Refactor documentation and GitHub Actions

The previous documentation sturcture cause all code and built modules to be
uploaded to the GitHub Pages, which is undesirable. This reorganizes the
documentation so that only the relevant files and uploaded and includes JavaDoc
generated documentation. It also rewrites the GitHub Actions to build those
tools.

.github/workflows/build.yml

@@ -0,0 +1,53 @@
+name: Maven Package
+
+on: ["release", "push"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: 17
+        distribution: adopt
+    - name: Install NodeJS
+      uses: actions/setup-node@v4
+      with:
+        node-version: 16
+    - name: Install TypeScript Compiler
+      run: npm install -g [email protected]
+    - name: Setup Repo credentials
+      uses: s4u/[email protected]
+    - name: Build Shesmu with Maven
+      run: mvn -B package --file pom.xml
+    - name: Build Shesmu JavaDoc with Maven
+      run: 'mvn javadoc:javadoc -pl shesmu-pluginapi --file pom.xml && mv shesmu-pluginapi/target/site/apidocs docs/javadoc'
+    - name: Build Jekyll Documentation
+      uses: actions/jekyll-build-pages@v1
+      with:
+        source: docs
+        verbose: true
+    - name: Upload Pages artifact
+      uses: actions/upload-pages-artifact@v3
+    - name: Build and Push Docker images
+      if: ${{ github.event_name == 'release' }}
+      uses: docker/[email protected]
+      with:
+        repository: oicr-gsi/shesmu
+        tags: latest
+        tag_with_ref: true
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      pages: write
+    steps:
+    - name: Upload Pages artifact
+      if: ${{ github.event_name == 'release' }}
+      uses: actions/deploy-pages@v4
+

