Using sopa as module in workflow leads to NameError: The name 'paths' is unknown in this context

[bednarsky]

Thanks once more for your amazing work!

Description

Using sopa as module in a larger workflow leads to NameError: The name 'paths' is unknown in this context. This seems to be related to a known snakemake issue: snakemake/snakemake#1688, but I don't know exactly how. A fix mentioned in this issue works, I will make a PR → don't directly use {paths.something} in the shell directive, but use it indirectly via params.

Reproducing the issue

can provide if needed, but fix is minimal anyways (no change in logic, slight increase in code complexity)

Expected behavior

I expect the rules to be added to my larger workflow and then sopa to run.

System

• OS: Linux
• Python version: 3.12.7
• Snakemake version (parent workflow): 8.20.1

Dependencies versions (sopa env, created as described in your doc)

> conda list

Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiobotocore 2.11.2 pypi_0 pypi
aiohappyeyeballs 2.4.3 pypi_0 pypi
aiohttp 3.11.1 pypi_0 pypi
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
anndata 0.11.1 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
array-api-compat 1.9.1 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
async-timeout 5.0.1 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
botocore 1.34.19 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pypi_0 pypi
charset-normalizer 3.4.0 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cloudpickle 3.1.0 pypi_0 pypi
colorcet 3.1.0 pypi_0 pypi
configargparse 1.7 pypi_0 pypi
connection-pool 0.0.3 pypi_0 pypi
contourpy 1.3.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2024.11.2 pypi_0 pypi
dask-expr 1.1.19 pypi_0 pypi
dask-image 2024.5.3 pypi_0 pypi
datashader 0.16.3 pypi_0 pypi
datrie 0.8.2 pypi_0 pypi
distributed 2024.11.2 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
dpath 2.2.0 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
fastjsonschema 2.20.0 pypi_0 pypi
fcsparser 0.2.8 pypi_0 pypi
filelock 3.16.1 pypi_0 pypi
flake8 7.1.1 pypi_0 pypi
fonttools 4.54.1 pypi_0 pypi
frozenlist 1.5.0 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
geopandas 1.0.1 pypi_0 pypi
gitdb 4.0.11 pypi_0 pypi
gitpython 3.1.43 pypi_0 pypi
h5py 3.12.1 pypi_0 pypi
humanfriendly 10.0 pypi_0 pypi
idna 3.10 pypi_0 pypi
imagecodecs 2024.9.22 pypi_0 pypi
imageio 2.36.0 pypi_0 pypi
importlib-metadata 8.5.0 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2024.10.1 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
lamin-utils 0.13.7 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
legacy-api-wrap 1.4 pypi_0 pypi
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsqlite 3.47.0 hadc24fc_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loompy 3.0.7 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.2 pypi_0 pypi
matplotlib 3.9.2 pypi_0 pypi
mccabe 0.7.0 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
msgpack 1.1.0 pypi_0 pypi
multidict 6.1.0 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiscale-spatial-image 1.0.1 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 he02047a_1 conda-forge
networkx 3.4.2 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numcodecs 0.13.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
numpy-groupies 0.11.2 pypi_0 pypi
nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi
nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi
nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi
nvidia-curand-cu12 10.3.2.106 pypi_0 pypi
nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi
nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi
nvidia-nccl-cu12 2.20.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.6.77 pypi_0 pypi
nvidia-nvtx-cu12 12.1.105 pypi_0 pypi
ome-zarr 0.9.0 pypi_0 pypi
opencv-python 4.10.0.84 pypi_0 pypi
openssl 3.4.0 hb9d3cd8_0 conda-forge
packaging 24.2 pypi_0 pypi
pandas 2.2.3 pypi_0 pypi
param 2.1.1 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
patsy 1.0.1 pypi_0 pypi
pillow 11.0.0 pypi_0 pypi
pims 0.7 pypi_0 pypi
pip 24.3.1 pyh8b19718_0 conda-forge
plac 1.4.3 pypi_0 pypi
platformdirs 4.3.6 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
propcache 0.2.0 pypi_0 pypi
psutil 6.1.0 pypi_0 pypi
pulp 2.7.0 pypi_0 pypi
pyarrow 18.0.0 pypi_0 pypi
pycodestyle 2.12.1 pypi_0 pypi
pyct 0.5.0 pypi_0 pypi
pyflakes 3.2.0 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pyogrio 0.10.0 pypi_0 pypi
pyparsing 3.2.0 pypi_0 pypi
pyproj 3.7.0 pypi_0 pypi
python 3.10.15 h4a871b0_2_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2024.2 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
readfcs 1.1.9 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
reretry 0.11.8 pypi_0 pypi
rich 13.9.4 pypi_0 pypi
rpds-py 0.21.0 pypi_0 pypi
s3fs 0.6.0 pypi_0 pypi
scanpy 1.10.4 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scikit-learn 1.5.2 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 75.3.0 pyhd8ed1ab_0 conda-forge
shapely 2.0.6 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
six 1.16.0 pypi_0 pypi
slicerator 1.1.0 pypi_0 pypi
smart-open 7.0.5 pypi_0 pypi
smmap 5.0.1 pypi_0 pypi
snakemake 7.32.4 pypi_0 pypi
sopa 1.1.5 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
spatial-image 1.1.0 pypi_0 pypi
spatialdata 0.2.5.post0 pypi_0 pypi
spatialdata-io 0.1.5 pypi_0 pypi
statsmodels 0.14.4 pypi_0 pypi
stdlib-list 0.11.0 pypi_0 pypi
stopit 1.1.2 pypi_0 pypi
sympy 1.13.3 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tangram-sc 1.0.4 pypi_0 pypi
tblib 3.0.0 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
throttler 1.2.2 pypi_0 pypi
tifffile 2024.9.20 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
toposort 1.10 pypi_0 pypi
torch 2.3.1 pypi_0 pypi
tornado 6.4.1 pypi_0 pypi
tqdm 4.67.0 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
triton 2.3.1 pypi_0 pypi
typer 0.13.0 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2024.2 pypi_0 pypi
umap-learn 0.5.7 pypi_0 pypi
urllib3 2.0.7 pypi_0 pypi
wheel 0.45.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 pypi_0 pypi
xarray 2024.7.0 pypi_0 pypi
xarray-dataclasses 1.8.0 pypi_0 pypi
xarray-datatree 0.0.15 pypi_0 pypi
xarray-schema 0.0.3 pypi_0 pypi
xarray-spatial 0.4.0 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forge
yarl 1.17.1 pypi_0 pypi
yte 1.5.4 pypi_0 pypi
zarr 2.18.3 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.21.0 pypi_0 pypi