The workspace_root should be part of the source build path at this point: StripPrefixError(()) #5125
Description
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 shell -e devpixi.toml/pyproject.toml file that reproduces my issue:
[workspace]
preview = ["pixi-build"]
channels = ["https://prefix.dev/conda-forge"]
platforms = ["osx-arm64"]
[package]
name = "imbalanced-learn"
version = "0.14.0.dev0"
[package.build.backend]
name = "pixi-build-python"
version = "*"
[package.build.config]
noarch = true
[package.build.source]
path = "imbalanced-learn"
[package.build-dependencies]
python = "~=3.13.0"
[package.host-dependencies]
uv = "*"
python = "~=3.13.0"
setuptools = "*"
[package.run-dependencies]
python = "~=3.13.0"
numpy = ">=1.25.2,<3"
scipy = ">=1.11.4,<2"
joblib = ">=1.2.0,<2"
threadpoolctl = ">=3.1.0,<4"
scikit-learn = { path = "../scikit-learn" }
[feature.source.dependencies]
ninja = "*"
scikit-learn = { path = "../scikit-learn" }
imbalanced-learn = { path = "." }
[feature.dev.dependencies]
ipykernel = "*"
ipython = "*"
jupyterlab = "*"
twine = "*"
[feature.docs.dependencies]
matplotlib = ">=3.7.3,<4"
seaborn = ">=0.12.2,<1"
memory_profiler = ">=0.61.0,<1"
numpydoc = ">=1.5.0,<2"
sphinx = ">=8.0.2,<9"
sphinx-gallery = ">=0.13.0,<1"
sphinxcontrib-bibtex = ">=2.4.1,<3"
sphinx-copybutton = ">=0.5.2,<1"
pydata-sphinx-theme = ">=0.15.4,<1"
sphinx-design = ">=0.6.1,<1"
[feature.optional.dependencies]
pandas = ">=2.0.3,<3"
[feature.keras.dependencies]
keras = ">=3.3.3,<4"
[feature.tests.dependencies]
packaging = ">=23.2,<25"
pytest = ">=7.2.2,<9"
pytest-cov = ">=4.1.0,<6"
pytest-xdist = ">=3.5.0,<4"
[feature.docs.tasks]
build-docs = { cmd = "make html", cwd = "imbalanced-learn/doc" }
clean-docs = { cmd = "rm -rf _build/ && rm -rf auto_examples/ && rm -rf reference/generated/", cwd = "imbalanced-learn/doc" }
[feature.lint.tasks]
lint = { cmd = "pre-commit install && pre-commit run -v --all-files --show-diff-on-failure", cwd = "imbalanced-learn" }
[feature.tests.tasks]
tests = { cmd = "pytest -vsl --cov=imblearn --cov-report=xml imblearn", cwd = "imbalanced-learn" }
[environments]
dev = { features = ["source", "dev", "docs", "lint", "tests", "optional", "keras"], no-default-feature = true }pixi info output:
System
------------
Pixi version: 0.61.0
Platform: osx-arm64
Virtual packages: __unix=0=0
: __osx=15.6.1=0
: __archspec=1=m2
Cache dir: /Users/glemaitre/Library/Caches/rattler/cache
Auth storage: /Users/glemaitre/.rattler/credentials.json
Config locations: No config files found
Global
------------
Bin dir: /Users/glemaitre/.pixi/bin
Environment dir: /Users/glemaitre/.pixi/envs
Manifest dir: /Users/glemaitre/.pixi/manifests/pixi-global.toml
Workspace
------------
Name: imbalanced-learn
Manifest file: /Users/glemaitre/Documents/packages/python-stack/imbalanced-learn/pixi.toml
Last updated: 13-12-2025 14:05:50
Environments
------------
Environment: default
Features: default
Channels: https://prefix.dev/conda-forge
Dependency count: 0
Target platforms: osx-arm64
Prefix location: /Users/glemaitre/Documents/packages/python-stack/imbalanced-learn/.pixi/envs/default
Environment: dev
Features: source, dev, docs, lint, tests, optional, keras
Channels: https://prefix.dev/conda-forge
Dependency count: 23
Dependencies: ninja, scikit-learn, imbalanced-learn, ipykernel, ipython, jupyterlab, twine, matplotlib, seaborn, memory_profiler, numpydoc, sphinx, sphinx-gallery, sphinxcontrib-bibtex, sphinx-copybutton, pydata-sphinx-theme, sphinx-design, packaging, pytest, pytest-cov, pytest-xdist, pandas, keras
Target platforms: osx-arm64
Prefix location: /Users/glemaitre/Documents/packages/python-stack/imbalanced-learn/.pixi/envs/dev
Tasks: tests, lint, clean-docs, build-docs
Other files (e.g. script files, source files, etc.):
Issue description
I recently upgraded from 0.59 to 0.61 (but the bug appear already in 0.60).
I'm building a workspace where I'm using an out of tree source package while developing for a library (see toml below - developing for imbalanced-learn package using scikit-learn source).
This configuration was working in 0.59 but start to fail in 0.60 when activating the shell with the following traceback:
> RUST_BACKTRACE=full pixi shell -e dev
thread 'main2' panicked at crates/pixi_record/src/pinned_source.rs:266:73:
the workspace_root should be part of the source build path at this point: StripPrefixError(())
stack backtrace:
0: 0x1044e493c - __mh_execute_header
1: 0x1033afe50 - __mh_execute_header
2: 0x1044e306c - __mh_execute_header
3: 0x1044e47dc - __mh_execute_header
4: 0x1044e2c00 - __mh_execute_header
5: 0x104516dcc - __mh_execute_header
6: 0x104516d3c - __mh_execute_header
7: 0x10451bd90 - __mh_execute_header
8: 0x104beeb4c - __mh_execute_header
9: 0x104beef90 - __mh_execute_header
10: 0x103def374 - __mh_execute_header
11: 0x103df98d8 - __mh_execute_header
12: 0x102f2d470 - __mh_execute_header
13: 0x102f24b98 - __mh_execute_header
14: 0x102f12818 - __mh_execute_header
15: 0x102ed0d94 - __mh_execute_header
16: 0x102ecf494 - __mh_execute_header
17: 0x102e17430 - __mh_execute_header
18: 0x102dd1184 - __mh_execute_header
19: 0x102cb4d0c - __mh_execute_header
20: 0x102a79314 - __mh_execute_header
21: 0x102ac3388 - __mh_execute_header
22: 0x10451c138 - __mh_execute_header
23: 0x18e18bc0c - __pthread_cond_wait
thread 'main' panicked at crates/pixi/src/main.rs:49:10:
Tokio executor failed, was there a panic?: Any { .. }
stack backtrace:
0: 0x1044e493c - __mh_execute_header
1: 0x1033afe50 - __mh_execute_header
2: 0x1044e306c - __mh_execute_header
3: 0x1044e47dc - __mh_execute_header
4: 0x1044e2c00 - __mh_execute_header
5: 0x104516dcc - __mh_execute_header
6: 0x104516d3c - __mh_execute_header
7: 0x10451bd90 - __mh_execute_header
8: 0x104beeb4c - __mh_execute_header
9: 0x104beef90 - __mh_execute_header
10: 0x102fdf60c - __mh_execute_header
11: 0x102a7a428 - __mh_execute_header
12: 0x102fdfc98 - __mh_execute_headerExpected behavior
I would expect no error.