quentinblampey
commented
1 month ago Thanks for reporting this!
Do you have the same issue if you install sopa without snakemake, and then have a second environment with snakemake only? This way you can run the pipeline inside the snakemake environment, which will then call the sopa env
Still, I have to fix this. I'm working remotely until late august, and, since I don't have a windows, I'll need to wait to reproduce this on the computer of some collegues
josenimo
Description
Installing sopa for snakemake (git cloning repo and running pip install -e) pops an error in Windows. Cant run snakemake because of this.
Reproducing the issue
Installation traceback
```python (base) mamba create -n sopa python==3.10 (went to downloaded github repo, I want to run snakemake) (sopa) C:\Users\jnimoca\Desktop\SOPA\sopa>pip install -e ".[snakemake,cellpose,baysor,tangram]" Obtaining file:///C:/Users/jnimoca/Desktop/SOPA/sopa Installing build dependencies ... done Checking if build backend supports build_editable ... done Getting requirements to build editable ... done Preparing editable metadata (pyproject.toml) ... done Collecting botocore==1.34.19 (from sopa==1.1.1) Using cached botocore-1.34.19-py3-none-any.whl.metadata (5.6 kB) Collecting flake8<8.0.0,>=7.0.0 (from sopa==1.1.1) Using cached flake8-7.1.0-py2.py3-none-any.whl.metadata (3.8 kB) Collecting scanpy>=1.9.8 (from sopa==1.1.1) Using cached scanpy-1.10.2-py3-none-any.whl.metadata (9.3 kB) Requirement already satisfied: setuptools>=69.2.0 in c:\users\jnimoca\appdata\local\miniforge3\envs\sopa\lib\site-packages (from sopa==1.1.1) (71.0.1) Collecting spatialdata>=0.2.0 (from sopa==1.1.1) Using cached spatialdata-0.2.1-py3-none-any.whl.metadata (9.4 kB) Collecting spatialdata-io>=0.1.3 (from sopa==1.1.1) Using cached spatialdata_io-0.1.3.post0-py3-none-any.whl.metadata (6.0 kB) Collecting typer>=0.9.0 (from sopa==1.1.1) Using cached typer-0.12.3-py3-none-any.whl.metadata (15 kB) Collecting jmespath<2.0.0,>=0.7.1 (from botocore==1.34.19->sopa==1.1.1) Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) Collecting python-dateutil<3.0.0,>=2.1 (from botocore==1.34.19->sopa==1.1.1) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting urllib3<2.1,>=1.25.4 (from botocore==1.34.19->sopa==1.1.1) Using cached urllib3-2.0.7-py3-none-any.whl.metadata (6.6 kB) Collecting loompy>=3.0.7 (from sopa==1.1.1) Using cached loompy-3.0.7-py3-none-any.whl Collecting toml>=0.10.2 (from sopa==1.1.1) Using cached toml-0.10.2-py2.py3-none-any.whl.metadata (7.1 kB) Collecting pulp<2.8,>=2.3.1 (from sopa==1.1.1) Using cached PuLP-2.7.0-py3-none-any.whl.metadata (5.1 kB) Collecting snakemake<8.0.0,>=7.32.4 (from sopa==1.1.1) Using cached snakemake-7.32.4-py3-none-any.whl Collecting cellpose>=3.0.5 (from sopa==1.1.1) Using cached cellpose-3.0.10-py3-none-any.whl.metadata (24 kB) Collecting opencv-python>=4.8.0.76 (from sopa==1.1.1) Using cached opencv_python-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB) Collecting torch!=2.0.1,!=2.1.0,>=2.0.0 (from sopa==1.1.1) Using cached torch-2.3.1-cp310-cp310-win_amd64.whl.metadata (26 kB) Collecting tangram-sc>=1.0.4 (from sopa==1.1.1) Using cached tangram_sc-1.0.4-py3-none-any.whl.metadata (8.1 kB) Collecting numpy<2.0.0,>=1.20.0 (from cellpose>=3.0.5->sopa==1.1.1) Using cached numpy-1.26.4-cp310-cp310-win_amd64.whl.metadata (61 kB) Collecting scipy (from cellpose>=3.0.5->sopa==1.1.1) Using cached scipy-1.14.0-cp310-cp310-win_amd64.whl.metadata (60 kB) Collecting natsort (from cellpose>=3.0.5->sopa==1.1.1) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting tifffile (from cellpose>=3.0.5->sopa==1.1.1) Using cached tifffile-2024.7.2-py3-none-any.whl.metadata (30 kB) Collecting tqdm (from cellpose>=3.0.5->sopa==1.1.1) Using cached tqdm-4.66.4-py3-none-any.whl.metadata (57 kB) Collecting numba>=0.53.0 (from cellpose>=3.0.5->sopa==1.1.1) Using cached numba-0.60.0-cp310-cp310-win_amd64.whl.metadata (2.8 kB) Collecting llvmlite (from cellpose>=3.0.5->sopa==1.1.1) Using cached llvmlite-0.43.0-cp310-cp310-win_amd64.whl.metadata (4.9 kB) Collecting opencv-python-headless (from cellpose>=3.0.5->sopa==1.1.1) Using cached opencv_python_headless-4.10.0.84-cp37-abi3-win_amd64.whl.metadata (20 kB) Collecting fastremap (from cellpose>=3.0.5->sopa==1.1.1) Using cached fastremap-1.14.2-cp310-cp310-win_amd64.whl.metadata (9.9 kB) Collecting imagecodecs (from cellpose>=3.0.5->sopa==1.1.1) Using cached imagecodecs-2024.6.1-cp310-cp310-win_amd64.whl.metadata (19 kB) Collecting roifile (from cellpose>=3.0.5->sopa==1.1.1) Using cached roifile-2024.5.24-py3-none-any.whl.metadata (4.6 kB) Collecting mccabe<0.8.0,>=0.7.0 (from flake8<8.0.0,>=7.0.0->sopa==1.1.1) Using cached mccabe-0.7.0-py2.py3-none-any.whl.metadata (5.0 kB) Collecting pycodestyle<2.13.0,>=2.12.0 (from flake8<8.0.0,>=7.0.0->sopa==1.1.1) Using cached pycodestyle-2.12.0-py2.py3-none-any.whl.metadata (4.5 kB) Collecting pyflakes<3.3.0,>=3.2.0 (from flake8<8.0.0,>=7.0.0->sopa==1.1.1) Using cached pyflakes-3.2.0-py2.py3-none-any.whl.metadata (3.5 kB) Collecting h5py (from loompy>=3.0.7->sopa==1.1.1) Using cached h5py-3.11.0-cp310-cp310-win_amd64.whl.metadata (2.5 kB) Collecting click (from loompy>=3.0.7->sopa==1.1.1) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting numpy-groupies (from loompy>=3.0.7->sopa==1.1.1) Using cached numpy_groupies-0.11.1-py3-none-any.whl.metadata (18 kB) Collecting anndata>=0.8 (from scanpy>=1.9.8->sopa==1.1.1) Using cached anndata-0.10.8-py3-none-any.whl.metadata (6.6 kB) Collecting joblib (from scanpy>=1.9.8->sopa==1.1.1) Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) Collecting legacy-api-wrap>=1.4 (from scanpy>=1.9.8->sopa==1.1.1) Using cached legacy_api_wrap-1.4-py3-none-any.whl.metadata (1.8 kB) Collecting matplotlib>=3.6 (from scanpy>=1.9.8->sopa==1.1.1) Using cached matplotlib-3.9.1-cp310-cp310-win_amd64.whl.metadata (11 kB) Collecting networkx>=2.7 (from scanpy>=1.9.8->sopa==1.1.1) Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB) Collecting packaging>=21.3 (from scanpy>=1.9.8->sopa==1.1.1) Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB) Collecting pandas>=1.5 (from scanpy>=1.9.8->sopa==1.1.1) Using cached pandas-2.2.2-cp310-cp310-win_amd64.whl.metadata (19 kB) Collecting patsy (from scanpy>=1.9.8->sopa==1.1.1) Using cached patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB) Collecting pynndescent>=0.5 (from scanpy>=1.9.8->sopa==1.1.1) Using cached pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB) Collecting scikit-learn>=0.24 (from scanpy>=1.9.8->sopa==1.1.1) Using cached scikit_learn-1.5.1-cp310-cp310-win_amd64.whl.metadata (12 kB) Collecting seaborn>=0.13 (from scanpy>=1.9.8->sopa==1.1.1) Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting session-info (from scanpy>=1.9.8->sopa==1.1.1) Using cached session_info-1.0.0-py3-none-any.whl Collecting statsmodels>=0.13 (from scanpy>=1.9.8->sopa==1.1.1) Using cached statsmodels-0.14.2-cp310-cp310-win_amd64.whl.metadata (9.5 kB) Collecting umap-learn!=0.5.0,>=0.5 (from scanpy>=1.9.8->sopa==1.1.1) Using cached umap_learn-0.5.6-py3-none-any.whl.metadata (21 kB) Collecting appdirs (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) Collecting configargparse (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB) Collecting connection-pool>=0.0.3 (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached connection_pool-0.0.3-py3-none-any.whl Collecting datrie (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached datrie-0.8.2.tar.gz (63 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting docutils (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB) Collecting gitpython (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached GitPython-3.1.43-py3-none-any.whl.metadata (13 kB) Collecting humanfriendly (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) Collecting