From c78702324f55bbd491635d8d66420659d025220e Mon Sep 17 00:00:00 2001
From: Cecile Ane <cecileane@users.noreply.github.com>
Date: Thu, 12 Sep 2024 14:11:02 -0400
Subject: [PATCH] Files generated by PkgTemplates

PkgTemplates version: 0.7.52
---
 .github/dependabot.yml             |   7 +++
 .github/workflows/CI.yml           |  78 +++++++++++++++++++++++++++++
 .github/workflows/CompatHelper.yml |  16 ++++++
 .github/workflows/TagBot.yml       |  31 ++++++++++++
 .gitignore                         |   9 ++++
 CITATION.bib                       |   8 +++
 LICENSE                            |  21 ++++++++
 Project.toml                       |   7 +++
 README.md                          |  13 +++++
 docs/Project.toml                  |   3 ++
 docs/make.jl                       |  23 +++++++++
 docs/src/assets/logo-dark.png      | Bin 0 -> 3346 bytes
 docs/src/assets/logo.png           | Bin 0 -> 3170 bytes
 docs/src/index.md                  |  14 ++++++
 src/PhyLiNC.jl                     |   5 ++
 test/Project.toml                  |   3 ++
 test/runtests.jl                   |  10 ++++
 17 files changed, 248 insertions(+)
 create mode 100644 .github/dependabot.yml
 create mode 100644 .github/workflows/CI.yml
 create mode 100644 .github/workflows/CompatHelper.yml
 create mode 100644 .github/workflows/TagBot.yml
 create mode 100644 .gitignore
 create mode 100644 CITATION.bib
 create mode 100644 LICENSE
 create mode 100644 Project.toml
 create mode 100644 README.md
 create mode 100644 docs/Project.toml
 create mode 100644 docs/make.jl
 create mode 100644 docs/src/assets/logo-dark.png
 create mode 100644 docs/src/assets/logo.png
 create mode 100644 docs/src/index.md
 create mode 100644 src/PhyLiNC.jl
 create mode 100644 test/Project.toml
 create mode 100644 test/runtests.jl

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..700707c
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
new file mode 100644
index 0000000..798713a
--- /dev/null
+++ b/.github/workflows/CI.yml
@@ -0,0 +1,78 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    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 }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.2'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      contents: write
+      statuses: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v2
+      - name: Configure doc environment
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - name: Run doctests
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Documenter: DocMeta, doctest
+          using PhyLiNC
+          DocMeta.setdocmeta!(PhyLiNC, :DocTestSetup, :(using PhyLiNC); recursive=true)
+          doctest(PhyLiNC)
diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
new file mode 100644
index 0000000..61d898c
--- /dev/null
+++ b/.github/workflows/CompatHelper.yml
@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 28 01 16 * ?
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
new file mode 100644
index 0000000..0cd3114
--- /dev/null
+++ b/.github/workflows/TagBot.yml
@@ -0,0 +1,31 @@
+name: TagBot
+on:
+  issue_comment:
+    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'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..d1d68d4
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,9 @@
+**/.DS_Store
+*.jl.*.cov
+*.jl.cov
+*.jl.mem
+.DS_Store
+/Manifest.toml
+/docs/Manifest.toml
+/docs/build/
+/test/Manifest.toml
diff --git a/CITATION.bib b/CITATION.bib
new file mode 100644
index 0000000..b68d019
--- /dev/null
+++ b/CITATION.bib
@@ -0,0 +1,8 @@
+@misc{PhyLiNC.jl,
+	author  = {Cecile Ane <cecileane@users.noreply.github.com>, Cora Allen-Savietta <coraallensavietta@users.noreply.github.com>, and contributors},
+	title   = {PhyLiNC.jl},
+	url     = {https://github.com/JuliaPhylo/PhyLiNC.jl},
+	version = {v1.0.0-DEV},
+	year    = {2024},
+	month   = {9}
+}
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..124343d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Cecile Ane <cecileane@users.noreply.github.com>, Cora Allen-Savietta <coraallensavietta@users.noreply.github.com>, and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/Project.toml b/Project.toml
new file mode 100644
index 0000000..8489621
--- /dev/null
+++ b/Project.toml
@@ -0,0 +1,7 @@
+name = "PhyLiNC"
+uuid = "cc80c543-84d2-42fd-beda-26c7d0f745cc"
+authors = ["Cecile Ane <cecileane@users.noreply.github.com>", "Cora Allen-Savietta <coraallensavietta@users.noreply.github.com>", "and contributors"]
+version = "0.1.0-DEV"
+
+[compat]
+julia = "1.2"
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..610367b
--- /dev/null
+++ b/README.md
@@ -0,0 +1,13 @@
+# PhyLiNC
+
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaPhylo.github.io/PhyLiNC.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaPhylo.github.io/PhyLiNC.jl/dev/)
+[![Build Status](https://github.com/JuliaPhylo/PhyLiNC.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaPhylo/PhyLiNC.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/JuliaPhylo/PhyLiNC.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaPhylo/PhyLiNC.jl)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
+
+## Citing
+
+See [`CITATION.bib`](CITATION.bib) for the relevant reference(s).
