DeprecationWarning:

[erinyoung]

I don't think this is an error, but I wanted to let you know that there's a DepreciationWarning with heatcluster due to pandas' new dependency.

heatcluster.py --help
/heatcluster/heatcluster.py:13: DeprecationWarning:
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

usage: heatcluster.py [-h] [-i INPUT] [-o OUT] [-t TYPE] [-v]

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input SNP matrix file name
  -o OUT, --out OUT     final file name
  -t TYPE, --type TYPE  file extension for final image
  -v, --version         print version and exit

[DrB-S]

Would it be wise to move from Pandas to Polars? See [https://pola.rs/posts/polars-string-type/]

[erinyoung]

I think pandas is better documented

[DrB-S]

I have created a branch of HeatCluster - v1.1.0.20240131 using Polars. How can I test that within github without modifying main?

[erinyoung]

If all your changed are on a branch, then you can push to your github repo and then create a PR. That should trigger your tests.

[DrB-S]

Doesn’t the PR pull from the new branch to main? Also, when I try running the tests, I am getting errors. When I correct the files (heatcluster.yml, and heatcluster.py) and commit changes, the test is still using the old version of the files and gives me the same error. For instance, I changed (tabs = pl.scan_csv(file, nrows=1, sep='\t').shape[1]) to (tabs = pl.scan_csv(file, n_rows=1, sep='\t').shape[1]) in heatcluster.py and committed the change. But when I run the test, it gives me the same error, that nrows is incorrect!