Issues with docker and library incompatibilities #17
Description
I initially faced issues with running the docker image for baysor, so I skipped that step. My docker image did not run_baysor.sh but when i cloned it to my local directory I could find the run_baysor.sh in the xb directory. But, locally I was unable to baysor because I could not successfully install julia.
Then I finally skipped that step and moved to the next steps, which worked fine until I reached the banksy portion where there were some library incompatibilities due to which i couldnt install banksy in the xenium_benchmarking env
Some errors that I faced are below --
The one below is what I constantly ran into -
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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.
typeguard 4.4.4 requires typing_extensions>=4.14.0, but you have typing-extensions 4.8.0 which is incompatible.
scikit-image 0.25.2 requires scipy>=1.11.4, but you have scipy 1.11.3 which is incompatible.
omnipath 1.0.10 requires packaging>=24.2, but you have packaging 23.2 which is incompatible.
Successfully installed array-api-compat-1.4 certifi-2023.7.22 igraph-0.10.6 ipykernel-6.25.2 jupyter-1.0.0 packaging-23.2 pip-23.3 scipy-1.11.3 typing_extensions-4.8.0
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ERROR: Ignored the following versions that require a different python version: 0.10.0 Requires-Python >=3.9; 0.10.0rc1 Requires-Python >=3.9; 0.10.1 Requires-Python >=3.9; 0.10.2 Requires-Python >=3.9; 0.10.3 Requires-Python >=3.9; 0.10.4 Requires-Python >=3.9; 0.10.5 Requires-Python >=3.9; 0.10.5.post1 Requires-Python >=3.9; 0.10.6 Requires-Python >=3.9; 0.10.7 Requires-Python >=3.9; 0.10.8 Requires-Python >=3.9; 0.10.9 Requires-Python >=3.9; 0.11.0 Requires-Python >=3.10; 0.11.0rc1 Requires-Python >=3.9; 0.11.0rc2 Requires-Python >=3.9; 0.11.0rc3 Requires-Python >=3.10; 0.11.1 Requires-Python >=3.10; 0.11.2 Requires-Python >=3.10; 0.11.3 Requires-Python >=3.10; 0.11.4 Requires-Python >=3.10; 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.9.0 Requires-Python >=3.8; 0.9.0rc1 Requires-Python >=3.8; 0.9.1 Requires-Python >=3.8; 0.9.2 Requires-Python >=3.8
ERROR: Could not find a version that satisfies the requirement anndata==0.10.2 (from versions: 0.1, 0.2, 0.2.1, 0.3, 0.3.0.1, 0.3.0.2, 0.3.0.3, 0.3.1, 0.3.2, 0.3.3, 0.3.4, 0.4, 0.4.1, 0.4.2, 0.4.3, 0.4.4, 0.5, 0.5.1, 0.5.2, 0.5.3, 0.5.4, 0.5.5, 0.5.6, 0.5.7, 0.5.8, 0.5.8.post1, 0.5.9, 0.5.10, 0.5.10.post1, 0.5.10.post2, 0.6, 0.6.1, 0.6.2, 0.6.3, 0.6.4, 0.6.5, 0.6.6, 0.6.7, 0.6.8, 0.6.9, 0.6.10, 0.6.11, 0.6.12, 0.6.13, 0.6.14, 0.6.15, 0.6.16, 0.6.17, 0.6.18, 0.6.19, 0.6.20, 0.6.21, 0.6.22rc1, 0.6.22, 0.6.22.post1, 0.7rc1, 0.7rc2, 0.7, 0.7.1, 0.7.2a1, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8.0rc1, 0.8.0)
ERROR: No matching distribution found for anndata==0.10.2
Thank you!