diff --git a/docs/Project.toml b/docs/Project.toml
new file mode 100644
index 0000000..d910a27
--- /dev/null
+++ b/docs/Project.toml
@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+PhyLiNC = "cc80c543-84d2-42fd-beda-26c7d0f745cc"
diff --git a/docs/make.jl b/docs/make.jl
new file mode 100644
index 0000000..47261cb
--- /dev/null
+++ b/docs/make.jl
@@ -0,0 +1,23 @@
+using PhyLiNC
+using Documenter
+
+DocMeta.setdocmeta!(PhyLiNC, :DocTestSetup, :(using PhyLiNC); recursive=true)
+
+makedocs(;
+    modules=[PhyLiNC],
+    authors="Cecile Ane <cecileane@users.noreply.github.com>, Cora Allen-Savietta <coraallensavietta@users.noreply.github.com>, and contributors",
+    sitename="PhyLiNC.jl",
+    format=Documenter.HTML(;
+        canonical="https://JuliaPhylo.github.io/PhyLiNC.jl",
+        edit_link="main",
+        assets=String[],
+    ),
+    pages=[
+        "Home" => "index.md",
+    ],
+)
+
+deploydocs(;
+    repo="github.com/JuliaPhylo/PhyLiNC.jl",
+    devbranch="main",
+)
diff --git a/docs/src/assets/logo-dark.png b/docs/src/assets/logo-dark.png
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diff --git a/docs/src/assets/logo.png b/docs/src/assets/logo.png
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diff --git a/docs/src/index.md b/docs/src/index.md
new file mode 100644
index 0000000..37e32ea
--- /dev/null
+++ b/docs/src/index.md
@@ -0,0 +1,14 @@
+```@meta
+CurrentModule = PhyLiNC
+```
+
+# PhyLiNC
+
+Documentation for [PhyLiNC](https://github.com/JuliaPhylo/PhyLiNC.jl).
+
+```@index
+```
+
+```@autodocs
+Modules = [PhyLiNC]
+```
diff --git a/src/PhyLiNC.jl b/src/PhyLiNC.jl
new file mode 100644
index 0000000..0cf70aa
--- /dev/null
+++ b/src/PhyLiNC.jl
@@ -0,0 +1,5 @@
+module PhyLiNC
+
+# Write your package code here.
+
+end
diff --git a/test/Project.toml b/test/Project.toml
new file mode 100644
index 0000000..b35b5ed
--- /dev/null
+++ b/test/Project.toml
@@ -0,0 +1,3 @@
+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/test/runtests.jl b/test/runtests.jl
new file mode 100644
index 0000000..8cc9d1e
--- /dev/null
+++ b/test/runtests.jl
@@ -0,0 +1,10 @@
+using PhyLiNC
+using Test
+using Aqua
+
+@testset "PhyLiNC.jl" begin
+    @testset "Code quality (Aqua.jl)" begin
+        Aqua.test_all(PhyLiNC)
+    end
+    # Write your tests here.
+end