jinja2<4.0,>=3.0 (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB) Collecting jsonschema (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB) Collecting nbformat (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB) Collecting psutil (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached psutil-6.0.0-cp37-abi3-win_amd64.whl.metadata (22 kB) Collecting pyyaml (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached PyYAML-6.0.1-cp310-cp310-win_amd64.whl.metadata (2.1 kB) Collecting requests (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) Collecting reretry (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached reretry-0.11.8-py2.py3-none-any.whl.metadata (5.5 kB) Collecting smart-open>=3.0 (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached smart_open-7.0.4-py3-none-any.whl.metadata (23 kB) Collecting stopit (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached stopit-1.1.2-py3-none-any.whl Collecting tabulate (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached tabulate-0.9.0-py3-none-any.whl.metadata (34 kB) Collecting throttler (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached throttler-1.2.2-py3-none-any.whl.metadata (7.4 kB) Collecting toposort>=1.10 (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached toposort-1.10-py3-none-any.whl.metadata (4.1 kB) Collecting wrapt (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached wrapt-1.16.0-cp310-cp310-win_amd64.whl.metadata (6.8 kB) Collecting yte<2.0,>=1.5.1 (from snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached yte-1.5.4-py3-none-any.whl.metadata (3.4 kB) Collecting dask-image (from spatialdata>=0.2.0->sopa==1.1.1) Using cached dask_image-2024.5.3-py3-none-any.whl.metadata (2.8 kB) Collecting dask>=2024.4.1 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached dask-2024.7.0-py3-none-any.whl.metadata (3.8 kB) Collecting fsspec<=2023.6 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached fsspec-2023.6.0-py3-none-any.whl.metadata (6.7 kB) Collecting geopandas>=0.14 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached geopandas-1.0.1-py3-none-any.whl.metadata (2.2 kB) Collecting multiscale-spatial-image>=1.0.0 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached multiscale_spatial_image-1.0.0-py3-none-any.whl.metadata (21 kB) Collecting ome-zarr>=0.8.4 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached ome_zarr-0.9.0-py3-none-any.whl.metadata (3.4 kB) Collecting pooch (from spatialdata>=0.2.0->sopa==1.1.1) Using cached pooch-1.8.2-py3-none-any.whl.metadata (10 kB) Collecting pyarrow (from spatialdata>=0.2.0->sopa==1.1.1) Downloading pyarrow-17.0.0-cp310-cp310-win_amd64.whl.metadata (3.4 kB) Collecting rich (from spatialdata>=0.2.0->sopa==1.1.1) Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB) Collecting scikit-image (from spatialdata>=0.2.0->sopa==1.1.1) Using cached scikit_image-0.24.0-cp310-cp310-win_amd64.whl.metadata (14 kB) Collecting shapely>=2.0.1 (from spatialdata>=0.2.0->sopa==1.1.1) Downloading shapely-2.0.5-cp310-cp310-win_amd64.whl.metadata (7.2 kB) Collecting spatial-image>=1.0.0 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached spatial_image-1.1.0-py3-none-any.whl.metadata (5.5 kB) Collecting typing-extensions>=4.8.0 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB) Collecting xarray (from spatialdata>=0.2.0->sopa==1.1.1) Using cached xarray-2024.6.0-py3-none-any.whl.metadata (11 kB) Collecting xarray-datatree (from spatialdata>=0.2.0->sopa==1.1.1) Using cached xarray_datatree-0.0.14-py3-none-any.whl.metadata (6.9 kB) Collecting xarray-schema (from spatialdata>=0.2.0->sopa==1.1.1) Using cached xarray_schema-0.0.3-py3-none-any.whl.metadata (4.3 kB) Collecting xarray-spatial>=0.3.5 (from spatialdata>=0.2.0->sopa==1.1.1) Using cached xarray_spatial-0.4.0-py3-none-any.whl.metadata (16 kB) Collecting zarr (from spatialdata>=0.2.0->sopa==1.1.1) Using