We have SharePoint 2016 with a custom visual web parts, we want to show these web parts responsive in the mobile view
Do we need to use bootstrap? If yes it should be in the web part it self or master page?
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You can use Bootstrap or Media queries or Device channels based on your application needs and use of Third party plugin like bootstrap.
if you want to make webpart responsive so i assume you need to have SharePoint Classic Page layouts also responsive in nature .better to include plugin in Page layouts which will be using Responsive page Design. Refrence
If you are going for Modern Pages then all the pages are Responsive by nature so you should include the Bootstrap or Media Query in your webpart only and develop SPFX webparts
you can use bootstrap if you want, but you can also use pure CSS... the advantage to use bootstrap is about winning time, so you can focus on webpart functionality instead of design :)
1- you might want to declare
<meta name="viewport" content="width=device-width, initial-scale=1.0"> on your masterPage to ensure that the masterPage is responsive and implment also bootstrap libraries/classes
2- use thise libraries in your webparts