT/testing",
    "--pyargs",
    "numba.cuda.tests.benchmarks",
    "--benchmark-only",
    "--benchmark-enable",
    "--benchmark-group-by=name",
    "--benchmark-compare",
] }

[target.linux.tasks.bench-against]
cmd = ["python", "$PIXI_PROJECT_ROOT/scripts/bench-against.py"]

[target.linux.tasks.build-docs]
cmd = ["make", "-C", "$PIXI_PROJECT_ROOT/docs", "html"]

[target.linux.tasks.test]
cmd = ["pytest", "$PIXI_PROJECT_ROOT/testing"]
env = { NUMBA_CUDA_TEST_BIN_DIR = "$PIXI_PROJECT_ROOT/testing" }
depends-on = [{ task = "build-tests" }]

[target.linux.tasks.simtest]
cmd = ["pytest", "$PIXI_PROJECT_ROOT/testing"]

[target.linux.tasks.simtest.env]
NUMBA_CUDA_TEST_BIN_DIR = "$PIXI_PROJECT_ROOT/testing"
NUMBA_ENABLE_CUDASIM = "1"

[package]
name = "numba-cuda"
version = "0.23.0"

[package.build]
backend = { name = "pixi-build-python", version = "*" }
# makes the package not noarch which is required for build-variants to work and
# because numba-cuda has c(++) extensions
config.compilers = ["cxx"]

[package.build-dependencies]
# this can't be in `config.compilers` otherwise CUDA_HOME isn't defined
cuda-compiler = "*"

[package.host-dependencies]
python = "*"
setuptools = "*"
numpy = ">=2.1"

[package.run-dependencies]
python = "*"
packaging = "*"
numba = ">=0.60"
cuda-core = ">=0.3,<1"
cuda-bindings = ">=12.9,<14"
cuda-python = ">=12.9,<14"

pixi info output:

System
------------
       Pixi version: 0.62.2
        TLS backend: rustls
           Platform: linux-64
   Virtual packages: __unix=0=0
                   : __linux=6.12.61=0
                   : __glibc=2.40=0
                   : __cuda=13.1=0
                   : __archspec=1=zen2
   Config locations: No config files found

Global
------------

Workspace
------------
               Name: numba-cuda

Environments
------------
        Environment: default
           Features: default
           Channels: conda-forge
   Dependency count: 1
       Dependencies: numba-cuda
   Target platforms: linux-aarch64, linux-64, win-64
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: bench-against
           Features: test
           Channels: conda-forge
   Dependency count: 7
       Dependencies: make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: win-64, linux-64, linux-aarch64

        Environment: cu-12-0-py310
           Features: cu-12-0, test, cu, cu-12, py310, default
        Solve group: cu-12-0-py310
           Channels: conda-forge
   Dependency count: 17
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-aarch64, win-64, linux-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-0-py311
           Features: cu-12-0, test, cu, cu-12, py311, default
        Solve group: cu-12-0-py311
           Channels: conda-forge
   Dependency count: 17
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-64, linux-aarch64, win-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-2-py311
           Features: cu-12-2, test, cu, cu-12, nvvm, py311, default
        Solve group: cu-12-2-py311
           Channels: conda-forge
   Dependency count: 18
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-aarch64, linux-64, win-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-8-py310
           Features: cu-12-8, test, cu, cu-12, cu-rt, nvvm, py310, default
        Solve group: cu-12-8-py310
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: win-64, linux-64, linux-aarch64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-8-py311
           Features: cu-12-8, test, cu, cu-12, cu-rt, nvvm, py311, default
        Solve group: cu-12-8-py311
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: win-64, linux-aarch64, linux-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-8-py312
           Features: cu-12-8, test, cu, cu-12, cu-rt, nvvm, py312, default
        Solve group: cu-12-8-py312
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-aarch64, win-64, linux-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-8-py313
           Features: cu-12-8, test, cu, cu-12, cu-rt, nvvm, py313, default
        Solve group: cu-12-8-py313
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: win-64, linux-aarch64, linux-64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-12-9-py312
           Features: cu-12-9, test, bench, cu, cu-12, cu-rt, nvvm, py312, default
        Solve group: cu-12-9-py312
           Channels: conda-forge
   Dependency count: 23
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, pytorch, pytorch-gpu, libtorch, cupy, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-64, win-64, linux-aarch64
System requirements: cuda = "12"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-13-0-py312
           Features: cu-13-0, test, cu, cu-13, cu-rt, nvvm, py312, default
        Solve group: cu-13-0-py312
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-aarch64, linux-64, win-64
System requirements: cuda = "13"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-13-0-py313
           Features: cu-13-0, test, cu, cu-13, cu-rt, nvvm, py313, default
        Solve group: cu-13-0-py313
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-aarch64, win-64, linux-64
System requirements: cuda = "13"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-13-0-py314
           Features: cu-13-0, test, cu, cu-13, cu-rt, nvvm, py314, default
        Solve group: cu-13-0-py314
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: linux-64, linux-aarch64, win-64
System requirements: cuda = "13"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: cu-13-1-py314
           Features: cu-13-1, test, cu, cu-13, cu-rt, nvvm, py314, default
        Solve group: cu-13-1-py314
           Channels: conda-forge
   Dependency count: 19
       Dependencies: cuda-version, make, pre-commit, psutil, cffi, pytest, pytest-xdist, pytest-benchmark, cuda-nvcc, cuda-nvcc-impl, cuda-cuobjdump, cuda-nvrtc, libnvjitlink, cuda-cccl, libcurand, cuda-runtime, cuda-nvvm, python, numba-cuda
  PyPI Dependencies: ml_dtypes, filecheck
   Target platforms: win-64, linux-64, linux-aarch64
System requirements: cuda = "13"
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

        Environment: docs
           Features: docs, default
        Solve group: docs
           Channels: conda-forge
   Dependency count: 6
       Dependencies: make, psutil, sphinx, sphinx-rtd-theme, numpydoc, numba-cuda
  PyPI Dependencies: nvidia-sphinx-theme
   Target platforms: win-64, linux-64, linux-aarch64
              Tasks: bench-against, build-docs, simtest, test, clean-tests, bench, benchcmp, build-tests

Other files (e.g. script files, source files, etc.):

Issue description

Running pixi lock && pixi install --locked reports

❯ pixi lock && pixi install --locked
✔ Updated lock-file
Error:   × lock-file not up-to-date with the workspace

This seems to cause our CI to fail.

Expected behavior

I would expect that pixi lock updates the lockfile such that --locked on any subcommand that supports it would succeed.

[cpcloud]

Running with -v:

❯ pixi install -v --locked
 INFO pixi_core::lock_file::outdated: the dependencies of environment 'cu-13-0-py312' for platform linux-64 are out of date because the locked metadata of 'numba-cuda' package changed (see trace logs for details)
 INFO pixi_core::lock_file::outdated: the dependencies of environment 'cu-13-0-py313' for platform linux-64 are out of date because the locked metadata of 'numba-cuda' package changed (see trace logs for details)
Error:   × lock-file not up-to-date with the workspace

I can't really tell even with -vvvv what exactly is out of date.

git status shows no unstaged changes, so I'm not sure what is constantly out of date here.

[baszalmstra]

Thanks for the detailed report!

I did a bit of a deep dive, and it turns out that this is caused by different system requirements, which produce two slightly different output packages (one with cuda and one without). However, from the perspective of the lock file these are the same. The lock-file does not have the possibility to discern the subtle differences in the package. But then, when we check whether the lock file is satisfiable, this subtle difference is detected, and the lock file is invalidated.

I'll cook up a fix.