cached zarr-2.18.2-py3-none-any.whl.metadata (5.7 kB) Collecting readfcs (from spatialdata-io>=0.1.3->sopa==1.1.1) Using cached readfcs-1.1.8-py2.py3-none-any.whl.metadata (1.9 kB) Requirement already satisfied: pip in c:\users\jnimoca\appdata\local\miniforge3\envs\sopa\lib\site-packages (from tangram-sc>=1.0.4->sopa==1.1.1) (24.0) Collecting filelock (from torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached filelock-3.15.4-py3-none-any.whl.metadata (2.9 kB) Collecting sympy (from torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached sympy-1.13.0-py3-none-any.whl.metadata (12 kB) Collecting mkl<=2021.4.0,>=2021.1.1 (from torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached mkl-2021.4.0-py2.py3-none-win_amd64.whl.metadata (1.4 kB) Collecting shellingham>=1.3.0 (from typer>=0.9.0->sopa==1.1.1) Using cached shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB) Collecting array-api-compat!=1.5,>1.4 (from anndata>=0.8->scanpy>=1.9.8->sopa==1.1.1) Using cached array_api_compat-1.7.1-py3-none-any.whl.metadata (1.5 kB) Collecting exceptiongroup (from anndata>=0.8->scanpy>=1.9.8->sopa==1.1.1) Downloading exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB) Collecting colorama (from click->loompy>=3.0.7->sopa==1.1.1) Using cached colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB) Collecting cloudpickle>=1.5.0 (from dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached cloudpickle-3.0.0-py3-none-any.whl.metadata (7.0 kB) Collecting partd>=1.4.0 (from dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB) Collecting toolz>=0.10.0 (from dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached toolz-0.12.1-py3-none-any.whl.metadata (5.1 kB) Collecting importlib-metadata>=4.13.0 (from dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached importlib_metadata-8.0.0-py3-none-any.whl.metadata (4.6 kB) Collecting pyogrio>=0.7.2 (from geopandas>=0.14->spatialdata>=0.2.0->sopa==1.1.1) Using cached pyogrio-0.9.0-cp310-cp310-win_amd64.whl.metadata (3.9 kB) Collecting pyproj>=3.3.0 (from geopandas>=0.14->spatialdata>=0.2.0->sopa==1.1.1) Using cached pyproj-3.6.1-cp310-cp310-win_amd64.whl.metadata (31 kB) Collecting MarkupSafe>=2.0 (from jinja2<4.0,>=3.0->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached MarkupSafe-2.1.5-cp310-cp310-win_amd64.whl.metadata (3.1 kB) Collecting contourpy>=1.0.1 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached contourpy-1.2.1-cp310-cp310-win_amd64.whl.metadata (5.8 kB) Collecting cycler>=0.10 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached fonttools-4.53.1-cp310-cp310-win_amd64.whl.metadata (165 kB) Collecting kiwisolver>=1.3.1 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached kiwisolver-1.4.5-cp310-cp310-win_amd64.whl.metadata (6.5 kB) Collecting pillow>=8 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached pillow-10.4.0-cp310-cp310-win_amd64.whl.metadata (9.3 kB) Collecting pyparsing>=2.3.1 (from matplotlib>=3.6->scanpy>=1.9.8->sopa==1.1.1) Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB) Collecting intel-openmp==2021.* (from mkl<=2021.4.0,>=2021.1.1->torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached intel_openmp-2021.4.0-py2.py3-none-win_amd64.whl.metadata (1.2 kB) Collecting tbb==2021.* (from mkl<=2021.4.0,>=2021.1.1->torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached tbb-2021.13.0-py3-none-win_amd64.whl.metadata (1.1 kB) Collecting aiohttp<4 (from ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiohttp-3.9.5-cp310-cp310-win_amd64.whl.metadata (7.7 kB) Collecting distributed (from ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached distributed-2024.7.0-py3-none-any.whl.metadata (3.4 kB) Collecting pytz>=2020.1 (from pandas>=1.5->scanpy>=1.9.8->sopa==1.1.1) Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas>=1.5->scanpy>=1.9.8->sopa==1.1.1) Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB) Collecting