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🚧 switch mamba installation #81

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🚧 switch mamba installation #81

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enryH
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@enryH enryH commented Oct 7, 2024

  • see if snakemake envs are somehow cached

enryH and others added 26 commits October 7, 2024 10:53
@enryH
🚧 switch mamba installation
442ad85 
- see if snakemake envs are somehow cached
@enryH
🐛 specify python version, move ls
057647f
@enryH
🚧 deactivate some workflow, run relatvie ls command
66dbb88
@enryH
try not to cache
9de1e37
@enryH
🚧 test using venv created by codespace with python 3.12
4e4965c 
- might be that I need to create (not sure what change in runner configurations)
@enryH
try to use full snakemake installation
7dc1168
@enryH
🚧 use miniconda for pypi installation test
be2699e
@enryH
try miniconda again
0f011a1 
- snakemake environment has it's own mamba installation
- auto-activate environment "test"
@enryH
install build dependencies, fix ubuntu first
1b35c28
@enryH
🐛 try to put mamba below 2.0
e732f8c 
snakemake/snakemake#3108
@enryH
test should be activate per default
98b7279
@enryH
🚧 conda env not activated...
180141c
@enryH
🐛 pip does not install in environment
9d2c4a4
@enryH
🚧 experiment
2b90edd
@enryH
🐛 shell was not iniated
1b9f2ac
@enryH
🐛 test installing njab separately
86f57b3
@enryH
🐛 order matters!
a97968d
@enryH
try again new order, add umap-learn explicitly
49f4902
@enryH
🐛 do not re-install njab
4d202cb
@enryH
restrict scipy (trapz missing in lifelines)
6a17b90 
latest scipy not supported by lifelines
@enryH
🐛 exclude numpy 2.0 for now
85b386c
@enryH
numpy try two
e6db81f
@enryH
swap numpy and njab, adapt other pkg to what it was before
481ac9f
@enryH
add back umap learn, relax constraints
8326220
@enryH
🚧 in package single requirement
47988cf 
single packages cannot be specified to just ignore the dependencies.
@enryH
➖ remove scipy dependency
d3fa813 
- leave it to njab to install dependencies in a second step.
@enryH
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enryH commented Oct 9, 2024 

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.
blis 1.0.1 requires numpy<3.0.0,>=2.0.0, but you have numpy 1.26.4 which is incompatible.
thinc 8.3.2 requires numpy<2.1.0,>=2.0.0; python_version >= "3.9", but you have numpy 1.26.4 which is incompatible.
Successfully installed autograd-1.7.0 autograd-gamma-0.5.0 category-encoders-2.6.4 formulaic-1.0.2 interface-meta-1.3.0 lifelines-0.29.0 llvmlite-0.43.0 mrmr-selection-0.2.8 njab-0.0.8 numba-0.60.0 numpy-1.26.4 polars-1.9.0 pynndescent-0.5.13 umap-learn-0.5.6

lifelines currently still relies on numpy below 2.0

  • other packages use later numpy version. lifelines is installed partly by njab, where it is used to plot km curves. Better to not include it in the default installation then.

Errors were created installing njab separatly without pimms.

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