Make first pass at full doc coverage for structure.g[di]

To do this, the structure of the manual needed to be elaborated, which was
accomplished with a skeleton file, doc/chapters.autodoc, which is explicitly
loaded first.

Note that this portion of the manual may still need polishing; in particular,
perhaps it could use more examples, which would then double as tests in
tst/testall.g

PackageInfo.g

@@ -2,7 +2,7 @@ SetPackageInfo( rec(
   PackageName := "RAQ",
   Subtitle := "Racks And Quandles in GAP",
   Version := "0.1.0",
-  Date := "2018-Oct-1",
+  Date := "2018/10/01",
   PackageWWWPrefix := Concatenation("http://code.studioinfinity.org/",
                                     ~.PackageName),
   PackageWWWHome := Concatenation(~.PackageWWWPrefix, "/wiki"),
@@ -49,7 +49,7 @@ SetPackageInfo( rec(
     "quasigroups, but more more particularly with racks and quandles. ",
     "This package builds on fundamentals of non-associative algebra ",
     "established in the <span class=\"pkgname\">LOOPS</span> package, and ",
-    "and provides enhanced functionality, libraries, and implementations ",
+    "provides enhanced functionality, libraries, and implementations ",
     "as compared to the earlier <span class=\"pkgname\">RIG</span> package ",
     "on which <span class=\"pkgname\">RAQ</span> is generally modeled."
   ),

README.md

@@ -8,7 +8,10 @@
 #! @Chapter Introduction
 #! @AutoDocPlainText -->
 The &RAQ; package provides a variety of facilities for constructing and
-computing with one-sided quasigroups, racks, and quandles in ⪆.
+computing with one-sided quasigroups, racks, and quandles in ⪆. Highlights
+include:
+* Constructing quandles from operation tables, groups, or other quandles.
+* And more to come..
 
 <!--@Section Installation
 @AutoDocPlainText -->
@@ -53,4 +56,12 @@ Note in particular that &RAQ; generally, unless otherwise specifically
 requested, produces __left__ quandles and racks. (That is to say, quandles in
 which for any fixed element $l$, the "left-multiplication by $l$" operation
 $x\mapsto l*x$ is a permutation of the quandle.)
+
+<!--@Copyright
+@AutoDocPlainText -->
+&copyright; 2018 by Glen Whitney.
+
+This package may be distributed under the terms and conditions of the GNU
+Public License version 3. See the <C>LICENSE</C> file in the package directory
+for details.
 <!--@EndAutoDocPlainText -->

doc/chapters.autodoc

@@ -0,0 +1,11 @@
+@Chapter construct
+@ChapterTitle Constructing One-Sided Quasigroups, Racks, and Quandles.
+
+@Chapter operate
+@ChapterTitle Operations on One-Sided Quasigroups, Racks, and Quandles.
+
+@Chapter basic
+@ChapterTitle Basic Notions
+
+@Chapter technical
+@ChapterTitle Technical Details

doc/makedoc.g

@@ -3,7 +3,7 @@
 
 LoadPackage("AutoDoc");
 AutoDoc(rec(
-    autodoc := rec(files := ["README.md"]),
+    autodoc := rec(files := ["README.md", "doc/chapters.autodoc"]),
     maketest := rec(name := "tst/AutoDoc_tests.g")
 ));
 QUIT;

lib/structure.gd

@@ -2,7 +2,14 @@
 
 ## GAP Categories and representations
 
-## Info class for RAQ
+#! @Chapter technical
+#!   This chapter covers computational/operational aspects of &RAQ;
+#!   rather than mathematical ones.
+#! @Section Messages
+#! @Description Controls the level of verbosity of &RAQ;'s informative
+#!   messages. Use `SetInfoLevel` to set it to 0 to quiet &RAQ;
+#!   entirely, or to values greater than 1 to yield more details of &RAQ;'s
+#!   internal algorithms.
 DeclareInfoClass("InfoRAQ");
 
 ## Self-distributivity
@@ -14,63 +21,146 @@ DeclareInfoClass("InfoRAQ");
 # (cf. https://arxiv.org/abs/0910.4760). Hence, we implement them in RAQ with
 # new, non-conflicting terms.
 
