[doc] minor doc fixes

Author: h-2

LICENSE.md

@@ -1,12 +1,11 @@
 # Copyright {#core_copyright}
 
-| Summary                   |                                                                                        |
-|---------------------------|----------------------------------------------------------------------------------------|
+| Summary                   |                                                                                                         |
+|---------------------------|---------------------------------------------------------------------------------------------------------|
 | Copyright holders         | deCODE Genetics, Knut Reinert, [FU-Berlin](https://fu-berlin.de), [MPI MolGen](https://molgen.mpg.de/)  |
-| Library source code       | ![](doc/about/copyright/bsdl_badge.svg)                                                |
-| Documentation             | ![](doc/about/copyright/ccby_badge.svg)                                                |
-| Snippets and examples     | ![](doc/about/copyright/cc0_badge.svg)                                                 |
-| Dependencies              | ![](doc/about/copyright/copyfree_badge.svg)                                            |
+| Library source code       | 3-clause BSD license                                                                                    |
+| Documentation             | CC-BY-3.0 (Creative Commons Attribution 3.0 Unported)                                                   |
+| Snippets and examples     | CC0-1.0 (Creative Commons Public Domain Dedication)                                                     |
 
 # Source code license
 

doc/biocpp/customisation.md

@@ -22,11 +22,11 @@ BioC++ library. We call these "customisation points" (also known as "extension p
 # Customisation points
 
 An example is the bio::alphabet::alphabet concept. One part of this concept's requirements are from
-bio::alphabet::semialphabet which requires `to_rank()` to available on an object of the type. `to_rank()`
+bio::alphabet::semialphabet which requires `to_rank()` to be available on an object of the type. `to_rank()`
 is a "customisation point".
 
 Instead of the bio::alphabet::semialphabet concept looking directly for `.to_rank()` member functions, it checks for
-a valid definition of bio::alphabet::to_rank which in turn calls `tag_invoke()` with certain parameters.
+a valid definition of bio::alphabet::to_rank which in turn calls `tag_invoke()`.
 This mechanism is widely employed in Modern C++ and may be standardised in the future
 ([P1895](https://wg21.link/P1895)).
 There are (hidden) implementations of `tag_invoke()` that typically redirect to the respective member functions.
@@ -38,7 +38,7 @@ The first argument of `tag_invoke()` is the "tag" used to select the implementat
 exactly like the function that you otherwise call, except that they are in a `cpo` subnamespace.
 E.g. bio::alphabet::to_rank looks for `tag_invoke(bio::alphabet::cpo::to_rank, YOUR_TYPE)`.
 
-If you need to specialise the behaviour for a third party type, and you cannot open that types namespace (or it doesn't have
+If you need to specialise the behaviour for a third party type, and you cannot open that type's namespace (or it doesn't have
 one), you can also add your overload of `tag_invoke()` to our customisation namespace, e.g. `bio::alphabet::cpo`.
 Only do this, if there is no other solution.
 
@@ -51,3 +51,5 @@ and never explicitly specialise one of our templates (except those in `cpo` name
 
 The \link core_custom_alphabet HowTo on creating your own alphabet \endlink provides many examples of how to
 satisfy the requirements of customisation point objects.
+
+Since the customisation point objects are functors, *you can take their address* and use them in higher order functions.

doc/biocpp/overview.md

@@ -21,12 +21,16 @@ More modules are planned!
 
 | Library                                       | Module(s)  | Include          |Namespaces        | Code-Owner | Cite               |
 |-----------------------------------------------|------------|------------------|------------------|------------|--------------------|
-| [Core](https://github.com/biocpp/biocpp-core) | Alphabet   | <bio/alphabet/*> |`bio::a{lphabet}` | `@h-2` | [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1) |
+| [Core](https://github.com/biocpp/biocpp-core) | Alphabet   | <bio/alphabet/*> |`bio::alphabet`   | `@h-2` | [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1) |
 |                                               | Ranges     | <bio/ranges/*>   | `bio::ranges`, `bio::{ranges::}views` | `@h-2` | [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1) |
-|                                               | Meta       | <bio/meta/*>     |`bio:meta`        | `@h-2` | [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1) |
+|                                               | Meta       | <bio/meta/*>     |`bio::meta`       | `@h-2` | [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1) |
 | [I/O](https://github.com/biocpp/biocpp-io)    | I/O        | <bio/io/*>       |`bio::io`         | `@h-2` |  |
 
 
 The primary namespace for BioC++ is `bio::`, and each Module is found in a sub-namespace (usually identical to the module name). Some namespaces are aliased into the primary namespace, so `bio::ranges::views` is identical to `bio::views`. Only top-level namespaces are displayed here.
 
+Some modules provide literals in an `inline namespace` within their main namespace. This allows doing e.g.
+`using namespace bio::alphabet::literals;` to get easy access to the alphabet literals without importing the rest
+of the module into your namespace.
+
 If no citable publication is listed for a Module, please cite [10.1007/978-3-030-90990-1](https://link.springer.com/book/10.1007/978-3-030-90990-1), which is a book by the main author of BioC++.

doc/core/tutorial_concepts/index.md

@@ -228,13 +228,3 @@ In some parts of the documentation concepts are called "interfaces", please don'
 And the "verbose syntax" introduced above is not visible at all in the automatically generated documentation.
 That's why it's important to read the detailed documentation section where all requirements are documented.
 
-TODO(bio) the following needs to be updated
-
-Have a look at the documentation of bio::alphabet::argument_parser::add_positional_option().
-It has two template parameters, one seems unconstrained (`typename` in the signature) and one is constrained
-(`validator` in the signature).
-But in fact both are constrained as the detailed documentation reveals.
-
-Now, follow the link to bio::alphabet::validator. We will check in the next section whether you understand the
-documentation for the concept.
-

doc/core/write_an_alphabet/index.md

@@ -6,8 +6,6 @@ This HowTo documents how to write a custom alphabet that can be used with the al
 
 \tutorial_head{Moderate, 45 min, \ref core_concepts\, \ref core_alphabets, \ref alphabet}
 
-TODO(bio) this needs to be updated; equality, inequality, order should all go in one step; needs tag_invoke
-
 # Motivation
 
 In the [alphabet tutorial](\ref core_alphabets) you have learned that alphabets are a core component in BioC++