safepy

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sf.define_domains() - ValueError: The number of observations cannot be determined on an empty distance matrix.

3

Hi, thanks for this great package! I am trying to use SAFE for the annotation of metadata on a low-dimensional graph representation of microbiome abundance information (similar to: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1871-4). For...

m-petersen

Hi, I am trying to install safepy in a python 3.10 envirnoment. I am getting a version conflict, with many packages (pandas, matplotlib, ..) requiring a slightly newer version of...

samwindels

Windows paths

4

`sf.load_network()` Fails to work with windows paths in ini file: `re.sub` crashes in [`load_network_from_gpickle` from `safe_io.py`](https://github.com/baryshnikova-lab/safepy/blob/master/safe_io.py#L95) I think it's due to path concatenation or escaping error Try using pathlib

maxim1317

Bumps [ipython](https://github.com/ipython/ipython) from 8.6.0 to 8.10.0. Commits 15ea1ed release 8.10.0 560ad10 DOC: Update what's new for 8.10 (#13939) 7557ade DOC: Update what's new for 8.10 385d693 Merge pull request from...

dependabot[bot]

Bumps [numpy](https://github.com/numpy/numpy) from 1.14.1 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

plot_composite_network

1

Is there an option to save the composite_network in pdf? Thanks!

lacpromoter