.github/workflows/release.yml

@@ -0,0 +1,266 @@
+# Copyright 2022-2023, axodotdev
+# SPDX-License-Identifier: MIT or Apache-2.0
+#
+# CI that:
+#
+# * checks for a Git Tag that looks like a release
+# * builds artifacts with cargo-dist (archives, installers, hashes)
+# * uploads those artifacts to temporary workflow zip
+# * on success, uploads the artifacts to a Github Release
+#
+# Note that the Github Release will be created with a generated
+# title/body based on your changelogs.
+
+name: Release
+
+permissions:
+  contents: write
+
+# This task will run whenever you push a git tag that looks like a version
+# like "1.0.0", "v0.1.0-prerelease.1", "my-app/0.1.0", "releases/v1.0.0", etc.
+# Various formats will be parsed into a VERSION and an optional PACKAGE_NAME, where
+# PACKAGE_NAME must be the name of a Cargo package in your workspace, and VERSION
+# must be a Cargo-style SemVer Version (must have at least major.minor.patch).
+#
+# If PACKAGE_NAME is specified, then the announcement will be for that
+# package (erroring out if it doesn't have the given version or isn't cargo-dist-able).
+#
+# If PACKAGE_NAME isn't specified, then the announcement will be for all
+# (cargo-dist-able) packages in the workspace with that version (this mode is
+# intended for workspaces with only one dist-able package, or with all dist-able
+# packages versioned/released in lockstep).
+#
+# If you push multiple tags at once, separate instances of this workflow will
+# spin up, creating an independent announcement for each one. However Github
+# will hard limit this to 3 tags per commit, as it will assume more tags is a
+# mistake.
+#
+# If there's a prerelease-style suffix to the version, then the release(s)
+# will be marked as a prerelease.
+on:
+  push:
+    tags:
+      - '**[0-9]+.[0-9]+.[0-9]+*'
+  pull_request:
+
+jobs:
+  # Run 'cargo dist plan' (or host) to determine what tasks we need to do
+  plan:
+    runs-on: ubuntu-latest
+    outputs:
+      val: ${{ steps.plan.outputs.manifest }}
+      tag: ${{ !github.event.pull_request && github.ref_name || '' }}
+      tag-flag: ${{ !github.event.pull_request && format('--tag={0}', github.ref_name) || '' }}
+      publishing: ${{ !github.event.pull_request }}
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Install cargo-dist
+        # we specify bash to get pipefail; it guards against the `curl` command
+        # failing. otherwise `sh` won't catch that `curl` returned non-0
+        shell: bash
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh"
+      # sure would be cool if github gave us proper conditionals...
+      # so here's a doubly-nested ternary-via-truthiness to try to provide the best possible
+      # functionality based on whether this is a pull_request, and whether it's from a fork.
+      # (PRs run on the *source* but secrets are usually on the *target* -- that's *good*
+      # but also really annoying to build CI around when it needs secrets to work right.)
+      - id: plan
+        run: |
+          cargo dist ${{ (!github.event.pull_request && format('host --steps=create --tag={0}', github.ref_name)) || 'plan' }} --output-format=json > plan-dist-manifest.json
+          echo "cargo dist ran successfully"
+          cat plan-dist-manifest.json
+          echo "manifest=$(jq -c "." plan-dist-manifest.json)" >> "$GITHUB_OUTPUT"
+      - name: "Upload dist-manifest.json"
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifacts-plan-dist-manifest
+          path: plan-dist-manifest.json
+
+  # Build and packages all the platform-specific things
+  build-local-artifacts:
+    name: build-local-artifacts (${{ join(matrix.targets, ', ') }})
+    # Let the initial task tell us to not run (currently very blunt)
+    needs:
+      - plan
+    if: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix.include != null && (needs.plan.outputs.publishing == 'true' || fromJson(needs.plan.outputs.val).ci.github.pr_run_mode == 'upload') }}
+    strategy:
+      fail-fast: false
+      # Target platforms/runners are computed by cargo-dist in create-release.
+      # Each member of the matrix has the following arguments:
+      #
+      # - runner: the github runner
+      # - dist-args: cli flags to pass to cargo dist
+      # - install-dist: expression to run to install cargo-dist on the runner
+      #
+      # Typically there will be:
+      # - 1 "global" task that builds universal installers
+      # - N "local" tasks that build each platform's binaries and platform-specific installers
+      matrix: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix }}
+    runs-on: ${{ matrix.runner }}
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      BUILD_MANIFEST_NAME: target/distrib/${{ join(matrix.targets, '-') }}-dist-manifest.json
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - uses: swatinem/rust-cache@v2
+      - name: Install cargo-dist
+        run: ${{ matrix.install_dist }}
+      # Get the dist-manifest
+      - name: Fetch local artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: artifacts-*
+          path: target/distrib/
+          merge-multiple: true
+      - name: Install dependencies
+        run: |
+          ${{ matrix.packages_install }}
+      - name: Build artifacts
+        run: |
+          # Actually do builds and make zips and whatnot
