Merge pull request #36 from YiboK/master

try to build documentaiton

.github/workflows/CI.yml

@@ -1,16 +1,13 @@
+
+
 name: CI
+
 on:
   push:
     branches:
       - master
-    tags: ['*']
+    tags: '*'
   pull_request:
-  workflow_dispatch:
-concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: only if it is a pull request build.
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -19,19 +16,48 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.0'
-          - '1.7'
-          - 'nightly'
+          - '1' # will expand to the latest stable 1.x release of Julia.
         os:
           - ubuntu-latest
+          - macos-latest
+          - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.7'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - uses: julia-actions/julia-runtest@v1
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+        run: julia --project=docs/ --code-coverage=user docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1

.github/workflows/documentation.yml

@@ -0,0 +1,21 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - master
+    tags: '*'
+  pull_request:
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.8'
+      - 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 }} # For authentication with GitHub Actions token
+        run: julia --project=docs/ docs/make.jl

CONTRIBUTING.md

@@ -11,15 +11,19 @@ For reporting a bug or a failed function or requesting a new feature, you can si
 To make contributions to `PhyloClustering.jl`, you need to set up your [GitHub](https://github.com) 
 account if you do not have and sign in, and request your change(s) or contribution(s) via 
 a pull request against the ``develop``
-branch of the [PhyloClustering.jl repository](https://github.com/solislemuslab/ml-phylo-trees). 
+branch of the [PhyloClustering.jl repository](https://github.com/solislemuslab/PhyloClustering.jl
+). 
 
 Please use the following steps:
 
-1. Open a new issue for new feature or failed function in the [issue tracker](https://github.com/solislemuslab/ml-phylo-trees/issues)
-2. Fork the [PhyloClustering.jl repository](https://github.com/solislemuslab/ml-phylo-trees) to your GitHub account
+1. Open a new issue for new feature or failed function in the [issue tracker](https://github.com/solislemuslab/PhyloClustering.jl
+/issues)
+2. Fork the [PhyloClustering.jl repository](https://github.com/solislemuslab/PhyloClustering.jl
+) to your GitHub account
 3. Clone your fork locally:
 ```
-$ git clone https://github.com/your-username/ml-phylo-trees.git
+$ git clone https://github.com/your-username/PhyloClustering.jl
+.git
 ```   
 4. Make your change(s) in the `master` (or `development`) branch of your cloned fork
 5. Make sure that all tests (`test/runtests.jl`) are passed without any errors
@@ -32,7 +36,9 @@ Make sure to include the following information in your pull request:
 
 * **Code** which you are contributing to this package
 
-* **Documentation** of this code if it provides new functionality. This should be a description of new functionality added to the [docs](https://solislemuslab.github.io/ml-phylo-trees/dev/). Check out the [docs folder](https://github.com/solislemuslab/ml-phylo-trees.jl/tree/main/docs) for instructions on how to update the documentation.
+* **Documentation** of this code if it provides new functionality. This should be a description of new functionality added to the [docs](https://solislemuslab.github.io/PhyloClustering.jl
+/dev/). Check out the [docs folder](https://github.com/solislemuslab/PhyloClustering.jl
+.jl/tree/main/docs) for instructions on how to update the documentation.
 
 - **Tests** of this code to make sure that the previously failed function or the new functionality now works properly
 

Manifest.toml

@@ -3,6 +3,11 @@
 julia_version = "1.7.3"
 manifest_format = "2.0"
 
+[[deps.ANSIColoredPrinters]]
+git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
+uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
+version = "0.0.1"
+
 [[deps.AbstractFFTs]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
 git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
@@ -335,6 +340,12 @@ git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
+[[deps.Documenter]]
+deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "Test", "Unicode"]
+git-tree-sha1 = "43aa88b72dffff46b1b19f66483ea3e2f907c4fa"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "1.2.0"
+
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -540,6 +551,18 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046"
 uuid = "78b55507-aeef-58d4-861c-77aaff3498b1"
 version = "0.21.0+0"
 
+[[deps.Git]]
+deps = ["Git_jll"]
+git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d"
+uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
+version = "1.3.0"
+
+[[deps.Git_jll]]
+deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
+git-tree-sha1 = "bb8f7cc77ec1152414b2af6db533d9471cfbb2d1"
+uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
+version = "2.42.0+0"
+
 [[deps.Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
 git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17"
@@ -581,6 +604,12 @@ git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685"
 uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
 version = "0.3.23"
 
+[[deps.IOCapture]]
+deps = ["Logging", "Random"]
+git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6"
+uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
+version = "0.2.3"
+
 [[deps.ImageAxes]]
 deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"]
 git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8"
@@ -757,6 +786,11 @@ git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.3.1"
 
+[[deps.LazilyInitializedFields]]
+git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612"
+uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf"
+version = "1.2.2"
+
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
 uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
@@ -891,6 +925,12 @@ version = "0.4.2"
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
+[[deps.MarkdownAST]]
+deps = ["AbstractTrees", "Markdown"]
+git-tree-sha1 = "465a70f0fc7d443a00dcdc3267a497397b8a3899"
+uuid = "d0879d2d-cac2-40c8-9cee-1863dc0c7391"
+version = "0.1.2"
+
 [[deps.MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
 git-tree-sha1 = "70ea2892b8bfffecc0387ba1a6a21192814f120c"
@@ -1259,6 +1299,12 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "1.2.2"
 
+[[deps.RegistryInstances]]
+deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"]
+git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51"
+uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3"
+version = "0.1.0"
+
 [[deps.RelocatableFolders]]
 deps = ["SHA", "Scratch"]
 git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864"
@@ -1422,12 +1468,6 @@ git-tree-sha1 = "30edbce1c797dc7d4c74bc07b2b6a57b891bead3"
 uuid = "c5dd0088-6c3f-4803-b00e-f31a60c170fa"
 version = "1.1.0"
 
-[[deps.StableRNGs]]
-deps = ["Random", "Test"]
-git-tree-sha1 = "3be7d49667040add7ee151fefaf1f8c04c8c8276"
-uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
-version = "1.0.0"
-
 [[deps.StackViews]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"

Project.toml

@@ -8,6 +8,7 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
 GaussianMixtures = "cc18c42c-b769-54ff-9e2a-b28141a64aae"
 MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"

README.md

@@ -1,9 +1,9 @@
 # PhyloClustering.jl
 
-[![Build Status](https://github.com/YiboK/ml-phylo-trees/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/YiboK/ml-phylo-trees/actions/workflows/CI.yml?query=branch%3Amaster)
-
+[![Build Status](https://github.com/YiboK/PhyloClustering.jl/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/YiboK/PhyloClustering.jl/actions/workflows/CI.yml?query=branch%3Amaster)
+[![](https://img.shields.io/badge/docs-dev-blue.svg)](https://solislemuslab.github.io/PhyloClustering.jl/dev)
 
 ## License
 
 `PhyloClustering.jl` is licensed under a
-[MIT License](https://github.com/solislemuslab/ml-phylo-trees/blob/master/LICENSE).
+[MIT License](https://github.com/solislemuslab/PhyloClustering.jl/blob/master/LICENSE).