Better links in the readme

Author: james-d-mitchell

README.md

@@ -23,7 +23,7 @@ monoids. The main algorithms implemented in `libsemigroups` are:
   by a generating set consisting of elements whose multiplication and equality is
   decidable (such as [transformations, partial permutations, permutations][],
   [bipartitions][], and [matrices over a semiring][]) in the
-  `libsemigroups::FroidurePin` class template; 
+  [`libsemigroups::FroidurePin`][] class template; 
 - Kambites' algorithm for solving the word problem in small overlap monoids
   from ["Small overlap monoids I: The word problem"][], and the algorithm from
   ["An explicit algorithm for normal forms in small overlap monoids"][] in the
@@ -33,23 +33,23 @@ monoids. The main algorithms implemented in `libsemigroups` are:
 - a version of Sims' low index subgroup algorithm for computing congruences of a
   semigroup or monoid from 
   ["Computing finite index congruences of finitely presented semigroups and monoids"][] 
-  in the classes `libsemigroups::Sims1` and `libsemigroups::Sims2`;
+  in the classes [`libsemigroups::Sims1`][] and [`libsemigroups::Sims2`][];
 - a generalized version of the algorithms described in 
   ["Green's equivalences in finite semigroups of binary relations"][] by 
   Konieczny, and 
   ["On the determination of Green's relations in finite transformation semigroups"][] 
   by Lallement and Mcfadden for computing finite semigroups and monoids
   admitting a pair of actions with particular properties, in the class template
-  `libsemigroups::Konieczny`;
+  [`libsemigroups::Konieczny`][];
 - the algorithm from ["Efficient Testing of Equivalence of Words in a Free Idempotent Semigroup"][] 
-  by Radoszewski and Rytter in the function `libsemigroups::freeband_equal_to`;
+  by Radoszewski and Rytter in the function [`libsemigroups::freeband_equal_to`][];
 - a non-random version of the [Schreier-Sims algorithm][]
-  for permutation groups in the class template `libsemigroups::SchreierSims`;
+  for permutation groups in the class template [`libsemigroups::SchreierSims`][];
 - a version of Stephen's procedure from 
   ["Applications of automata theory to presentations of monoids and inverse monoids"][]
   for finitely presented inverse semigroups and monoids (for a given word \\(w\\) this
   procedure is for determining words equivalent to \\(w\\) or that are
-  left divisors of \\(w\\)) in the class template `libsemigroups::Stephen`;
+  left divisors of \\(w\\)) in the class template [`libsemigroups::Stephen`][];
 - the [Todd-Coxeter algorithm][] for finitely presented semigroups and monoids; 
   in the class template [`libsemigroups::ToddCoxeter`][]; see also 
   ["The Todd–Coxeter algorithm for semigroups and monoids"][].
@@ -59,9 +59,6 @@ monoids. The main algorithms implemented in `libsemigroups` are:
 [Expository Slides][], and [Semigroupe 2.01][] by [Jean-Eric Pin][].
 
 [Froidure-Pin algorithm]: https://www.irif.fr/~jep/PDF/Rio.pdf
-[transformations, partial permutations, permutations]: group__transf__group.html
-[bipartitions]: group__bipart__group.html
-[matrices over a semiring]: group__matrix__group.html
 ["Small overlap monoids I: The word problem"]: https://doi.org/10.1016/j.jalgebra.2008.09.038
 ["An explicit algorithm for normal forms in small overlap monoids"]: https://doi.org/10.1016/j.jalgebra.2023.04.019
 [Knuth-Bendix algorithm]: https://en.wikipedia.org/wiki/Knuth%E2%80%93Bendix_completion_algorithm
@@ -73,7 +70,6 @@ monoids. The main algorithms implemented in `libsemigroups` are:
 [Todd-Coxeter algorithm]: https://en.wikipedia.org/wiki/Todd%E2%80%93Coxeter_algorithm
 ["The Todd–Coxeter algorithm for semigroups and monoids"]: https://doi.org/10.1007/s00233-024-10431-z
 [Schreier-Sims algorithm]: https://en.wikipedia.org/wiki/Schreier%E2%80%93Sims_algorithm
-[`libsemigroups::ToddCoxeter`]: group__todd__coxeter__group.html
 [Expository Slides]: https://www.irif.fr/~jep/PDF/Exposes/StAndrews.pdf
 [Semigroupe 2.01]: https://www.irif.fr/~jep/Logiciels/Semigroupe2.0/semigroupe2.html
 [Jean-Eric Pin]: https://www.irif.fr/~jep/
@@ -89,47 +85,39 @@ related projects are [here](https://github.com/libsemigroups).
 ## Design principles
 
