Workflow for libraries

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Hello,
My colleague and I have always worked in Eagle. At some point we got interested to get the 3D export from our PCB designs. So we converted all our libraries to managed ones an used Fusion to create the components so we could use the "Push to Fusion" feature in Eagle. This all worked quite well but felt a bit unnecessary to use 2 programs since fusion can do all the parts from eagle as well.
So we started in Fusion but got very confused with how you're supposed to work with the different libraries, the situation is as follows.
- we have a couple libraries in a shared team project
- each library is synced to library.io
- Our PCB designs are also in a synced team project
If I go to the library manager in my PCB design I can find the library twice, one from teams and one from library.io. This create a conflict once I press the "update design from library" button since fusion doesn't know which one of the two it needs to use.
I could get rid of this conflict by deleted the local version of the library.io libraries and only have the teams one in use. However every time I edit this library the library.io version will just come back in the library manger with the [version]+Edits.
By now we are very confused about what the intended workflow is with these two co-existing management systems.
Do you guys have some tips to push me in right direction?