Integrations to log automatically
Here are some popular sites that you could pull data from to update goal progress automatically:
Fitbit - steps, miles, sleep time, calories
MyFitnessPal - calories, nutritional information
Runkeeper - miles ran, other exercises
Toodledo - tasks completed
With the Shortcuts app you can log your progress with triggers set in the Automation tab. This is a powerful way to track with integrations, though we still plan to build a separate Apple Health integration.
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RC commented
If you don't want to go all the way with an API and make a full Oauth2 solution (which I don't think you need to) you can give each user a private key and then have some basic API actions so that users can update their own goals from another app.
Some of the useful actions would be:
Add/Edit/Delete an entry for a goal
Edit goal settings
Pull stats from a goal