Merge pull request #1 from anton083/dev

Dev

.github/workflows/TagBot.yml

@@ -4,22 +4,6 @@ on:
     types:
       - created
   workflow_dispatch:
-    inputs:
-      lookback:
-        default: 3
-permissions:
-  actions: read
-  checks: read
-  contents: write
-  deployments: read
-  issues: read
-  discussions: read
-  packages: read
-  pages: read
-  pull-requests: read
-  repository-projects: read
-  security-events: read
-  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -28,4 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/documentation.yml

@@ -0,0 +1,24 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - main
+      - dev
+    tags: '*'
+  pull_request:
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.9'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia --project=docs/ docs/make.jl

README.md

@@ -4,4 +4,10 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/license/MIT)
 [![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://anton083.github.io/VectorizedKmers.jl/stable/)
 [![Status](https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/anton083/VectorizedKmers.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/anton083/VectorizedKmers.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/anton083/VectorizedKmers.jl)
+[![Coverage](https://codecov.io/gh/anton083/VectorizedKmers.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/anton083/VectorizedKmers.jl)
+
+VectorizedKmers.jl is a Julia package for fast $k$-mer counting of biological sequences. The core idea is that $k$-mers with an alphabet size $A$ are essentially integers in base $A$, and can be used as indices in a vector of size $A^k$ to count the corresponding $k$-mers.
+
+The `KmerCount` type is a wrapper for `AbstractVector`, which means that these vector k-mer counts are not limited to Julia's `Base.Vector` type; other kinds of vectors can be used as well, such as `CUDA.CuVector`, `SparseArrays.SparseVector` or even matrix views. To efficiently group k-mer counts together, the `KmerCountVector` stores them in a matrix as rows or columns. It can wrap any `AbstractMatrix`, such as `Matrix` or `CuMatrix`, and indexing it returns a `KmerCount` wrapped around a view of a row or column of the original matrix.
+
+This data structure can be used to quickly approximate distances between sequences. Most notably, the squared Euclidean distance was used to estimate edit distance in [this paper](https://doi.org/10.1093/nar/gkz657). The dot product has also proven to be a useful metric for comparing correlation between sequences.

docs/make.jl

@@ -4,16 +4,27 @@ using Documenter
 DocMeta.setdocmeta!(VectorizedKmers, :DocTestSetup, :(using VectorizedKmers); recursive=true)
 
 makedocs(;
-    modules=[VectorizedKmers],
-    authors="Anton",
-    repo="https://github.com/anton083/VectorizedKmers.jl/blob/{commit}{path}#{line}",
-    sitename="VectorizedKmers.jl",
-    format=Documenter.HTML(;
-        prettyurls=get(ENV, "CI", "false") == "true",
-        edit_link="main",
-        assets=String[],
+    modules = [VectorizedKmers],
+    authors = "Anton O. Sollman",
+    repo = "https://github.com/anton083/VectorizedKmers.jl/blob/{commit}{path}#{line}",
+    sitename = "VectorizedKmers.jl",
+    doctest = true,
+    format = Documenter.HTML(;
+        prettyurls = get(ENV, "CI", "false") == "true",
+        edit_link = "main",
+        assets = String[],
     ),
-    pages=[
+    pages = [
         "Home" => "index.md",
     ],
+    checkdocs = :all,
+)
+
+deploydocs(;
+    repo = "github.com/anton083/VectorizedKmers.jl",
+    push_preview = true,
+    branch = "gh-pages",
+    devbranch = "dev",
+    deps = nothing,
+    make = nothing
 )