+          cargo dist build ${{ needs.plan.outputs.tag-flag }} --print=linkage --output-format=json ${{ matrix.dist_args }} > dist-manifest.json
+          echo "cargo dist ran successfully"
+      - id: cargo-dist
+        name: Post-build
+        # We force bash here just because github makes it really hard to get values up
+        # to "real" actions without writing to env-vars, and writing to env-vars has
+        # inconsistent syntax between shell and powershell.
+        shell: bash
+        run: |
+          # Parse out what we just built and upload it to scratch storage
+          echo "paths<<EOF" >> "$GITHUB_OUTPUT"
+          jq --raw-output ".artifacts[]?.path | select( . != null )" dist-manifest.json >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
+
+          cp dist-manifest.json "$BUILD_MANIFEST_NAME"
+      - name: "Upload artifacts"
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifacts-build-local-${{ join(matrix.targets, '_') }}
+          path: |
+            ${{ steps.cargo-dist.outputs.paths }}
+            ${{ env.BUILD_MANIFEST_NAME }}
+
+  # Build and package all the platform-agnostic(ish) things
+  build-global-artifacts:
+    needs:
+      - plan
+      - build-local-artifacts
+    runs-on: "ubuntu-20.04"
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      BUILD_MANIFEST_NAME: target/distrib/global-dist-manifest.json
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Install cargo-dist
+        shell: bash
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh"
+      # Get all the local artifacts for the global tasks to use (for e.g. checksums)
+      - name: Fetch local artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: artifacts-*
+          path: target/distrib/
+          merge-multiple: true
+      - id: cargo-dist
+        shell: bash
+        run: |
+          cargo dist build ${{ needs.plan.outputs.tag-flag }} --output-format=json "--artifacts=global" > dist-manifest.json
+          echo "cargo dist ran successfully"
+
+          # Parse out what we just built and upload it to scratch storage
+          echo "paths<<EOF" >> "$GITHUB_OUTPUT"
+          jq --raw-output ".artifacts[]?.path | select( . != null )" dist-manifest.json >> "$GITHUB_OUTPUT"
+          echo "EOF" >> "$GITHUB_OUTPUT"
+
+          cp dist-manifest.json "$BUILD_MANIFEST_NAME"
+      - name: "Upload artifacts"
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifacts-build-global
+          path: |
+            ${{ steps.cargo-dist.outputs.paths }}
+            ${{ env.BUILD_MANIFEST_NAME }}
+  # Determines if we should publish/announce
+  host:
+    needs:
+      - plan
+      - build-local-artifacts
+      - build-global-artifacts
+    # Only run if we're "publishing", and only if local and global didn't fail (skipped is fine)
+    if: ${{ always() && needs.plan.outputs.publishing == 'true' && (needs.build-global-artifacts.result == 'skipped' || needs.build-global-artifacts.result == 'success') && (needs.build-local-artifacts.result == 'skipped' || needs.build-local-artifacts.result == 'success') }}
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: "ubuntu-20.04"
+    outputs:
+      val: ${{ steps.host.outputs.manifest }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Install cargo-dist
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh"
+      # Fetch artifacts from scratch-storage
+      - name: Fetch artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: artifacts-*
+          path: target/distrib/
+          merge-multiple: true
+      # This is a harmless no-op for Github Releases, hosting for that happens in "announce"
+      - id: host
+        shell: bash
+        run: |
+          cargo dist host ${{ needs.plan.outputs.tag-flag }} --steps=upload --steps=release --output-format=json > dist-manifest.json
+          echo "artifacts uploaded and released successfully"
+          cat dist-manifest.json
+          echo "manifest=$(jq -c "." dist-manifest.json)" >> "$GITHUB_OUTPUT"
+      - name: "Upload dist-manifest.json"
+        uses: actions/upload-artifact@v4
+        with:
+          # Overwrite the previous copy
+          name: artifacts-dist-manifest
+          path: dist-manifest.json
+
+  # Create a Github Release while uploading all files to it
+  announce:
+    needs:
+      - plan
+      - host
+    # use "always() && ..." to allow us to wait for all publish jobs while
+    # still allowing individual publish jobs to skip themselves (for prereleases).
+    # "host" however must run to completion, no skipping allowed!
+    if: ${{ always() && needs.host.result == 'success' }}
+    runs-on: "ubuntu-20.04"
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: "Download Github Artifacts"
+        uses: actions/download-artifact@v4
+        with:
+          pattern: artifacts-*
+          path: artifacts
+          merge-multiple: true
+      - name: Cleanup
+        run: |
+          # Remove the granular manifests
+          rm -f artifacts/*-dist-manifest.json
+      - name: Create Github Release
+        uses: ncipollo/release-action@v1
+        with:
+          tag: ${{ needs.plan.outputs.tag }}
+          name: ${{ fromJson(needs.host.outputs.val).announcement_title }}
+          body: ${{ fromJson(needs.host.outputs.val).announcement_github_body }}
+          prerelease: ${{ fromJson(needs.host.outputs.val).announcement_is_prerelease }}
+          artifacts: "artifacts/*"