Dependency conlfict when installing on Ubuntu

[kevinyamauchi]

Hello everyone! I tried installing on Ubuntu using the instructions on the readme. The installation completes successfully, but in the final SPAC installation step, pip raised the depedency conflict error below. The example notebook still runs so I guess the dependency pins are either too strict or those libraries aren't utilized in the notebook.

This is in connection with the JOSS review (openjournals/joss-reviews#8787).

  Running setup.py develop for spac
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
scimap 2.1.3 requires combat<0.4.0,>=0.3.3, which is not installed.
scimap 2.1.3 requires dask[array]<2024.0.0,>=2023.11.0, but you have dask 2024.2.1 which is incompatible.
scimap 2.1.3 requires mpl-scatter-density<0.8,>=0.7, but you have mpl-scatter-density 0.8 which is incompatible.
scimap 2.1.3 requires pytest<8.0.0,>=7.4.3, but you have pytest 8.4.1 which is incompatible.
scimap 2.1.3 requires scipy<=1.12.0,>1.11.3, but you have scipy 1.13.1 which is incompatible.
scimap 2.1.3 requires TiffFile<2024.0.0,>=2023.9.26, but you have tifffile 2024.6.18 which is incompatible.
Successfully installed scikit-learn-1.6.1 spac-0.9.0

