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retorquere / zotero-better-bibtex

Make Zotero effective for us LaTeX holdouts
https://retorque.re/zotero-better-bibtex/
MIT License
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Auto Exporting not staging and pushing bib with git with Flatpacked Zotero #1536

Closed clairekope closed 4 years ago

clairekope commented 4 years ago

Report ID: 692E5RD3-euc

Exporter used: Better BibLaTeX

Expected behavior: Auto export should be pushing the newly exported bib to Overleaf automatically.

Actual behavior: Modified bib files show as unstaged in the output directory and was not pushed to Overleaf. Credentials have been stored so that pulls and pushes should be able to proceed automatically.

Log indicates that Better BibTeX thinks the extension is not enabled? (3)(+0000001): {better-bibtex +1} git.pull {"enabled":false,"git":null} Even though it is:

push.default=simple
core.repositoryformatversion=0
core.filemode=true
core.bare=false
core.logallrefupdates=true
remote.origin.url=https://git.overleaf.com/5de56c54c5f3a3000196ff4f
remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
branch.master.remote=origin
branch.master.merge=refs/heads/master
credential.helper=store
zotero.betterbibtex.push=true
retorquere commented 4 years ago

It looks like the git executable is not in the $PATH that's available to Zotero. Can you go to Help -> Debug Output Logging -> Restart with logging enabled, let Zotero restart, and then send a new BBT log from the Help menu?

clairekope commented 4 years ago

Interesting, because it's in /usr/bin (at least that's the one that is being used when I use the command line). The new log is D801701768

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 4:21 AM Emiliano Heyns notifications@github.com wrote:

It looks like the git executable is not in the $PATH that's available to Zotero. Can you go to Help -> Debug Output Logging -> Restart with logging enabled, let Zotero restart, and then send a new BBT log from the Help menu?

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retorquere commented 4 years ago

That's a zotero log, I can't access those. I need a bbt debug log. Those always end in -euc or -apse.

clairekope commented 4 years ago

Whoops, the report # is 3W8BQH92-euc

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 1:05 PM Emiliano Heyns notifications@github.com wrote:

That's a zotero log, I can't access those. I need a bbt debug log. Those always end in -euc or -apse.

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retorquere commented 4 years ago

As far as Zotero knows, the $PATH is /app/bin:/usr/bin

retorquere commented 4 years ago

How did you install Zotero?

clairekope commented 4 years ago

I believe I installed it from the package installer built into Linux Mint

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 3:20 PM Emiliano Heyns notifications@github.com wrote:

How did you install Zotero?

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retorquere commented 4 years ago

That likely means it's a snap package. Those are very restricted in what binaries they can see.

clairekope commented 4 years ago

Ah, ok. Should I reinstall from the Zotero website then?

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 3:35 PM Emiliano Heyns notifications@github.com wrote:

That likely means it's a snap package. Those are very restricted in what binaries they can see.

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retorquere commented 4 years ago

It should be possible to configure a snap to get access to more paths.

The zotero binaries from the official downloads will work but there is some (very little) extra work you need to do to get launcher integration done. It's well documented on the zotero site.

Alternately, there's these: https://github.com/retorquere/zotero-deb. There's a one-time setup for that but the desktop integration stuff is done by the packager.

retorquere commented 4 years ago

No wait, you're more likely to have a flatpacked install. Mint had some philosophical objections to snap, and I see you're on Zotero 5.0.86, and flatpack is currently one release behind, so that'd fit.

I'm not familiar with either unfortunately. I obviously know zotero-deb -- I created the package -- but stuff that comes with your distro probably has your preference. You'd have to ask the flatpack project or mint how to add path access to flatpacks -- I have no idea how they work.

clairekope commented 4 years ago

Thank you for the information! I will look into it. I think this issue can now be closed, as the problem is on my end.

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 4:14 PM Emiliano Heyns notifications@github.com wrote:

No wait, you're more likely to have a flatpacked install. Mint had some philosophical objections to snap, and I see you're on Zotero 5.0.86, and flatpack is currently one release behind, so that'd fit.

I'm not familiar with either unfortunately. I obviously know zotero-deb -- I created the package -- but stuff that comes with your distro probably has your preference. You'd have to ask the flatpack project or mint how to add path access to flatpacks -- I have no idea how they work.

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blip-bloop commented 4 years ago

:robot: this is your friendly neighborhood build bot announcing test build 5.2.26.6634 ("really should be found? flatpacks are weird")

Install in Zotero by downloading test build 5.2.26.6634, opening the Zotero "Tools" menu, selecting "Add-ons", open the gear menu in the top right, and select "Install Add-on From File...".

retorquere commented 4 years ago

Could you give 6634 a try nonetheless?

clairekope commented 4 years ago

Exported bib shows as unstaged; report ZRSXCMC8-euc

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Thu, Jun 4, 2020 at 7:17 PM Emiliano Heyns notifications@github.com wrote:

Could you give 6634 a try nonetheless?

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blip-bloop commented 4 years ago

:robot: this is your friendly neighborhood build bot announcing test build 5.2.26.6637 ("more logging")

Install in Zotero by downloading test build 5.2.26.6637, opening the Zotero "Tools" menu, selecting "Add-ons", open the gear menu in the top right, and select "Install Add-on From File...".

retorquere commented 4 years ago

Can you give it one more go with 6637?

clairekope commented 4 years ago

Sure thing! New log is IK35KK9Y-euc

Claire Kopenhafer she/her Graduate Student Physics & Astronomy; Computational Math, Science, & Engineering Michigan State University

On Fri, Jun 5, 2020 at 4:40 PM Emiliano Heyns notifications@github.com wrote:

Can you give it one more go with 6637?

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retorquere commented 4 years ago

I got the logging wrong. I need to turn in now as I have an early start tomorrow, but a new build will drop here in 20 minutes or so -- I will be back around noon tomorrow and then I can take a further look.

clairekope commented 4 years ago

Ok; I'm happy to debug if you are committed to making this work but I was able to get it working with the install from the website

-Claire

On Fri, Jun 5, 2020, 19:11 Emiliano Heyns notifications@github.com wrote:

I got the logging wrong. I need to turn in now as I have an early start tomorrow, but a new build will drop here in 20 minutes or so -- I will be back around noon tomorrow and then I can take a further look.

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retorquere commented 4 years ago

Naah, I wouldn't have you install the flatpack just for this. Glad you got it work.

blip-bloop commented 4 years ago

:robot: this is your friendly neighborhood build bot announcing test build 5.2.26.6640 ("the comma is not optional my man")

Install in Zotero by downloading test build 5.2.26.6640, opening the Zotero "Tools" menu, selecting "Add-ons", open the gear menu in the top right, and select "Install Add-on From File...".

github-actions[bot] commented 3 years ago

This issue has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.