Python version conflicts in the Dockerfile

[dustincys]

Command executed:

mkdir "sample"
filter_genes --adata dataset.h5ad --n-top-by-standard-deviation 1000 --spot-threshold 0.9 --output "sample/dataset_filtered.h5ad"

cat <<-END_VERSIONS > versions.yml
"BAYESTME_BASIC_VISIUM_ANALYSIS:BAYESTME_FILTER_GENES":
bayestme: $( python -c 'from importlib.metadata import version;print(version("bayestme"))' )
END_VERSIONS

Command exit status:
1

Command output:
You are running 3.11.7
Only python versions 3.7~3.10 are currently tested, use at your own risk.

Command error:
2024-01-31 10:59:36,221 - bayestme.cli.filter_genes - INFO - filter_genes called with arguments: Namespace(adata='dataset.h5ad', output='sample/dataset_filtered.h5ad', filter_ribosomal_genes=False, n_top_by_stan$
ard_deviation=1000, spot_threshold=0.9, expression_truth=None, verbose=False)
2024-01-31 10:59:36,363 - bayestme.cli.filter_genes - INFO - Will filter the top 1000 genes by standard deviation.
Traceback (most recent call last):
File "/usr/local/bin/filter_genes", line 8, in
sys.exit(main())
^^^^^^
File "/usr/local/lib/python3.11/site-packages/bayestme/cli/filter_genes.py", line 66, in main
dataset = gene_filtering.select_top_genes_by_standard_deviation(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bayestme/gene_filtering.py", line 22, in select_top_genes_by_standard_deviation
ordering = utils.get_stddev_ordering(dataset.reads)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bayestme/utils.py", line 377, in get_stddev_ordering
return np.argsort(np.std(np.log(1 + reads), axis=0))[::-1]
~~^~~~~~~
File "/usr/local/lib/python3.11/site-packages/scipy/sparse/_base.py", line 529, in radd return self.add(other)
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/scipy/sparse/_base.py", line 516, in add
raise NotImplementedError('adding a nonzero scalar to a '
NotImplementedError: adding a nonzero scalar to a sparse array is not supported

Work dir:
/rsrch3/scratch/genomic_med/ychu2/projects/project26/code/software/bayestme/work/85/bc133fabbfc9ded2f2ec352996935b

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

[jeffquinn-msk]

Thanks for writing in. That initial log message about the python version is just a warning message from one of the imported third party libraries. It's not the root cause of this.

This issue is an unintended consequence of #137

Should be resolved by #139