Standardize yml (#15)

* Standardize yml

* Standardize make.jl

* Standardize docs

* Fix make

.github/dependabot.yml

@@ -1,7 +1,8 @@
 # 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
+  - package-ecosystem: github-actions
+    directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -2,20 +2,47 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '0 0 * * 0'
+    - cron: 0 0 * * 0 # weekly
   workflow_dispatch:
-
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+          # arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}  # optional
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
 
 # based on:
 # https://github.com/JuliaRegistries/CompatHelper.jl

.github/workflows/Documentation.yml

@@ -2,25 +2,25 @@ name: Documentation
 
 on:
   pull_request:
+    paths-ignore:
+      - 'README.md'
   push:
+    paths-ignore:
+      - 'README.md'
     branches:
       - 'main'
+      - 'release-'
     tags: '*'
 
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: ["1"]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
-          version: ${{ matrix.julia-version }}
-      - name: Cache artifacts
+          version: '1'
+      - name: CacheArtifacts
         uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
@@ -31,13 +31,17 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - name: Install dependencies
+      - name: InstallDependencies
         run: |
           julia --project=docs/ -e '
-          using Pkg
-          Pkg.develop(PackageSpec(path=pwd()))
-          Pkg.instantiate()'
+            ENV["JULIA_PKG_SERVER"] = ""
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
       - name: BuildAndDeploy
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN
+#         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
         run: julia --project=docs/ docs/make.jl

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@master

.github/workflows/TagBot.yml

@@ -1,9 +1,11 @@
 name: TagBot
+
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
+
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -12,4 +14,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.COMPATHELPER_PRIV }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/UnitTest.yml → .github/workflows/ci.yml

@@ -33,6 +33,18 @@ jobs:
         with:
           version: ${{ matrix.version }}
 
+      - name: Cache artifacts
+        uses: actions/cache@v4
+        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 }}-
+
 #     - name: "Unit Test"
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
@@ -43,3 +55,6 @@ jobs:
         if: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
         with:
           file: lcov.info
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/clean.yml

@@ -0,0 +1,28 @@
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#gh-pages-Branch
+
+name: DocPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.gitignore

@@ -16,9 +16,15 @@ deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+docs/src/generated/
 
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
+
+# other
+.DS_Store
+.*.*.swp
+.benchmarkci

docs/make.jl

@@ -1,29 +1,45 @@
-# push!(LOAD_PATH,"../src/")
-
-using AVSfldIO
-using Documenter
-
-DocMeta.setdocmeta!(AVSfldIO, :DocTestSetup, :(using AVSfldIO); recursive=true)
-
-makedocs(;
-    modules = [AVSfldIO],
-    authors = "Jeff Fessler <[email protected]> and contributors",
-#   repo = "https://github.com/JuliaIO/AVSfldIO.jl/blob/{commit}{path}#{line}",
-    sitename = "AVSfldIO.jl",
-    format = Documenter.HTML(;
-        prettyurls = get(ENV, "CI", "false") == "true",
-#       canonical = "https://JuliaIO.github.io/AVSfldIO.jl/stable",
-#       assets = String[],
-    ),
+execute = isempty(ARGS) || ARGS[1] == "run"
+
+org, reps = :JuliaIO, :AVSfldIO
+eval(:(using $reps))
+import Documenter
+#import Literate
+
+base = "$org/$reps.jl"
+
+
+repo = eval(:($reps))
+Documenter.DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
+
+
+isci = get(ENV, "CI", nothing) == "true"
+
+format = Documenter.HTML(;
+    prettyurls = isci,
+    edit_link = "main",
+    canonical = "https://$org.github.io/$repo.jl/stable/",
+    assets = ["assets/custom.css"],
+)
+
+Documenter.makedocs(;
+    modules = [repo],
+    authors = "Jeff Fessler and contributors",
+    sitename = "$repo.jl",
+    format,
     pages = [
         "Home" => "index.md",
+        "Methods" => "methods.md",
     ],
 )
 
-deploydocs(;
-    repo = "github.com/JuliaIO/AVSfldIO.jl.git",
-    devbranch = "main",
-#   devurl = "dev",
-#   versions = ["stable" => "v^", "dev" => "dev"],
-#   push_preview = true,
-)
+if isci
+    Documenter.deploydocs(;
+        repo = "github.com/$base",
+        devbranch = "main",
+        devurl = "dev",
+        versions = ["stable" => "v^", "dev" => "dev"],
+        forcepush = true,
+#       push_preview = true,
+        # see https://$org.github.io/$repo.jl/previews/PR##
+    )
+end

docs/src/assets/custom.css

@@ -0,0 +1,3 @@
+.docs-sourcelink {
+    opacity:1 !important;
+}

docs/src/index.md

@@ -14,14 +14,3 @@ CurrentModule = AVSfldIO
 File I/O routines for AVS `.fld` format data files;
 see
 [(AVSfldIO)](https://github.com/JuliaIO/AVSfldIO.jl)
-
-## Index
-
-```@index
-```
-
-## Functions
-
-```@autodocs
-Modules = [AVSfldIO]
-```

docs/src/methods.md

@@ -0,0 +1,10 @@
+## Methods list
+
+```@index
+```
+
+## Methods usage
+
+```@autodocs
+Modules = [AVSfldIO]
+```