six>=1.5 (from python-dateutil<3.0.0,>=2.1->botocore==1.34.19->sopa==1.1.1) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting markdown-it-py>=2.2.0 (from rich->spatialdata>=0.2.0->sopa==1.1.1) Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) Collecting pygments<3.0.0,>=2.13.0 (from rich->spatialdata>=0.2.0->sopa==1.1.1) Using cached pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB) Collecting threadpoolctl>=3.1.0 (from scikit-learn>=0.24->scanpy>=1.9.8->sopa==1.1.1) Using cached threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB) Collecting xarray-dataclasses>=1.1.0 (from spatial-image>=1.0.0->spatialdata>=0.2.0->sopa==1.1.1) Using cached xarray_dataclasses-1.8.0-py3-none-any.whl.metadata (10 kB) Collecting datashader>=0.15.0 (from xarray-spatial>=0.3.5->spatialdata>=0.2.0->sopa==1.1.1) Using cached datashader-0.16.3-py2.py3-none-any.whl.metadata (12 kB) Collecting dpath<3.0,>=2.1 (from yte<2.0,>=1.5.1->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached dpath-2.2.0-py3-none-any.whl.metadata (15 kB) Collecting plac<2.0.0,>=1.3.4 (from yte<2.0,>=1.5.1->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached plac-1.4.3-py2.py3-none-any.whl.metadata (5.9 kB) Collecting asciitree (from zarr->spatialdata>=0.2.0->sopa==1.1.1) Using cached asciitree-0.3.3-py3-none-any.whl Collecting numcodecs>=0.10.0 (from zarr->spatialdata>=0.2.0->sopa==1.1.1) Downloading numcodecs-0.13.0-cp310-cp310-win_amd64.whl.metadata (3.0 kB) Collecting fasteners (from zarr->spatialdata>=0.2.0->sopa==1.1.1) Using cached fasteners-0.19-py3-none-any.whl.metadata (4.9 kB) Collecting pims>=0.4.1 (from dask-image->spatialdata>=0.2.0->sopa==1.1.1) Using cached PIMS-0.7-py3-none-any.whl Collecting gitdb<5,>=4.0.1 (from gitpython->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB) Collecting pyreadline3 (from humanfriendly->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached pyreadline3-3.4.1-py3-none-any.whl.metadata (2.0 kB) Collecting attrs>=22.2.0 (from jsonschema->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB) Collecting referencing>=0.28.4 (from jsonschema->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB) Collecting rpds-py>=0.7.1 (from jsonschema->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached rpds_py-0.19.0-cp310-none-win_amd64.whl.metadata (4.2 kB) Collecting fastjsonschema>=2.15 (from nbformat->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB) Collecting jupyter-core!=5.0.*,>=4.12 (from nbformat->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB) Collecting traitlets>=5.1 (from nbformat->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached traitlets-5.14.3-py3-none-any.whl.metadata (10 kB) Collecting platformdirs>=2.5.0 (from pooch->spatialdata>=0.2.0->sopa==1.1.1) Using cached platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB) Collecting charset-normalizer<4,>=2 (from requests->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached charset_normalizer-3.3.2-cp310-cp310-win_amd64.whl.metadata (34 kB) Collecting idna<4,>=2.5 (from requests->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB) Collecting certifi>=2017.4.17 (from requests->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB) Collecting lamin_utils (from readfcs->spatialdata-io>=0.1.3->sopa==1.1.1) Using cached lamin_utils-0.13.2-py2.py3-none-any.whl.metadata (1.0 kB) Collecting fcsparser (from readfcs->spatialdata-io>=0.1.3->sopa==1.1.1) Using cached fcsparser-0.2.8-py3-none-any.whl.metadata (3.6 kB) Collecting imageio>=2.33 (from scikit-image->spatialdata>=0.2.0->sopa==1.1.1) Using cached imageio-2.34.2-py3-none-any.whl.metadata (4.9 kB) Collecting lazy-loader>=0.4 (from scikit-image->spatialdata>=0.2.0->sopa==1.1.1) Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB) Collecting stdlib-list (from session-info->scanpy>=1.9.8->sopa==1.1.1) Using cached stdlib_list-0.10.0-py3-none-any.whl.metadata (3.3 kB) Collecting mpmath<1.4,>=1.1.0 (from sympy->torch!