 The main classes in `libsemigroups` are named after the algorithms they
-implement; see, for example, `libsemigroups::FroidurePin`,
-`libsemigroups::Konieczny`, [`libsemigroups::ToddCoxeter`][],
+implement; see, for example, [`libsemigroups::FroidurePin`][],
+[`libsemigroups::Konieczny`][], [`libsemigroups::ToddCoxeter`][],
 [`libsemigroups::Kambites`][], [`libsemigroups::KnuthBendix`][],
-`libsemigroups::SchreierSims`, `libsemigroups::Sims1`, `libsemigroups::Sims2`,
-or `libsemigroups::Stephen`.
+[`libsemigroups::SchreierSims`][], [`libsemigroups::Sims1`][], [`libsemigroups::Sims2`][],
+or [`libsemigroups::Stephen`][].
 
 `libsemigroups` is a modern open source C++ library designed to be:
 
 -  **state of the art**: the mathematical underpinnings of several of the
    algorithms in `libsemigroups` originate from the authors and contributors; and the
    other algorithms are adapted from the literature (see above for details);
--  **extensible**: `libsemigroups::FroidurePin`, `libsemigroups::Konieczny`, and
-   `libsemigroups::SchreierSims` are generic and can be adapted to user-defined
+-  **extensible**: [`libsemigroups::FroidurePin`][], [`libsemigroups::Konieczny`][], and
+   [`libsemigroups::SchreierSims`][] are generic and can be adapted to user-defined
    types;
 -  **adaptable**: the behaviour of many algorithms implementing in `libsemigroups` 
    can be fine-tuned via many settings, and used interactively via the functions
-  `libsemigroups::Runner::run_for` and `libsemigroups::Runner::run_until`;
+  [`libsemigroups::Runner::run_for`][] and [`libsemigroups::Runner::run_until`][];
 -  **easy to use**: converting between different types of `libsemigroups`
    objects (see [the `to` function][]) is easy; there are many
    helper functions to streamline common tasks; high quality exception messages
    are implemented throughout the code base (although you don't have to use these
    if you don't want to); long running algorithms can provide detailed feedback on
-   their progress (see `libsemigroups::ReportGuard`); many data structures can be
-   visualised using graphviz (see `libsemigroups::Dot` and
+   their progress (see [`libsemigroups::ReportGuard`][]); many data structures can be
+   visualised using graphviz (see [`libsemigroups::Dot`][] and
    [Visualisation][]);
    and there are hundreds of examples in the [tests][] directory.
 -  **fast**: `libsemigroups` is designed with performance in mind; several
-  classes implement parallel algorithms (`libsemigroups::Sims1`,
-  `libsemigroups::Sims2`, [`libsemigroups::Congruence`][]; 
+  classes implement parallel algorithms ([`libsemigroups::Sims1`][],
+  [`libsemigroups::Sims2`][], [`libsemigroups::Congruence`][]); 
   we provide some "winner takes all" mechanisms for running algorithms
-  concurrently (see [`libsemigroups::Congruence`][]; there are
+  concurrently (see [`libsemigroups::Congruence`][]); there are
   `_no_checks` versions of most functions if performance is critical.
 
