Cleanup (#58)

* export fewer things, docs updates.

* document homology

* update tests

Project.toml

@@ -1,7 +1,7 @@
 name = "Ripserer"
 uuid = "aa79e827-bd0b-42a8-9f10-2b302677a641"
 authors = ["mtsch <matijacufar@gmail.com>"]
-version = "0.9.0"
+version = "0.10.0"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"

docs/src/api/filtrations.md

@@ -1,33 +1,41 @@
-# Filtrations
+# Filtration Interface
 
 ```@docs
-AbstractFiltration
+Ripserer.AbstractFiltration
 ```
 
 ```@docs
-n_vertices(::AbstractFiltration)
+Ripserer.n_vertices(::Ripserer.AbstractFiltration)
 ```
 
 ```@docs
-edges(::AbstractFiltration)
+Ripserer.edges(::Ripserer.AbstractFiltration)
 ```
 
 ```@docs
-diam(::AbstractFiltration, ::Any)
+Ripserer.diam(::Ripserer.AbstractFiltration, ::Any)
 ```
 
 ```@docs
-diam(::AbstractFiltration, ::AbstractSimplex, ::Any, ::Any)
+Ripserer.diam(::Ripserer.AbstractFiltration, ::Ripserer.AbstractSimplex, ::Any, ::Any)
 ```
 
 ```@docs
-birth(::AbstractFiltration, ::Any)
+Ripserer.birth(::Ripserer.AbstractFiltration, ::Any)
 ```
 
 ```@docs
-threshold(::AbstractFiltration)
+Ripserer.threshold(::Ripserer.AbstractFiltration)
 ```
 
 ```@docs
-AbstractFlagFiltration
+Ripserer.simplex_type
+```
+
+```@docs
+Ripserer.AbstractRipsFiltration
+```
+
+```@docs
+Ripserer.dist
 ```

docs/src/api/ripserer.md

@@ -1,4 +1,6 @@
-# Ripserer
+# Public API
+
+## Ripserer
 
 ```@docs
 ripserer
@@ -15,3 +17,59 @@ SparseRips
 ```@docs
 Cubical
 ```
+
+```@docs
+Mod
+```
+
+## Simplices
+
+```@docs
+Simplex
+```
+
+```@docs
+Cubelet
+```
+
+```@docs
+vertices
+```
+
+```@docs
+dim
+```
+
+## Persistence Diagrams
+
+See also: [PersistenceDiagrams.jl
+API](https://mtsch.github.io/PersistenceDiagrams.jl/dev/api/diagrams/). Ripserer reexports
+the following:
+
+```
+PersistenceDiagrams.birth
+```
+
+```
+PersistenceDiagrams.death
+```
+
+```
+PersistenceDiagrams.persistence
+```
+
+```
+PersistenceDiagrams.representative
+```
+
+```
+PersistenceDiagrams.birth_simplex
+```
+
+```
+PersistenceDiagrams.death_simplex
+```
+
+```
+PersistenceDiagrams.barcode
+```

docs/src/api/simplices.md

@@ -1,57 +1,49 @@
-# Simplices
+# Simplex Interface
 
 ```@docs
-AbstractSimplex
+Ripserer.AbstractSimplex
 ```
 
 ```@docs
-dim(::AbstractSimplex)
+dim(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-diam(::AbstractSimplex)
+diam(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-Base.sign(::AbstractSimplex)
+Base.sign(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-Base.:-(::AbstractSimplex)
+Base.:-(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-coface_type(::AbstractSimplex)
+Ripserer.coface_type(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-face_type(::AbstractSimplex)
+Ripserer.face_type(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-vertices(::AbstractSimplex)
+vertices(::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-coboundary(::Any, ::AbstractSimplex)
+Ripserer.coboundary(::Any, ::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-boundary(::Any, ::AbstractSimplex)
+Ripserer.boundary(::Any, ::Ripserer.AbstractSimplex)
 ```
 