=2.0.1,!=2.1.0,>=2.0.0->sopa==1.1.1) Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) Collecting aiosignal>=1.1.2 (from aiohttp<4->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiosignal-1.3.1-py3-none-any.whl.metadata (4.0 kB) Collecting frozenlist>=1.1.1 (from aiohttp<4->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached frozenlist-1.4.1-cp310-cp310-win_amd64.whl.metadata (12 kB) Collecting multidict<7.0,>=4.5 (from aiohttp<4->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached multidict-6.0.5-cp310-cp310-win_amd64.whl.metadata (4.3 kB) Collecting yarl<2.0,>=1.0 (from aiohttp<4->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached yarl-1.9.4-cp310-cp310-win_amd64.whl.metadata (32 kB) Collecting async-timeout<5.0,>=4.0 (from aiohttp<4->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached async_timeout-4.0.3-py3-none-any.whl.metadata (4.2 kB) Collecting dask-expr<1.2,>=1.1 (from dask[array,dataframe]>=2024.4.1->dask-image->spatialdata>=0.2.0->sopa==1.1.1) Using cached dask_expr-1.1.7-py3-none-any.whl.metadata (2.5 kB) Collecting colorcet (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata>=0.2.0->sopa==1.1.1) Using cached colorcet-3.1.0-py3-none-any.whl.metadata (6.3 kB) Collecting multipledispatch (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata>=0.2.0->sopa==1.1.1) Using cached multipledispatch-1.0.0-py3-none-any.whl.metadata (3.8 kB) Collecting param (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata>=0.2.0->sopa==1.1.1) Using cached param-2.1.1-py3-none-any.whl.metadata (7.2 kB) Collecting pyct (from datashader>=0.15.0->xarray-spatial>=0.3.5->spatialdata>=0.2.0->sopa==1.1.1) Using cached pyct-0.5.0-py2.py3-none-any.whl.metadata (7.4 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2024.6.1-py3-none-any.whl.metadata (1.6 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB) Collecting zipp>=0.5 (from importlib-metadata>=4.13.0->dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached zipp-3.19.2-py3-none-any.whl.metadata (3.6 kB) Collecting pywin32>=300 (from jupyter-core!=5.0.*,>=4.12->nbformat->snakemake<8.0.0,>=7.32.4->sopa==1.1.1) Using cached pywin32-306-cp310-cp310-win_amd64.whl.metadata (6.6 kB) Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->spatialdata>=0.2.0->sopa==1.1.1) Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB) Collecting locket (from partd>=1.4.0->dask>=2024.4.1->spatialdata>=0.2.0->sopa==1.1.1) Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB) Collecting slicerator>=0.9.8 (from pims>=0.4.1->dask-image->spatialdata>=0.2.0->sopa==1.1.1) Using cached slicerator-1.1.0-py3-none-any.whl.metadata (1.9 kB) Collecting msgpack>=1.0.0 (from distributed->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached msgpack-1.0.8-cp310-cp310-win_amd64.whl.metadata (9.4 kB) Collecting sortedcontainers>=2.0.5 (from distributed->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB) Collecting tblib>=1.6.0 (from distributed->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached tblib-3.0.0-py3-none-any.whl.metadata (25 kB) Collecting tornado>=6.0.4 (from distributed->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached tornado-6.4.1-cp38-abi3-win_amd64.whl.metadata (2.6 kB) Collecting zict>=3.0.0 (from distributed->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached zict-3.0.0-py2.py3-none-any.whl.metadata (899 bytes) Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.13.1-py3-none-any.whl.metadata (22 kB) INFO: pip is looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while. Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2024.6.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2024.5.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2024.3.1-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2024.3.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2024.2.