-# An element that knows that multiplication in its family is left
-# self-distributive:
+#! @Chapter basic
+#!   In order to build up and define one-sided quasigroups, racks, and
+#!   quandles, &RAQ; must define several lower-level objects and properties,
+#!   which are documented in this section. Although logically they come before
+#!   the domain constructors and operations, they are presented afterwards
+#!   because it's rare that one needs to use them directly when working with
+#!   &RAQ;.
+#! @Section elements
+#! @SectionTitle Categories of elements
+#! @Description An element <C>x</C> with the property
+#!   that for all elements <C>y</C> and <C>z</C> in its family, <C>x*(y*z) =
+#!   (x*y)*(x*z)</C>.
 DeclareCategory("IsLSelfDistElement", IsMultiplicativeElement);
+# Have to skip a line because of AutoDoc's convention on documenting
+# consecutive declarations.
 DeclareCategoryCollections("IsLSelfDistElement");
 
-# An element that knows that multiplication in its family is right
-# self-distributive:
+#! @Description An element <C>x</C> with the property
+#!   that for all elements <C>y</C> and <C>z</C> in its family, <C>(y*z)*x =
+#!   (y*x)*(z*x)</C>. 
 DeclareCategory("IsRSelfDistElement", IsMultiplicativeElement);
+
 DeclareCategoryCollections("IsRSelfDistElement");
 
-# Left self-distributive collections of elements:
+#! @Section collections
+#! @SectionTitle Categories of collections
+#! @Description A collection which satisfies the left self-distributive
+#!   property (see the description of
+#!   <Ref Filt="IsLSelfDistElement" Label="for IsMultiplicativeElement"/>)
+#!   for all triples of elements of the collection.
 DeclareProperty("IsLSelfDistributive", IsMultiplicativeElementCollection);
 InstallTrueMethod(IsLSelfDistributive, IsLSelfDistElementCollection);
 
-# Right self-distributive collections of elements:
+#! @Description A collection which satisfies the right self-distributive
+#!   property (see the description of
+#!   <Ref Filt="IsRSelfDistElement" Label="for IsMultiplicativeElement"/>)
+#!   for all triples of elements of the collection.
 DeclareProperty("IsRSelfDistributive", IsMultiplicativeElementCollection);
 InstallTrueMethod(IsRSelfDistributive, IsRSelfDistElementCollection);
 
 ## Idempotence
-# There is already a property IsIdempotent on elements, but to definw
+# There is already a property IsIdempotent on elements, but to define
 # structures which will automatically be quandles we need a corresponding
 # collections category:
 DeclareCategoryCollections("IsIdempotent");
 
 # Collections in which every element is idempotent
+#! @Description A collection in which every element <C>x</C> is
+#!   **idempotent**, i.e. satisfies <C>x*x=x</C>.
 DeclareProperty("IsElementwiseIdempotent", IsMultiplicativeElementCollection);
 InstallTrueMethod(IsElementwiseIdempotent, IsIdempotentCollection);
 
-## Left and right racks and quandles
+#! @Description Tests whether <A>obj</A> is a left rack, which by definition
+#!   is precisely that <A>obj</A> is a left quasigroup (i.e.,
+#!   <C>IsLeftQuasigroup(obj)</C>, defined in the &LOOPS;
+#!   package, is true) and is left self-distributive
+#!   (i.e., <C>IsLSelfDistributive(obj)</C> is true).
+#! @Arguments obj
+#! @ItemType Filt
 DeclareSynonym("IsLeftRack", IsLeftQuasigroup and IsLSelfDistributive);
+#! @Description Tests whether <A>obj</A> is a right rack, by definition
+#!   precisely that it is a right quasigroup and right self-distributive.
+#! @Arguments obj
+#! @ItemType Filt
 DeclareSynonym("IsRightRack", IsRightQuasigroup and IsRSelfDistributive);
 
+#! @Description Tests whether <A>obj</A> is a left quandle, which by definition
+#!   is precisely that <A>obj</A> is a left rack (i.e.,
+#!   <C>IsLeftRack(obj)</C> is true) and every element is idempotent
+#!   (i.e., <C>IsElementwiseIdempotent(obj)</C> is true).
+#! @Arguments obj
+#! @ItemType Filt
 DeclareSynonym("IsLeftQuandle", IsLeftRack and IsElementwiseIdempotent);
-DeclareSynonym("IsRightQuandle", IsRightRack and IsElementwiseIdempotent);
 
-## One-sided quasigroups and racks and quandles by generators
+#! @Description Tests whether <A>obj</A> is a right quandle, by definition
+#!   precisely that it is a right rack and every element is idempotent.
+#! @Arguments obj
+#! @ItemType Filt
+DeclareSynonym("IsRightQuandle", IsRightRack and IsElementwiseIdempotent);
 