-[`libsemigroups::Congruence`]: group__congruence__group.html
-[`libsemigroups::Kambites`]: group__kambites__group.html
-[`libsemigroups::KnuthBendix`]: group__knuth_bendix__group.html
-[`libsemigroups::ToddCoxeter`]: group__todd__coxeter__group.html
-[tests]: https://github.com/libsemigroups/libsemigroups/tree/main/tests
-[the `to` function]: group__to__group.html
-[Visualisation]: group__dot__group.html
-
 ## Thanks
 
 `libsemigroups` uses: 
@@ -156,7 +144,7 @@ See the documentation <https://libsemigroups.github.io/libsemigroups/>.
 ## Issues
 
 If you find any problems with `libsemigroups`, or have any suggestions
-for features that you\'d like to see, please use the [issue
+for features that you'd like to see, please use the [issue
 tracker](https://github.com/libsemigroups/libsemigroups/issues).
 
 ## Authors
@@ -231,13 +219,35 @@ We thank:
 * the Cyprus State Scholarship Foundation for their financial support for
   [Maria Tsalakou][].
 
-[Reinis Cirpons]: https://reinisc.id.lv
+[Finn Smith]: https://flsmith.github.io
 [Joseph Edwards]: https://github.com/Joseph-Edwards
 [Julius Jonušas]: http://julius.jonusas.work/
-[Finn Smith]: https://flsmith.github.io
 [Maria Tsalakou]: https://mariatsalakou.github.io/
 [Michael Young]: https://mtorpey.github.io/
+[Reinis Cirpons]: https://reinisc.id.lv
 [Samuel Lelièvre]: https://lelievre.perso.math.cnrs.fr/index-en.html
 
 [Carnegie Trust for the Universities of Scotland]: https://www.carnegie-trust.org/
 [School of Mathematics and Statistics, University of St Andrews]: https://www.st-andrews.ac.uk/mathematics-statistics/
+
+[Visualisation]: https://libsemigroups.github.io/libsemigroups/group__dot__group.html
+[`libsemigroups::Congruence`]: https://libsemigroups.github.io/libsemigroups/group__congruence__class__group.html
+[`libsemigroups::FroidurePin`]: https://libsemigroups.github.io/libsemigroups/classlibsemigroups_1_1_froidure_pin.html 
+[`libsemigroups::Kambites`]: https://libsemigroups.github.io/libsemigroups/group__kambites__class__group.html
+[`libsemigroups::KnuthBendix`]: https://libsemigroups.github.io/libsemigroups/group__knuth__bendix__class__group.html
+[`libsemigroups::Konieczny`]: https://libsemigroups.github.io/libsemigroups/group__konieczny__group.html
+[`libsemigroups::SchreierSims`]: https://libsemigroups.github.io/libsemigroups/group__schreier__sims__group.html
+[`libsemigroups::Sims1`]: https://libsemigroups.github.io/libsemigroups/classlibsemigroups_1_1_sims1.html
+[`libsemigroups::Sims2`]: https://libsemigroups.github.io/libsemigroups/classlibsemigroups_1_1_sims2.html
+[`libsemigroups::Stephen`]: https://libsemigroups.github.io/libsemigroups/group__stephen__group.html
+[`libsemigroups::ToddCoxeter`]: https://libsemigroups.github.io/libsemigroups/group__todd__coxeter__class__group.html
+[`libsemigroups::freeband_equal_to`]: https://libsemigroups.github.io/libsemigroups/group__freeband__group.html
+[bipartitions]: https://libsemigroups.github.io/libsemigroups/group__bipart__group.html
+[matrices over a semiring]: https://libsemigroups.github.io/libsemigroups/group__matrix__group.html
+[tests]: https://github.com/libsemigroups/libsemigroups/tree/main/tests
+[the `to` function]: https://libsemigroups.github.io/libsemigroups/group__to__group.html
+[transformations, partial permutations, permutations]: https://libsemigroups.github.io/libsemigroups/group__transf__group.html
+[`libsemigroups::ReportGuard`]: https://libsemigroups.github.io/libsemigroups/structlibsemigroups_1_1_report_guard.html
+[`libsemigroups::Dot`]: https://libsemigroups.github.io/libsemigroups/classlibsemigroups_1_1_dot.html
+[`libsemigroups::Runner::run_for`]: file:///Users/jdm/libsemigroups/docs/html/classlibsemigroups_1_1_runner.html
+[`libsemigroups::Runner::run_until`]: file:///Users/jdm/libsemigroups/docs/html/classlibsemigroups_1_1_runner.html