Docs updates, add midlife (#139)

* clean up index

* clean up api section

CHANGELOG.md

@@ -1,3 +1,7 @@
+# v0.16.3
+
+New function: `midlife`.
+
 # v0.16.0
 
 External changes:

Project.toml

@@ -1,7 +1,7 @@
 name = "Ripserer"
 uuid = "aa79e827-bd0b-42a8-9f10-2b302677a641"
 authors = ["mtsch <matijacufar@gmail.com>"]
-version = "0.16.2"
+version = "0.16.3"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
@@ -26,7 +26,7 @@ Distances = "0.8, 0.9, 0.10"
 IterTools = "1"
 LightGraphs = "1.3.3"
 MiniQhull = "0.2"
-PersistenceDiagrams = "0.8"
+PersistenceDiagrams = "^0.8.2"
 ProgressMeter = "1"
 RecipesBase = "1"
 StaticArrays = "0.12, 1"

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLMNet = "8d5ece8b-de18-5317-b113-243142960cc6"
 GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"

docs/make.jl

@@ -1,5 +1,6 @@
 @info "build started."
 using Documenter
+using Distances
 using Literate
 using Ripserer
 using PersistenceDiagrams
@@ -25,9 +26,9 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
-        "API" => ["Public" => "api/ripserer.md", "Interfaces" => "api/extensions.md"],
+        "Usage Guide" => "generated/basics.md",
+        "API" => "api.md",
         "Examples" => [
-            "generated/basics.md",
             "generated/stability.md",
             "generated/cocycles.md",
             "generated/cubical.md",

docs/src/api.md

@@ -0,0 +1,227 @@
+# API
+
+## Ripserer
+
+```@docs
+ripserer
+```
+
+## Filtrations
+
+```@docs
+Rips
+```
+
+```@docs
+Cubical
+```
+
+```@docs
+Custom
+```
+
+```@docs
+Alpha
+```
+
+```@docs
+EdgeCollapsedRips
+```
+
+## Persistence Diagrams
+
+Persistence diagrams live in a separate package,
+[PersistenceDiagrams.jl](https://github.com/mtsch/PersistenceDiagrams.jl). The package is
+documented in detail [here](https://mtsch.github.io/PersistenceDiagrams.jl/dev/).
+
+If you are looking for
+Wasserstein or bottleneck distances, persistence images, betti curves, landscapes, and
+similar, you will need to run `using PersistenceDiagrams`.
+
+For convenience, the following basic functionality is reexported by Ripserer:
+
+```@docs
+PersistenceDiagrams.PersistenceDiagram
+```
+
+```@docs
+PersistenceDiagrams.PersistenceInterval
+```
+
+```@docs
+birth(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+death(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+persistence(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+midlife
+```
+
+```@docs
+representative(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+birth_simplex(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+death_simplex(::PersistenceDiagrams.PersistenceInterval)
+```
+
+```@docs
+barcode
+```
+
+## Simplices and Representatives
+
+```@docs
+Ripserer.Simplex
+```
+
+```@docs
+Ripserer.Cube
+```
+
+```@docs
+Ripserer.dim(::Ripserer.AbstractCell)
+```
+
+```@docs
+Ripserer.birth(::Ripserer.AbstractCell)
+```
+
+```@docs
+Ripserer.index(::Ripserer.AbstractCell)
+```
+
+```@docs
+Ripserer.vertices(::Ripserer.AbstractCell)
+```
+
+```@docs
+Ripserer.Chain
+```
+
+```@docs
+Mod
+```
+
+## Experimental Features
+
+```@docs
+Ripserer.reconstruct_cycle
+```
+
+```@docs
+Ripserer.Partition
+```
+
+```@docs
+Ripserer.CircularCoordinates
+```
+
+## Abstract Types and Interfaces
+
+```@docs
+Ripserer.AbstractFiltration
+```
+
+```@docs
+Ripserer.nv(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.births(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.vertices(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.edges(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.simplex_type
+```
+
+```@docs
+Ripserer.simplex
+```
+
+```@docs
+Ripserer.unsafe_simplex
+```
+
+```@docs
+Ripserer.unsafe_cofacet
+```
+
+```@docs
+Ripserer.threshold(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.columns_to_reduce
+```
+
+```@docs
+Ripserer.emergent_pairs
+```
+
+```@docs
+Ripserer.postprocess_diagram
+```
+
+```@docs
+Ripserer.distance_matrix
+```
+
+```@docs
+Ripserer.AbstractRipsFiltration
+```
+
+```@docs
+Ripserer.adjacency_matrix(::Ripserer.AbstractFiltration)
+```
+
+```@docs
+Ripserer.AbstractCustomFiltration
+```
+
+```@docs
+Ripserer.simplex_dicts
+```
+
+```@docs
+Ripserer.AbstractCell
+```
+
+```@docs
+Ripserer.AbstractSimplex
+```
+
+```@docs
+Base.sign(::Ripserer.AbstractCell)
+```
+
+```@docs
+Base.:-(::Ripserer.AbstractCell)
+```
+
+```@docs
+Ripserer.coboundary
+```
+
+```@docs
+Ripserer.boundary
+```