> it doesn't distinguish between "isomorphism" and "canonical isomorphism"
You can distinguish these concepts in (higher )category theory, where isomorphisms are morphisms in groupoids and canonical isomorphisms are contractible spaces of morphisms. These sound like complicated concepts, but in HoTT you can discover the same phenomena as paths in types (i.e., equality) and a simple definition of contractibility which looks and works almost exactly like unique existence.
> In my opinion, Lean made a number pragmatic choices (impredicative Prop, non-classical logic including the axiom of global choice, uniqueness of identity proofs, etc.) that enable the practical formalization of mathematics as actually done by the vast majority of mathematicians who don't research logic, type theory, or category theory.
The authors of Lean are brilliant and I'm extremely happy that more mathematicians are looking into formalisations and recognizing the additional challenges that this brings. At the same time, it's a little bit depressing that we had finally gotten a good answer to many (not all!) of these additional challenges only to then retreat back to familiar ground.
Anyway, there were several responses to my original comment and instead of answering each individually, I'm just going to point to the article itself. The big example from section 5 is that of localisations of R-algebras. Here is how this whole discussion changes in HoTT:
1) We have a path R[1/f][1/g] = R[1/fg], therefore the original theorem is applicable in the case that the paper mentions.
2) The statements in terms of "an arbitrary localisation" and "for all particular localisations" are equivalent.
3) ...and this is essentially because in HoTT there is a way to define the localisation of an R-algebra at a multiplicative subset. This is a higher-inductive type and the problematic aspects of the definition in classical mathematics stem from the fact that this is not (automatically) a Set. A higher-inductive definition is a definition by a universal property, yet you can work with this in the same way as you would with a concrete construction and the theorems that the article mentions are provable.
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There is much more that can be said here and it's not all positive. The only point I want to make is that everybody who ever formalised anything substantial is well aware of the problem the article talks about: you need to pick the correct definitions to formalise, you can't just translate a random math textbook and expect it to work. Usually, you need to pick the correct generalisation of a statement which actually applies in all the cases where you need to use it.
Type theory is actually especially difficult here, because equality in type theory lacks many of the nice properties that you would expect it to have, on top of issues around isomorphisms and equality that are left vague in many textbooks/papers/etc. HoTT really does solve this issue. It presents a host of new questions and it's almost certain that we haven't found the best presentation of these ideas yet, but even the presentation we have solves the problems that the author talks about in this article.