Full error message

Obtaining file:///local1/code/SCSAWorkflow
  Preparing metadata (setup.py) ... done
Requirement already satisfied: pandas in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.5.3)
Requirement already satisfied: anndata in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (0.10.9)
Requirement already satisfied: numpy in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.26.4)
Requirement already satisfied: scikit-learn in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.5.2)
Requirement already satisfied: squidpy in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.2.2)
Requirement already satisfied: matplotlib in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (3.9.2)
Requirement already satisfied: seaborn in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (0.13.2)
Requirement already satisfied: scanpy in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.10.3)
Requirement already satisfied: phenograph in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (1.5.7)
Requirement already satisfied: zarr in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (2.10.3)
Requirement already satisfied: numba in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (0.58.1)
Requirement already satisfied: Pillow in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (11.0.0)
Requirement already satisfied: datashader in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (0.16.3)
Requirement already satisfied: plotly in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from spac==0.9.0) (5.24.1)
Requirement already satisfied: array-api-compat!=1.5,>1.4 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (1.11.2)
Requirement already satisfied: exceptiongroup in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (1.3.0)
Requirement already satisfied: h5py>=3.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (3.14.0)
Requirement already satisfied: natsort in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (8.4.0)
Requirement already satisfied: packaging>=20.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (25.0)
Requirement already satisfied: scipy>1.8 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from anndata->spac==0.9.0) (1.13.1)
Requirement already satisfied: python-dateutil>=2.8.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from pandas->spac==0.9.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from pandas->spac==0.9.0) (2025.2)
Requirement already satisfied: six>=1.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->spac==0.9.0) (1.17.0)
Requirement already satisfied: colorcet in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (3.1.0)
Requirement already satisfied: dask in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (2024.2.1)
Requirement already satisfied: multipledispatch in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (0.6.0)
Requirement already satisfied: param in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (2.2.1)
Requirement already satisfied: pyct in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (0.6.0)
Requirement already satisfied: requests in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (2.32.5)
Requirement already satisfied: toolz in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (1.0.0)
Requirement already satisfied: xarray in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from datashader->spac==0.9.0) (2023.7.0)
Requirement already satisfied: click>=8.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (8.1.8)
Requirement already satisfied: cloudpickle>=1.5.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (3.1.1)
Requirement already satisfied: fsspec>=2021.09.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (2025.7.0)
Requirement already satisfied: partd>=1.2.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (1.4.2)
Requirement already satisfied: pyyaml>=5.3.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (6.0.2)
Requirement already satisfied: importlib-metadata>=4.13.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask->datashader->spac==0.9.0) (8.7.0)
Requirement already satisfied: zipp>=3.20 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from importlib-metadata>=4.13.0->dask->datashader->spac==0.9.0) (3.23.0)
Requirement already satisfied: locket in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from partd>=1.2.0->dask->datashader->spac==0.9.0) (1.0.0)
Requirement already satisfied: typing-extensions>=4.6.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from exceptiongroup->anndata->spac==0.9.0) (4.14.1)
Requirement already satisfied: contourpy>=1.0.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (1.3.0)
Requirement already satisfied: cycler>=0.10 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (4.59.1)
Requirement already satisfied: kiwisolver>=1.3.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (1.4.7)
Requirement already satisfied: pyparsing>=2.3.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (3.2.3)
Requirement already satisfied: importlib-resources>=3.2.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from matplotlib->spac==0.9.0) (6.5.2)
Requirement already satisfied: llvmlite<0.42,>=0.41.0dev0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from numba->spac==0.9.0) (0.41.1)
Requirement already satisfied: leidenalg>=0.8.2 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from phenograph->spac==0.9.0) (0.10.2)
Requirement already satisfied: setuptools>=18.0.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from phenograph->spac==0.9.0) (80.9.0)
Requirement already satisfied: psutil>4 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from phenograph->spac==0.9.0) (7.0.0)
Requirement already satisfied: igraph<0.12,>=0.10.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from leidenalg>=0.8.2->phenograph->spac==0.9.0) (0.11.9)
Requirement already satisfied: texttable>=1.6.2 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from igraph<0.12,>=0.10.0->leidenalg>=0.8.2->phenograph->spac==0.9.0) (1.7.0)
Requirement already satisfied: joblib>=1.2.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scikit-learn->spac==0.9.0) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scikit-learn->spac==0.9.0) (3.6.0)
Requirement already satisfied: tenacity>=6.2.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from plotly->spac==0.9.0) (9.1.2)
Requirement already satisfied: charset_normalizer<4,>=2 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from requests->datashader->spac==0.9.0) (3.4.3)
Requirement already satisfied: idna<4,>=2.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from requests->datashader->spac==0.9.0) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from requests->datashader->spac==0.9.0) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from requests->datashader->spac==0.9.0) (2025.8.3)
