import the CI machinery, split into files to allow nicer docs

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - 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@v1
+        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 }}

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+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 }}

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1' # This is always the latest stable release in the 1.X series
+          - '1.6' # LTS
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - 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@latest
+      - run: |
+          git config --global user.name Tester
+          git config --global user.email [email protected]
+      - uses: julia-actions/julia-runtest@latest
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/docs.yml

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+
+# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+    tags: '*'
+  release:
+    types: [published, created]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+      - name: Install dependencies
+        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/pr-format.yml

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+on:
+  pull_request:
+  issue_comment:
+    types: [created]
+
+name: Formatting
+
+jobs:
+  formatting:
+    if: github.event_name == 'pull_request' || (github.event_name == 'issue_comment' && github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'OWNER' || github.event.issue.user.id == github.event.comment.user.id) && startsWith(github.event.comment.body, '/format') )
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone the repository
+        uses: actions/checkout@v3
+      - name: Checkout the pull request code # this checks out the actual branch so that one can commit into it
+        if: github.event_name == 'issue_comment'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr checkout ${{ github.event.issue.number }}
+      - name: Install JuliaFormatter and format
+        run: |
+          julia --color=yes -e 'import Pkg; Pkg.add("JuliaFormatter")'
+          julia --color=yes -e 'using JuliaFormatter; format(".")'
+      - name: Remove trailing whitespace
+        run: |
+          find -name '*.jl' -or -name '*.md' -or -name '*.toml' -or -name '*.yml' | while read filename ; do
+            # remove any trailing spaces
+            sed --in-place -e 's/\s*$//' "$filename"
+            # add a final newline if missing
+            if [[ -s "$filename" && $(tail -c 1 "$filename" |wc -l) -eq 0 ]] ; then
+              echo >> "$filename"
+            fi
+            # squash superfluous final newlines
+            sed -i -e :a -e '/^\n*$/{$d;N;};/\n$/ba' "$filename"
+          done
+      - name: Fail on formatting problems
+        if: github.event_name == 'pull_request'
+        run: |
+          if git diff --exit-code --quiet
+          then echo "Looks OK"
+          else echo "Formatting fixes required!"; git diff -p ; exit 1
+          fi
+      - name: Commit fixes
+        if: github.event_name == 'issue_comment'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          if [ `git status -s | wc -l` -ne 0 ] ; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit -a -m "automatic formatting" -m "triggered by @$GITHUB_ACTOR on PR #${{ github.event.issue.number }}"
+            if git push
+            then gh pr comment ${{ github.event.issue.number }} --body \
+              ":heavy_check_mark: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, commited as `git rev-parse HEAD`"
+            else gh pr comment ${{ github.event.issue.number }} --body \
+              ":x: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) failed, perhaps someone pushed to the PR in the meantime?"
+            fi
+          else
+            gh pr comment ${{ github.event.issue.number }} --body \
+              ":sunny: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, but the code was already formatted correctly."
+          fi

.gitignore

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+/docs/build/
+/Manifest.toml
+
+*.cov
+.*.swp

docs/Project.toml

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+[deps]
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

docs/make.jl

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+using Documenter, Literate, ConstraintTrees
+
+examples =
+    sort(filter(x -> endswith(x, ".jl"), readdir(joinpath(@__DIR__, "src"), join = true)))
+
+for example in examples
+    Literate.markdown(
+        example,
+        joinpath(@__DIR__, "src"),
+        repo_root_url = "https://github.com/COBREXA/ConstraintTrees.jl/blob/master",
+    )
+end
+
+example_mds = first.(splitext.(basename.(examples))) .* ".md"
+
+makedocs(
+    modules = [ConstraintTrees],
+    clean = false,
+    format = Documenter.HTML(
+        ansicolor = true,
+        canonical = "https://cobrexa.github.io/ConstraintTrees.jl/stable/",
+    ),
+    sitename = "ConstraintTrees.jl",
+    linkcheck = false,
+    pages = ["README" => "index.md"; example_mds; "Reference" => "reference.md"],
+    strict = [:missing_docs, :cross_references, :example_block],
+)
+
+deploydocs(
+    repo = "github.com/COBREXA/ConstraintTrees.jl.git",
+    target = "build",
+    branch = "gh-pages",
+    push_preview = false,
+)

docs/src/index.md

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+
+# ConstraintTrees.jl
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["ConstraintTrees.jl"]
+```

docs/src/reference.md

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+
+# Reference
+
+## Values (linear combinations of variables)
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["value.jl"]
+```
+
+## Constraints
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["constraint.jl"]
+```
+
+## Constraint trees
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["constraint_tree.jl"]
+```
+
+## Solution trees
+
+```@autodocs
+Modules = [ConstraintTrees]
+Pages = ["solution.jl"]
+```