Various updates to methods / installPackage / package / etc.

[mahrud]

• set warnings to be always printed
• added mutable symbols to items in package docs
• added briefDocumentation for method keys
• added routine that checks everything is documented
• overhauled warning and errors in installPackage
• fixed an issue in (package, Symbol), (package, Sequence)
• changed default errorDepth in CMake targets
• fixed methods to not show unexported methods
• simplified importFrom and added warning
• deleted unused key in Package
• added missing documentation for MonomialIdeal:RingElement
• moved and fixed (sort, List, Function)
• moved (jacobian, RingElement) to Core
• added helpers subclasses, descendants, allobjects
• downgraded a fatal error to an error signal
• undocumented all methods of Expressions
• added error when an unexported type is documented
• exported missing Bertini symbol
• exported missing VectorGraphics symbol

[mahrud]

@pzinn are the changes related to documentation of expressions here acceptable to you?

[pzinn]

As far as I understand you've only "undocumented" things that were not documented anyway. so I can't imagine why anyone would object to that.

[mahrud]

As far as I understand you've only "undocumented" things that were not documented anyway. so I can't imagine why anyone would object to that.

Not quite, there are two differences:

1. There are <160 nodes like - Expression which are currently just pointing to the documentation for Expression, this PR removes those from the index.
2. Even a missing documentation will appear under "Methods that use an expression" on the documentation for Expression. Marking them as undocumented removes this.

[pzinn]

2. Even a missing documentation will appear under "Methods that use an expression" on the documentation for Expression. Marking them as undocumented removes this.

I see. That's a bit radical. Maybe we do want to keep some of these methods listed? is there any way to do that w/o actually documenting them?

[mahrud]

Exactly, this is why I've been trying to ask you which things are important and should appear in the documentation! Adding them as secondary keys is the only other way I can think of (e.g. with this pr, value(Expression) still appears under Expression because it's a secondary of that node while assert(Expression) appears under Expression and links to assert because it's a secondary of assert:

M2/M2/Macaulay2/packages/Macaulay2Doc/debugging.m2

Lines 315 to 318 in 18a83cd

	Key
	assert
	(assert, Thing)
	(assert, Expression)

M2/M2/Macaulay2/packages/Macaulay2Doc/doc12.m2

Line 285 in 18a83cd

Key => { Expression, (value, Expression) },

I think this way undocumenting by default, except for nodes intentionally added as secondaries is probably easier to maintain.

ps: note that all the other methods still appear under methods Expression, they're just not listed online.

[mahrud]

Can this be merged? #3388 is on top of this.

[d-torrance]

Was there a reason to call help() here and not just use parent DIV? Or if we're trying to avoid importing DIV, code would work since it also returns a DIV object.

Calling help() can take a fair amount of memory (I seem to remember an issue about this but I can't find it...) and one of the PPA builds just crashed here.

[mahrud]

Oh sure, we can replace this with code of something. The important point is that we want to make sure methods still finds things for DIV even though it is not exported, because users can still access these methods, so they should be listed.