Requirement already satisfied: get-annotations in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (0.1.2)
Requirement already satisfied: legacy-api-wrap>=1.4 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (1.4)
Requirement already satisfied: networkx>=2.7 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (3.2.1)
Requirement already satisfied: patsy in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (1.0.1)
Requirement already satisfied: pynndescent>=0.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (0.5.13)
Requirement already satisfied: session-info in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (1.0.0)
Requirement already satisfied: statsmodels>=0.13 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (0.14.5)
Requirement already satisfied: tqdm in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (4.67.1)
Requirement already satisfied: umap-learn!=0.5.0,>=0.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scanpy->spac==0.9.0) (0.5.9.post2)
Collecting scikit-learn (from spac==0.9.0)
  Downloading scikit_learn-1.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Requirement already satisfied: stdlib-list in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from session-info->scanpy->spac==0.9.0) (0.11.1)
Requirement already satisfied: aiohttp>=3.8.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (3.12.15)
Requirement already satisfied: dask-image>=0.5.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (2023.3.0)
Requirement already satisfied: docrep>=0.3.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (0.3.2)
Requirement already satisfied: matplotlib-scalebar>=0.8.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (0.9.0)
Requirement already satisfied: omnipath>=1.0.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (1.0.8)
Requirement already satisfied: scikit-image>=0.19 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (0.24.0)
Requirement already satisfied: tifffile!=2022.4.22 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (2024.6.18)
Requirement already satisfied: validators>=0.18.2 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from squidpy->spac==0.9.0) (0.35.0)
Requirement already satisfied: aiohappyeyeballs>=2.5.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (2.6.1)
Requirement already satisfied: aiosignal>=1.4.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (1.4.0)
Requirement already satisfied: async-timeout<6.0,>=4.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (5.0.1)
Requirement already satisfied: attrs>=17.3.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (25.3.0)
Requirement already satisfied: frozenlist>=1.1.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (1.7.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (6.6.3)
Requirement already satisfied: propcache>=0.2.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (0.3.1)
Requirement already satisfied: yarl<2.0,>=1.17.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from aiohttp>=3.8.1->squidpy->spac==0.9.0) (1.20.1)
Requirement already satisfied: pims>=0.4.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from dask-image>=0.5.0->squidpy->spac==0.9.0) (0.7)
Requirement already satisfied: inflect>=4.1.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from omnipath>=1.0.5->squidpy->spac==0.9.0) (7.5.0)
Requirement already satisfied: wrapt>=1.12.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from omnipath>=1.0.5->squidpy->spac==0.9.0) (1.17.3)
Requirement already satisfied: more_itertools>=8.5.0 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from inflect>=4.1.0->omnipath>=1.0.5->squidpy->spac==0.9.0) (10.7.0)
Requirement already satisfied: typeguard>=4.0.1 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from inflect>=4.1.0->omnipath>=1.0.5->squidpy->spac==0.9.0) (4.4.4)
Requirement already satisfied: imageio in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from pims>=0.4.1->dask-image>=0.5.0->squidpy->spac==0.9.0) (2.37.0)
Requirement already satisfied: slicerator>=0.9.8 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from pims>=0.4.1->dask-image>=0.5.0->squidpy->spac==0.9.0) (1.1.0)
Requirement already satisfied: lazy-loader>=0.4 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from scikit-image>=0.19->squidpy->spac==0.9.0) (0.4)
Requirement already satisfied: asciitree in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from zarr->spac==0.9.0) (0.3.3)
Requirement already satisfied: fasteners in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from zarr->spac==0.9.0) (0.19)
Requirement already satisfied: numcodecs>=0.6.4 in /local0/home/kyamauch/miniforge3/envs/spac/lib/python3.9/site-packages (from zarr->spac==0.9.0) (0.12.1)
Downloading scikit_learn-1.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.5/13.5 MB 58.4 MB/s  0:00:00
Installing collected packages: scikit-learn, spac
  Attempting uninstall: scikit-learn
    Found existing installation: scikit-learn 1.5.2
    Uninstalling scikit-learn-1.5.2:
      Successfully uninstalled scikit-learn-1.5.2
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/2 [scikit-learn]  DEPRECATION: Legacy editable install of spac==0.9.0 from file:///local1/code/SCSAWorkflow (setup.py develop) is deprecated. pip 25.3 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457
  Running setup.py develop for spac
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
scimap 2.1.3 requires combat<0.4.0,>=0.3.3, which is not installed.
scimap 2.1.3 requires dask[array]<2024.0.0,>=2023.11.0, but you have dask 2024.2.1 which is incompatible.
scimap 2.1.3 requires mpl-scatter-density<0.8,>=0.7, but you have mpl-scatter-density 0.8 which is incompatible.
scimap 2.1.3 requires pytest<8.0.0,>=7.4.3, but you have pytest 8.4.1 which is incompatible.
scimap 2.1.3 requires scipy<=1.12.0,>1.11.3, but you have scipy 1.13.1 which is incompatible.
scimap 2.1.3 requires TiffFile<2024.0.0,>=2023.9.26, but you have tifffile 2024.6.18 which is incompatible.
Successfully installed scikit-learn-1.6.1 spac-0.9.0

[fangliu117]

Thank you @kevinyamauchi for flagging the pip conflict. We have resolved all 6 dependency conflicts reported with scimap 2.1.3 by pinning the following package versions in environment.yml:

scipy=1.12.0
dask=2023.12.1
tifffile=2023.9.26
mpl-scatter-density=0.7
pytest==7.4.4
combat==0.3.3
Verification:

We have tested the full Docker build completed with zero dependency conflicts and also on the local macOS conda environments
All imports (spac, scimap 2.3.5, scipy, pandas, dask) work without errors

We also added jupyter to environment.yml to support local notebook execution

The fixes are currently merged in the address-reviewer-comments branch.