doc: added man and lib pages from PhyloNetworks

docs/make.jl

@@ -5,19 +5,41 @@ DocMeta.setdocmeta!(SNaQ, :DocTestSetup, :(using SNaQ, PhyloNetworks); recursive
 
 makedocs(;
     modules=[SNaQ],
-    authors="Claudia Solis-Lemus <[email protected]>, Paul Bastide <[email protected]>, Cecile Ane <[email protected]>, and contributors",
+    authors="Claudia Solis-Lemus <[email protected]>, Cécile Ané <[email protected]>, and contributors",
     sitename="SNaQ.jl",
     format=Documenter.HTML(;
         canonical="https://JuliaPhylo.github.io/SNaQ.jl",
         edit_link="dev",
         assets=String[],
+        prettyurls = get(ENV, "CI", nothing) == "true", # easier local build
+        size_threshold = 600 * 2^10,
+        size_threshold_warn = 500 * 2^10, # 600 KiB
     ),
+    # exception, so warning-only for :missing_docs. List all others:
+    warnonly = Documenter.except(:autodocs_block, :cross_references, :docs_block,
+        :doctest, :eval_block, :example_block, :footnote, :linkcheck_remotes,
+        :linkcheck, :meta_block, :parse_error, :setup_block),
     pages=[
         "Home" => "index.md",
+        "Manual" => [
+            "Input Data for SNaQ" => "man/inputdata.md",
+            "TICR pipeline" => "man/ticr_howtogetQuartetCFs.md",
+            "Network estimation and display" => "man/snaq_plot.md",
+            "Network comparison and manipulation" => "man/dist_reroot.md",
+            "Candidate Networks" => "man/fixednetworkoptim.md",
+            "Extract Expected CFs" => "man/expectedCFs.md",
+            "Bootstrap" => "man/bootstrap.md",
+            "Multiple Alleles" => "man/multiplealleles.md",
+        ],
+        "Library" => [
+            "Public" => "lib/public.md",
+            "Internals" => "lib/internals.md",
+        ]
     ],
 )
 
 deploydocs(;
     repo="github.com/JuliaPhylo/SNaQ.jl",
-    devbranch="dev",
+    push_preview = true,
+    devbranch="main",
 )

docs/src/index.md

@@ -1,14 +1,40 @@
-```@meta
-CurrentModule = SNaQ
-```
-
 # SNaQ
 
-Documentation for [SNaQ](https://github.com/JuliaPhylo/SNaQ.jl).
+[SNaQ](https://github.com/JuliaPhylo/SNaQ.jl) is a [Julia](http://julialang.org)
+package that implements the SNaQ method by
+[Solís-Lemus & Cécile Ané (2016)](https://doi.org/10.1371/journal.pgen.1005896)
+to estimate a phylogenetic network from quartet concordance factors.
+See the [PhyloNetworks](https://github.com/JuliaPhylo/PhyloNetworks.jl)
+package, which SNaQ depends on, for background on phylogenetic networks
+and for how to get help.
+
+## references
 
-```@index
+See them in
+[bibtex format](https://github.com/juliaphylo/SNaQ.jl/blob/master/CITATION.bib).
+
+## Manual
+
+```@contents
+Pages = [
+    "man/inputdata.md",
+    "man/ticr_howtogetQuartetCFs.md",
+    "man/snaq_plot.md",
+    "man/dist_reroot.md",
+    "man/fixednetworkoptim.md",
+    "man/expectedCFs.md",
+    "man/bootstrap.md",
+    "man/multiplealleles.md",
+]
+Depth = 3
 ```
 
-```@autodocs
-Modules = [SNaQ]
+For help on individual functions, see the library:
+
+```@contents
+Pages = [
+    "lib/public.md",
+    "lib/internal.md",
+]
+Depth = 3
 ```

docs/src/lib/internals.md

@@ -0,0 +1,21 @@
+# internal documentation
+
+Documentation for `SNaQ`'s internal functions.
+These functions are not exported and their access (API) should not be
+considered stable. But they can still be used, like this for example:
+`SNaQ.foo()` for a function named `foo()`.
+
+
+## functions & types
+
+```@autodocs
+Modules = [SNaQ]
+Public  = false
+Order   = [:type,:function,:constant]
+```
+
+## index
+
+```@index
+Pages = ["internal.md"]
+```

docs/src/lib/public.md

@@ -0,0 +1,17 @@
+# public documentation
+
+Documentation for `SNaQ`'s public (exported) interface.
+
+## functions & types
+
+```@autodocs
+Modules = [SNaQ]
+Private = false
+Order   = [:function,:type]
+```
+
+## index
+
+```@index
+Pages = ["public.md"]
+```