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Incompatibility issue with cooler=0.9.1 #853

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JSegueni opened this issue May 3, 2023 · 5 comments
Open

Incompatibility issue with cooler=0.9.1 #853

JSegueni opened this issue May 3, 2023 · 5 comments

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@JSegueni
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JSegueni commented May 3, 2023 •
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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.
robomics added a commit to paulsengroup/2022-mcf10a-cancer-progression that referenced this issue May 16, 2023
@robomics
Address several version compatibility issues in Dockerfiles
cf3c0b6 
- Bump bioframe to v0.4.1 to patch the bug outlined [here](https://github.com/open2c/bioframe/releases/tag/v0.4.1).
  We are not using any of the select functions (at least not directly),
  but better safe than sorry.
- Restrict pandas version to v1.* when installing together with cooler
  to workaround [this](open2c/cooler#324) bug
- Restrict cooler version to v0.8.11 in HiCExplorer Dockerfile to
  workadound [this](deeptools/HiCExplorer#853) bug
robomics added a commit to paulsengroup/2022-mcf10a-cancer-progression that referenced this issue May 16, 2023
@robomics
Address several version compatibility issues in Dockerfiles (#79)
c9d5b1e 
- Bump bioframe to v0.4.1 to patch the bug outlined [here](https://github.com/open2c/bioframe/releases/tag/v0.4.1).
  We are not using any of the select functions (at least not directly),
  but better safe than sorry.
- Restrict pandas version to v1.* when installing together with cooler
  to workaround [this](open2c/cooler#324) bug
- Restrict cooler version to v0.8.11 in HiCExplorer Dockerfile to
  workadound [this](deeptools/HiCExplorer#853) bug
@lldelisle
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Thank you very much for spotting this.

@kysrpex
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kysrpex commented Jun 21, 2024

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

@lldelisle
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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
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kysrpex commented Jun 21, 2024

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

@kysrpex kysrpex mentioned this issue Jun 21, 2024
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3 participants
@lldelisle @kysrpex @JSegueni