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.12.2-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.12.1-py3-none-any.whl.metadata (1.6 kB) INFO: pip is still looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while. Using cached s3fs-2023.10.0-py3-none-any.whl.metadata (1.6 kB) Collecting aiobotocore~=2.7.0 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.7.0-py3-none-any.whl.metadata (20 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2023.9.2-py3-none-any.whl.metadata (1.6 kB) Collecting aiobotocore~=2.5.4 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.5.4-py3-none-any.whl.metadata (19 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2023.9.1-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.9.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.6.0-py3-none-any.whl.metadata (1.6 kB) INFO: pip is looking at multiple versions of aiobotocore to determine which version is compatible with other requirements. This could take a while. Collecting aiobotocore~=2.5.0 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.5.3-py3-none-any.whl.metadata (19 kB) Using cached aiobotocore-2.5.2-py3-none-any.whl.metadata (19 kB) Using cached aiobotocore-2.5.1-py3-none-any.whl.metadata (19 kB) Using cached aiobotocore-2.5.0-py3-none-any.whl.metadata (19 kB) INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C. Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2023.5.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.4.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2023.3.0-py3-none-any.whl.metadata (1.6 kB) Collecting aiobotocore~=2.4.2 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.4.2-py3-none-any.whl.metadata (19 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2023.1.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2022.11.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2022.10.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2022.8.2-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2022.8.1-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2022.8.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2022.7.1-py3-none-any.whl.metadata (1.5 kB) Collecting aiobotocore~=2.3.4 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.3.4-py3-none-any.whl.metadata (19 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2022.7.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2022.5.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2022.3.0-py3-none-any.whl.metadata (1.5 kB) Collecting aiobotocore~=2.2.0 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.2.0.tar.gz (59 kB) Preparing metadata (setup.py) ... done Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2022.2.0-py3-none-any.whl.metadata (1.5 kB) Collecting aiobotocore~=2.1.0 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.1.2-py3-none-any.whl.metadata (18 kB) Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2022.1.0-py3-none-any.whl.metadata (1.6 kB) Using cached s3fs-2021.11.1-py3-none-any.whl.metadata (1.6 kB) Collecting aiobotocore~=2.0.1 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.0.1.tar.gz (54 kB) Preparing metadata (setup.py) ... done Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2021.11.0-py3-none-any.whl.metadata (1.6 kB) Collecting aiobotocore~=1.4.1 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-1.4.2.tar.gz (52 kB) Preparing metadata (setup.py) ... done Collecting s3fs (from fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached s3fs-2021.10.1-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.10.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.9.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.8.1-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.8.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.7.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.6.1-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.6.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.5.