 ```@docs
-IndexedSimplex
+Ripserer.IndexedSimplex
 ```
 
 ```@docs
-index(::AbstractSimplex)
-```
-
-```@docs
-Simplex
-```
-
-```@docs
-Cubelet
+Ripserer.index(::Ripserer.AbstractSimplex)
 ```

docs/src/index.md

@@ -66,11 +66,10 @@ benchmarking on my computer or a CI system to be too unreliable.
 
 ## Extending
 
-Ripserer is designed to be easily extended with new simplex or filtration types. The
-interfaces are specified in the docstrings for `AbstractSimplex` and
-`AbstractFiltration`. Also see the [Filtrations](@ref) and [Simplices](@ref) API sections
-for more info. To see an example of an extension, check out the implementation of cubical
-simplices and filtrations in
+Ripserer is designed to be easily extended with new simplex or filtration types. See the
+[Filtration Interface](@ref) and [Simplex Interface](@ref) API sections for more info. To
+see an example of an extension, check out the implementation of cubical simplices and
+filtrations in
 [`src/cubical.jl`](https://github.com/mtsch/Ripserer.jl/blob/master/src/cubical.j).
 
 If you have written an extension or have trouble implementing one, please open a pull

src/Ripserer.jl

@@ -26,18 +26,12 @@ using TupleTools
 # reexporting basics these makes Ripserer usable without having to import another package.
 import PersistenceDiagrams: birth, threshold
 export
-    PersistenceDiagram, PersistenceInterval, RepresentativeInterval,
     birth, death, persistence, representative, birth_simplex, death_simplex, barcode
 
 export
-    Mod,
-    AbstractSimplex, diam, coface_type, face_type, vertices, coboundary, boundary, dim,
-    IndexedSimplex, index, Simplex,
-    AbstractFiltration, n_vertices, edges, threshold,
-    AbstractFlagFiltration, Rips, SparseRips,
-    Cubelet, Cubical,
-    simplex, coefficient,
-    ripserer
+    Mod, Simplex, Cubelet, vertices, diam, dim, threshold, simplex, coefficient,
+    Rips, SparseRips, Cubical, ripserer
+
 
 include("primefield.jl")
 

src/abstractfiltration.jl

@@ -4,16 +4,15 @@
 A filtration is used to find the edges in filtration and to determine diameters of
 simplices.
 
-`T` is the distance type, accessible by `dist_type` and S is the edge type, accesible by
-`vertex_type`.
+`T` is the distance type, accessible by `dist_type` and `S` is the simplex type.
 
 # Interface
 
 * [`n_vertices(::AbstractFiltration)`](@ref)
 * [`edges(::AbstractFiltration)`](@ref)
 * [`diam(::AbstractFiltration, vertices)`](@ref)
-* [`diam(::AbstractFiltration, ::AbstractSimplex, ::Any, ::Any)`](@ref) - only used for
-  `Simplex`.
+* [`diam(::AbstractFiltration, ::AbstractSimplex, ::Any, ::Any)`](@ref) - only used when
+  [`simplex_type`](@ref) is an [`IndexedSimplex`](@ref).
 * [`birth(::AbstractFiltration, v)`](@ref) - optional, defaults to returning `zero(T)`.
 * [`threshold(::AbstractFiltration)`](@ref) - optional, defaults to returning `missing`.
 * [`simplex_type(::AbstractFiltration, dim)`](@ref)
@@ -25,9 +24,9 @@ function Base.show(io::IO, flt::AbstractFiltration)
 end
 
 """
-    simplex_type(::AbstractFiltration, dim)
+    simplex_type(::AbstractFiltration, d)
 
-Return the `dim`-dimensional simplex in the filtration.
+Return the `d`-dimensional simplex type in the filtration.
 """
 simplex_type(::AbstractFiltration, dim)
 
@@ -46,30 +45,32 @@ n_vertices(::AbstractFiltration)
     edges(filtration::AbstractFiltration)
 
 Get edges in distance matrix in `filtration`, sorted by decresing length and increasing
-combinatorial index. Edges should be of type `edge_type(filtration)`.
+combinatorial index. Edges should be of type [`simplex_type`](@ref)(filtration, 1)`.
 """
 edges(::AbstractFiltration)
 
 """
-    diam(flt::AbstractFiltration, vertices)
+    diam(::AbstractFiltration, vertices)
 
-Get the diameter of list of vertices i.e. diameter of simplex with `vertices`. Retrun
-`missing` if `vertices` do not form a valid simplex.
+Get the diameter of a simplex with the vertex set `vertices`. Should return `missing` if
+`vertices` do not form a valid simplex.
 """
 diam(::AbstractFiltration, ::Any)
 
 """
-    diam(flt::AbstractFiltration, simplex, vertices, vertex)
+    diam(::AbstractFiltration, simplex, vertices, new_vertex)
 
-Get the diameter of coface of a `Simplex` that is formed by adding `vertex` to `vertices`.
-Return `missing` if new simplex is not valid.
+Get the diameter of coface of a `Simplex` that is formed by adding `new_vertex` to
+`vertices`. Should return `missing` if new simplex is not valid.
+
+This functions is used with the [`coboundary`](@ref) function for [`IndexedSimplex`](@ref)
 """
 diam(::AbstractFiltration, ::AbstractSimplex, ::Any, ::Any)
 
 """
     birth(::AbstractFiltration, v)
 
-Get the birth time of vertex `v`.
+Get the birth time of vertex `v` in filtration. Defaults to 0.
 """
 birth(::AbstractFiltration{T}, _) where T = zero(T)