[Bug]: TopoStats error on yaml dump due to depreciation

MaxGamill-Sheffield commented 5 months ago

Checklist

[X] Re-run analysis with topostats process --core 1.
[X] Describe the bug.
[X] Include the configuration file.
[X] Copy of the output.
[X] The exact command that failed. This is what you typed at the command line, including any options.
[X] TopoStats version, this is reported by topostats --version
[X] Operating System and Python Version

Describe the bug

When using pip install topostats in a new conda environment, all is installed ok. But when I run the test file using topostats process, it fails at the very end with the below error:

Copy of the output

Include the configuration file

This is the default_config.yaml file as one is not being specified.

To Reproduce

Create a new environment with python (I used 3.11). Seems to be an issue with the imported library run-yaml as version 0.18. fails but 0.17. works.

TopoStats Version

2.1.2

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

asttokens==2.4.1 contextlib2==21.6.0 contourpy==1.2.0 cycler==0.12.1 decorator==5.1.1 executing==2.0.1 fonttools==4.47.2 h5py==3.10.0 igor2==0.5.3 imageio==2.33.1 ipython==8.20.0 jedi==0.19.1 joblib==1.3.2 kiwisolver==1.4.5 lazy_loader==0.3 matplotlib==3.8.2 matplotlib-inline==0.1.6 networkx==3.2.1 numpy==1.26.3 packaging==23.2 pandas==2.2.0 parso==0.8.3 pexpect==4.9.0 pillow==10.2.0 prompt-toolkit==3.0.43 psutil==5.9.8 ptyprocess==0.7.0 pure-eval==0.2.2 pyfiglet==1.0.2 Pygments==2.17.2 pyparsing==3.1.1 pyspm==0.6.0 python-dateutil==2.8.2 pytz==2023.3.post1 PyYAML==6.0.1 ruamel.yaml==0.18.5 ruamel.yaml.clib==0.2.8 schema==0.7.5 scikit-image==0.22.0 scikit-learn==1.4.0 scipy==1.12.0 seaborn==0.13.1 six==1.16.0 stack-data==0.6.3 threadpoolctl==3.2.0 tifffile==2023.12.9 topostats==2.1.2 tqdm==4.66.1 traitlets==5.14.1 tzdata==2023.4 wcwidth==0.2.13

MaxGamill-Sheffield commented 5 months ago

This is an issue only with the pip installable version, not with the current version @ns-rse can we make a release after the cmap PR is sorted? Seems like you already fixed this previously @ns-rse :)

ns-rse commented 5 months ago

Probably #450 by the sounds of it?

Bug fix release can definitely be made, happy to include #777 if you don't mind giving that PR a the rubber stamp I'll do so tomorrow (just in time for the Computer Science Newsletter where I include new software releases :smile: )

AFM-SPM / TopoStats