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-2021.4.0-py3-none-any.whl.metadata (1.5 kB) Using cached s3fs-0.6.0-py3-none-any.whl.metadata (1.4 kB) Collecting aiobotocore>=1.0.1 (from s3fs->fsspec[s3]!=2021.07.0,>=0.8->ome-zarr>=0.8.4->spatialdata>=0.2.0->sopa==1.1.1) Using cached aiobotocore-2.13.0-py3-none-any.whl.metadata (21 kB) Using cached aiobotocore-2.12.4-py3-none-any.whl.metadata (21 kB) INFO: pip is still looking at multiple versions of aiobotocore to determine which version is compatible with other requirements. This could take a while. 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Using cached kiwisolver-1.4.5-cp310-cp310-win_amd64.whl (56 kB) Using cached lazy_loader-0.4-py3-none-any.whl (12 kB) Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB) Using cached MarkupSafe-2.1.5-cp310-cp310-win_amd64.whl (17 kB) Using cached mpmath-1.3.0-py3-none-any.whl (536 kB) Downloading numcodecs-0.13.0-cp310-cp310-win_amd64.whl (832 kB) ---------------------------------------- 832.4/832.4 kB 8.7 MB/s eta 0:00:00 Using cached partd-1.4.2-py3-none-any.whl (18 kB) Using cached pillow-10.4.0-cp310-cp310-win_amd64.whl (2.6 MB) Using cached plac-1.4.3-py2.py3-none-any.whl (22 kB) Using cached platformdirs-4.2.2-py3-none-any.whl (18 kB) Using cached pygments-2.18.0-py3-none-any.whl (1.2 MB) Using cached pyogrio-0.9.0-cp310-cp310-win_amd64.whl (15.9 MB) Using cached pyparsing-3.1.2-py3-none-any.whl (103 kB) Using cached pyproj-3.6.1-cp310-cp310-win_amd64.whl (6.1 MB) Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB) Using cached referencing-0.35.1-py3-none-any.whl (26 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dask_expr-1.1.7-py3-none-any.whl (241 kB) Using cached frozenlist-1.4.1-cp310-cp310-win_amd64.whl (50 kB) Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB) Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) Using cached msgpack-1.0.8-cp310-cp310-win_amd64.whl (75 kB) Using cached multidict-6.0.5-cp310-cp310-win_amd64.whl (28 kB) Using cached pywin32-306-cp310-cp310-win_amd64.whl (9.2 MB) Using cached slicerator-1.1.0-py3-none-any.whl (10 kB) Using cached smmap-5.0.1-py3-none-any.whl (24 kB) Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB) Using cached tblib-3.0.0-py3-none-any.whl (12 kB) Using cached tornado-6.4.1-cp38-abi3-win_amd64.whl (438 kB) Using cached yarl-1.9.4-cp310-cp310-win_amd64.whl (76 kB) Using cached zict-3.0.0-py2.py3-none-any.whl (43 kB) Using cached zipp-3.19.2-py3-none-any.whl (9.0 kB) Using cached colorcet-3.1.0-py3-none-any.whl (260 kB) Using cached multipledispatch-1.0.0-py3-none-any.whl (12 kB) Using cached param-2.1.1-py3-none-any.whl (116 kB) Using cached pyct-0.5.0-py2.py3-none-any.whl (15 kB) Using cached s3fs-0.6.0-py3-none-any.whl (23 kB) Using cached aiobotocore-2.11.2-py3-none-any.whl (76 kB) Using cached aioitertools-0.11.0-py3-none-any.whl (23 kB) Checking if build backend supports build_editable ... done Building wheels for collected packages: sopa, datrie Building editable for sopa (pyproject.toml) ... done Created wheel for sopa: filename=sopa-1.1.1-py3-none-any.whl size=5100 sha256=0e338900efe7778e45f00eac320168dbb1889c011557d36ad8e6ee6fc4f4d027 Stored in directory: C:\Users\jnimoca\AppData\Local\Temp\4\pip-ephem-wheel-cache-y2l4i0g1\wheels\50\ee\8a\3715c996f3d9166d0833bfc2d09cd19ba8a3c915b3b90a4a60 Building wheel for datrie (pyproject.toml) ... error error: subprocess-exited-with-error × Building wheel for datrie (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [5 lines of output] running bdist_wheel running build running build_clib building 'datrie' library error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/ [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for datrie Successfully built sopa Failed to build datrie ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects ```Expected behavior
normal installation I guess
System