Comments (15)
Released in https://pypi.org/project/jupyterlab-fasta/3.2.0
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This seems to be msa / Firefox related: wilzbach/msa#257
Xref: jupyterlite/jupyterlite#284
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jupyterlab: 3.1.2
jupyterlab-fasta: 3.1.1
chromium: 92.0.4515.131
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Replace if(this.seqs=[],!t instanceof Array||"at"in t))
by if(this.seqs=[],!t instanceof Array||"on"in t)
.
I guess there was a typo "at" --> "on".
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Thanks @guignonv! Would you like to open a PR?
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So the upstream library (https://github.com/wilzbach/msa) looks abandoned (last PR in 2018 and the NPM package was pushed 5 years ago).
The root issue isn't in that library, however, but is in https://github.com/wilzbach/stat.seqs, which also looks abandoned.
Specifically, it's in https://github.com/wilzbach/stat.seqs/blob/master/lib/index.js#L52.
The issue can't easily be fixed here (unless you do a hacky find and replace at the end of the build stage).
It can't be fixed upstream given they seem abandoned.
Thankfully, there's a fork with fixes - https://github.com/niaid/msa. The specific fix is niaid/msa@e82512e.
Unfortunately, this isn't published to NPM and is a bit of a pain to get working.
- Update the
"msa"
entry ofpackage.json
in thefasta-extension
folder to point to"https://github.com/niaid/msa"
. - Run the install steps, which fails due to the
bio.io
package not being built. - Go into
bio.io
innode_modules
and manually 'build' it by runningbabel -d lib src
. - Repeat the install step and you'll have a working FASTA viewer.
Hopefully, this helps a little...
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Thanks @zacharyrs for investigating this.
Thankfully, there's a fork with fixes - https://github.com/niaid/msa. The specific fix is niaid/msa@e82512e.
It would have been interesting to see if they planned to open a PR to merge the fixes upstream. Although as you mentioned it doesn't seem to be actively maintained unfortunately.
Another option would also be to maintain a fork of the msa
library, for example in https://github.com/jupyterlab-contrib (and move the jupyterlab-renderers
there too). But this adds quite a bit of maintenance cost.
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Personally I suspect we'd be best to move to their fork.
For reference, NIAID is the National Institute of Allergy and Infectious Diseases, so I suspect their fork will be well maintained.
I've contacted them to find out if they'll be publishing it to NPM, else I suppose we'll need a fork...
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Hey @jtpio! Unfortunately I don't thing NIAID will be publishing their fork to NPM. I think it might be worth forking it to https://github.com/jupyterlab-contrib and publishing that to NPM ourselves.
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Thanks @zacharyrs for following up here.
Would you like to help with this and releasing to npm? Probably we could then fork to https://github.com/jupyterlab-contrib and add you as maintainer of the repo?
The package could be published under the @jlab-contrib/msa
name for example.
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Hey @jtpio, I'm keen to give it a go but I'll be honest that I'm not sure how much time I have to dedicate long-term. I can at least get the NPM builds working though so we can use it!
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@zacharyrs I fork the NIAID msa repository in jupyterlab-contrib and you should have receive an invitation to become admin: https://github.com/jupyterlab-contrib/msa
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Would you mind giving me your npm user id so I can invite you to the NPM organization?
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@zacharyrs I fork the NIAID msa repository in jupyterlab-contrib and you should have receive an invitation to become admin: https://github.com/jupyterlab-contrib/msa
Awesome! I've just accepted that.
Would you mind giving me your npm user id so I can invite you to the NPM organization?
Should be zacharyrs
.
Thanks!
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Thanks I invited you to the jlab-contrib npm organization. Let us know if you have trouble publishing the package.
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