Comments (10)
@shuail - are you able to take a look/have you run into this? If not I'll have to dig in.
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Yes, I take a look and it seems that the lomap package in conda is out of data. I think all my previous tests and the travis tests are all tested using the source code directly not through the conda package.
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Ah, OK. So this means I just need to refresh my memory on how to update the conda version and update that.
In the meantime, @skfegan , you should be able to resolve your issue by installing from source.
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I have installed lomap from source and am still having the same problem. Is there a specific version of NetworkX that I should have (currently version 2.1 is installed)? I am running this on my Ubuntu 16.04 workstation.
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@skfegan Yes, I think the current Lomap is compatible with networkx 1.11 but not networkx 2.0 and beyond #30, could you try to downgrade your networkx and see if it works?
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@shuail - do you have any thoughts about updating to be networkx 2 compatible?
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@davidlmobley here is a note I found https://networkx.github.io/documentation/stable/release/migration_guide_from_1.x_to_2.0.html, will take a deep look this weekend and see if I could find all incompatible pieces.
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Switching to networkx 1.11 works.
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@skfegan - thanks. I'll reopen so we remember to investigate networkx 2 compatibility
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Create a pull request here #34 to make the code compatible with networkx > 2.0. Sorry that it takes longer than I thought, ends up that I need to manually port the test template pickle file to be read by networkx version 2.0.
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Related Issues (20)
- Change the code to be compatible with networkx 2.0
- Add a fingerprint similarity option to calculate the structure similarity HOT 1
- Add a fast graphing option HOT 1
- Output problems for example.py and import problems for dbmol.py HOT 12
- Installing lomap via mobleylab conda channel HOT 10
- graph visualisation issues HOT 3
- Enhacement questions HOT 14
- Finish getting `dev` branch up to speed and merged into master HOT 1
- Confusion about example output HOT 2
- Problem specifying the hub molecule HOT 6
- can't read reference graph pickle HOT 1
- MCS test fails with most recent version of rdkit HOT 2
- Colouring code for connecting compounds in FEP HOT 7
- Issues with current perturbation map generation HOT 4
- Wishlist HOT 2
- Documentation HOT 1
- Developper guide as a wiki page? HOT 5
- [WIP] Lomap Refactoring HOT 6
- How to plot the graph?
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