-# Returns the closure of <gens> under * and LeftQuotient;
-# the family of elements of M may be specified, and must be if <gens>
-# is empty (in which case M will be empty as well).
+#! @Chapter construct
+#! @Section from_scratch
+#! @SectionTitle Direct constructors
+#!   All of the functions in this section produce magmas (of one of the
+#!   categories with which &RAQ; is concerned) from data of other (non-domain)
+#!   types.
+#! @BeginAutoDoc
+#! @BeginGroup basic_constructors
+#! @GroupTitle Basic constructors (from generators)
+#! @Description These are the fundamental constructors of these
+#!   categories. They produce the closure of the specified <A>generators</A>,
+#!   which are considered to be of the given <A>family</A>, under both the
+#!   binary operation of the magma, which is always considered to be * in
+#!   &RAQ;, and the quotient on the specified side. (If
+#!   <A>family</A> is omitted, these functions attempt to infer it from the
+#!   <A>generators</A>; if there are no <A>generators</A> then the
+#!   <A>family</A> must be specified, and note that the resulting magma will
+#!   be empty.) The resulting magma must satisfy the defining
+#!   characteristics of the respective category: for the quasigroups, all
+#!   quotients on the specified side must exist; racks must also satisfy the
+#!   appropriate self-distributive law; and quandles must also have every
+#!   element idempotent.
+#! @Returns a magma of the named category
+#! @GroupInitialArguments [family], [generators]
 DeclareGlobalFunction("LeftQuasigroup");
-DeclareGlobalFunction("LeftQuasigroupNC");
 DeclareGlobalFunction("RightQuasigroup");
-DeclareGlobalFunction("RightQuasigroupNC");
 DeclareGlobalFunction("LeftRack");
-DeclareGlobalFunction("LeftRackNC");
 DeclareGlobalFunction("RightRack");
-DeclareGlobalFunction("RightRackNC");
 DeclareGlobalFunction("LeftQuandle");
-DeclareGlobalFunction("LeftQuandleNC");
 DeclareGlobalFunction("RightQuandle");
+#! @EndGroup
+#! @BeginGroup unchecked_basic_constructors
+#! @GroupTitle Unchecked basic constructors
+#! @Description Each function is the same as its checked counterpart, but the
+#!   <A>family</A> of elements must be specified and no checks that the
+#!   appropriate axioms are satisfied are performed. They may be used for
+#!   efficiency when those properties are guaranteed to be satisfied by the
+#!   <A>generators</A>. NOTE that the behavior of &RAQ; is undefined if the
+#!   unchecked versions are called on <A>generators</A> that do **not**
+#!   satisfy the proper axioms.
+#! @Returns a magma of the named category
+#! @GroupInitialArguments family, generators
+DeclareGlobalFunction("LeftQuasigroupNC");
+DeclareGlobalFunction("RightQuasigroupNC");
+DeclareGlobalFunction("LeftRackNC");
+DeclareGlobalFunction("RightRackNC");
+DeclareGlobalFunction("LeftQuandleNC");
 DeclareGlobalFunction("RightQuandleNC");
+#! @EndGroup
+#! @EndAutoDoc
 
 # Underlying operation
 DeclareGlobalFunction("CloneOfTypeByGenerators");
 
 ## Opposite structures
+#! @Section from_quasigroups
+#! @SectionTitle Constructors from other one-sided quasigroups
+#!   All of the functions in this section produce magmas from other objects of
+#!   similar domain categories.
+
 DeclareCategory("IsOppositeObject", IsMultiplicativeElement);
 DeclareCategoryCollections("IsOppositeObject");
 DeclareAttribute("OppositeFamily", IsFamily);
@@ -80,20 +170,44 @@ DeclareSynonym("IsDefaultOppositeObject",
 DeclareAttribute("OppositeObj", IsMultiplicativeElement);
 DeclareAttribute("UnderlyingMultiplicativeElement", IsOppositeObject);
 
+#! @Chapter operate
+#! @Section basic_info
+#! @SectionTitle Basic information
+
 # Attributes for the generators
 
-# Generates the structure by \* and LeftQuotient. Note that for finite
-# structures, these are the same as the GeneratorsOfMagma but in general more
-# elements might be required to generate the structure just under *
+#! @Arguments q
+#! @Returns list of elements generating <A>q</A>
+#! @Description This produces a list of elements that generate <A>q</A> by
+#!   `\*` and `LeftQuotient`. There are no guarantees that the list is minimal
+#!   in any respect. Note that for finite structures, the
+#!   `GeneratorsOfMagma(q)` will suffice,  but in general more
+#!   elements might be required to generate the structure just under `\*`.
 DeclareAttribute("GeneratorsOfLeftQuasigroup", IsLeftQuasigroup);
 
-# Generates the structure by \* and \/, same considerations as above
+#! @Arguments q
+#! @Returns list of elements generating <A>q</A>
+#! @Description This produces a list of elements that generate <A>q</A> by
+#!   `\*` and `\/`, with the same caveats as above.
 DeclareAttribute("GeneratorsOfRightQuasigroup", IsRightQuasigroup);
 
