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diegozea / MIToS.jl

A Julia package to analyze protein sequences, structures, and evolutionary information
https://diegozea.github.io/MIToS.jl/stable/
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Switch to GitHub Actions, fix constructor #64

Closed timholy closed 1 year ago

timholy commented 1 year ago

This goes partway to fixing tests on this package, and switches to GitHub Actions for CI.

Issues that this does not fix include:

This also fixes the URL for downloading Pfam data, see https://xfam.wordpress.com/2022/08/04/pfam-website-decommission/

timholy commented 1 year ago

Oh, and if you want to keep supporting Julia 1.0, we should add it to the CI list before merging this PR. (It's bad to claim to support Julia versions you don't test.) If you'd rather drop Julia 1.0 support, then we'd need to bump the version to 2.10 because General requires a minor version bump if you change the supported Julia versions.

timholy commented 1 year ago

The change in the filename encoding for the Pfam download might necessitate a breaking change, unless we come up with a way of making it backward compatible.

timholy commented 1 year ago

Bump

diegozea commented 1 year ago

Hi @timholy ! Thanks you very much for taking care of this. I will merge the PR and try to solve the remaining issues before doing a new release and bumping the minor version.

diegozea commented 1 year ago

Thanks a lot @timholy !

I have solved most of these issues in MIToS 2.10

  • there seems to be a Pkg bug that prevents testing with GaussDCA (it generates a conflict on DelimitedFiles, which is a standard library 😕). For now, comment out that test

https://github.com/diegozea/MIToS.jl/commit/5349591ce730445096fbf2f1bbb21b5cf6bc7d03

  • the scripts fail if you don't have MIToS in your default environment

https://github.com/diegozea/MIToS.jl/commit/d519fc2abba861fc6a46e39c5a9dff0c9985b21b

This also fixes the URL for downloading Pfam data, see https://xfam.wordpress.com/2022/08/04/pfam-website-decommission/

https://github.com/diegozea/MIToS.jl/commit/4d732dce915d3b8e9d3d027435df1aeb092c82a8

Cheers!

timholy commented 1 year ago

Thanks, greatly appreciated!