Incompatibility issue with cooler=0.9.1

[JSegueni]

Hi everyone,

I noticed an incompatibility issue with cooler 0.9.1.

Versions: python 3.10 hicexplorer version 3.7.2 cooler 0.9.1 numpy 1.24.2

Command hicInfo -m matrix.cool

Output (error) AttributeError: module 'cooler' has no attribute 'io'

---Fix---

Versions: python 3.10 hicexplorer version 3.7.2 cooler 0.8.11 numpy 1.23.5 (downgraded because of the cooler downgrade)

Command hicInfo -m matrix.cool

Output (no error) # Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2 ....

Hopefully, this can help someone with the same issue.

[lldelisle]

Thank you very much for spotting this.

[kysrpex]

Can the problem be fixed adjusting setup.py? In other words, is there a version of cooler with which all "sub-tools" work?

[lldelisle]

As written above with cooler version 0.8.11, everything works. To change the setup.py we need to release. If we release, it is better to support the last version of cooler.

[kysrpex]

I am in fact writing because of the bug report we have received at usegalaxy.eu related to this issue. According to the README, this tool is supposed to work with conda, thus I guess it makes sense either to pin cooler to 0.8.11 in setup.py and release, or make it compatible with the newest version.

[lldelisle]

The bug report is from me ;-). Can you contact me on element (@lldelisle:matrix.org)?