 ## Conversions into quasigroup/rack/quandle
+#! @Chapter construct
+#! @Section from_scratch
+#! @BeginAutoDoc
+#! @BeginGroup conversions
+#! @GroupTitle Conversions
+#! @Description These functions convert a potentially arbitrary
+#!   <A>collection</A> of elements to one of the categories of objects with
+#!   which &RAQ; is concerned. The <A>collection</A> must be closed under *
+#!   and satisfy the appropriate axioms for the conversion to succeed.
+#! @Returns a magma of the named category
+#! @GroupInitialArguments collection
 DeclareAttribute("AsLeftQuasigroup", IsCollection);
 DeclareAttribute("AsLeftRack", IsCollection);
 DeclareAttribute("AsLeftQuandle", IsCollection);
 DeclareAttribute("AsRightQuasigroup", IsCollection);
 DeclareAttribute("AsRightRack", IsCollection);
 DeclareAttribute("AsRightQuandle", IsCollection);
+#! @EndGroup
+#! @EndAutoDoc

lib/structure.gi

@@ -489,7 +489,23 @@ OppHelper@ := function(Q, whichgens, cnstr)
   return opp;
 end;
 
-
+#! @Chapter construct
+#! @Section from_quasigroups
+#! @Arguments magma
+#! @ItemType Attr
+#! @Label for various finitely-generated magmas
+#! @Description Given `q`, one of the structures covered in &RAQ;,
+#!   `Opposite(q)` returns a structure which is just the same except the order
+#!   of the operation is exactly reversed: `a*b` in the new structure means
+#!   exactly what `b*a` did in the original structure. (This is the same
+#!   operation as transposing the Cayley table.) Actually, this operation is
+#!   originally defined in &LOOPS;, and it is extended in &RAQ; to one-sided
+#!   quasigroups, racks, and quandles. Moreover, since Opposite actually makes
+#!   sense for an arbitrary magma, &RAQ; makes an effort to extend it to as
+#!   wide a class of arguments as are easily implemented. Note for example
+#!   Opposite has no effect on a commutative magma, and &RAQ;
+#!   recognizes this fact.
+#! @Returns a magma of the same category
 InstallMethod(Opposite, "for a left quasigroup",
   [IsLeftQuasigroup and HasGeneratorsOfLeftQuasigroup],
   Q -> OppHelper@(Q, GeneratorsOfLeftQuasigroup, RightQuasigroupNC)
@@ -549,6 +565,15 @@ RoughJoinOfFilters@ := function(list, first)
   return jof;
 end;
 
+#! @ItemType Meth
+#! @Arguments list-of-factors, distinguished-factor
+#! @Returns a magma with only the structure common to all factors
+#! @Description Extends the `DirectProduct` operation to allow factors that
+#!   are not even quasigroups, such as the one-sided quasigroups, racks, and
+#!   quandles with which &RAQ; is concerned. This direct product operation
+#!   makes its best effort to find the most structured category for the result
+#!   that it can, given that every factor in the product must lie in that
+#!   category.
 InstallOtherMethod(DirectProductOp, "for a list and non-quasigroup magma",
   [IsList, IsMagma],
   function (list, first)
@@ -669,18 +694,18 @@ end);
 
 
 ## Coversions among the structure types
-InstallMethod(AsLeftQuasigroup, "for a left quasigroup", 
+InstallMethod(AsLeftQuasigroup, "for a left quasigroup",
               [IsLeftQuasigroup], IdFunc);
-InstallMethod(AsLeftRack, "for a left rack", 
+InstallMethod(AsLeftRack, "for a left rack",
               [IsLeftRack], IdFunc);
-InstallMethod(AsLeftQuandle, "for a left quandle", 
+InstallMethod(AsLeftQuandle, "for a left quandle",
               [IsLeftQuandle], IdFunc);
-InstallMethod(AsRightQuasigroup, "for a right quasigroup", 
+InstallMethod(AsRightQuasigroup, "for a right quasigroup",
               [IsRightQuasigroup], IdFunc);
-InstallMethod(AsRightRack, "for a right rack", 
+InstallMethod(AsRightRack, "for a right rack",
               [IsRightRack], IdFunc);
-InstallMethod(AsRightQuandle, "for a left quandle", 
-              [IsLeftQuandle], IdFunc);
+InstallMethod(AsRightQuandle, "for a right quandle",
+              [IsRightQuandle], IdFunc);
 
 AsAStructure@ := function(struc, D)
   local T,S;