massive cleanup + stabilization

.github/workflows/CompatHelper.yml

@@ -37,8 +37,7 @@ jobs:
       - name: "Run CompatHelper"
         run: |
           import CompatHelper
-          CompatHelper.main(master_branch="develop")
+          CompatHelper.main()
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+  pull_request:
 
 jobs:
   test:
@@ -13,36 +14,30 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - 'nightly'
+          - '1' # This is always the latest stable release in the 1.X series
+          - '1.10' # LTS
+          #- 'nightly'
         os:
           - ubuntu-latest
-          - macOS-latest
+          #- macOS-latest
           #- windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - 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/cache@v2
       - uses: julia-actions/julia-buildpkg@latest
       - run: |
           git config --global user.name Tester
           git config --global user.email te@st.er
       - uses: julia-actions/julia-runtest@latest
         continue-on-error: ${{ matrix.version == 'nightly' }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docker.yml

@@ -1,24 +1,40 @@
-name: Publish Docker image
+
+name: build docker image
 
 on:
   push:
-    tags:
-      - "v*"
-  release:
-    types: [published, created]
+    branches:
+      - master
+    tags: '*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: lcsb-biocore/gigasom.jl # lowercase of ${{ github.repository }}
 
 jobs:
-  push_to_registry:
-    name: Push Docker image to GitHub Packages
+  build:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
     steps:
-      - name: Check out the repo
-        uses: actions/checkout@v2
-      - name: Push to GitHub Registry
-        uses: mr-smithers-excellent/docker-build-push@v5
-        with:
-          image: gigasom.jl
-          tags: latest
-          registry: ghcr.io
-          username: cylon-x
-          password: ${{ secrets.docker_token }}
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: log into docker registry
+      uses: docker/login-action@v3
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: extract metadata
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+    - name: build and push the docker container
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docs.yml

@@ -1,26 +1,24 @@
+
 # ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
 name: Documentation
 
 on:
+  pull_request:
   push:
     branches:
-      - develop
       - master
     tags: '*'
-  release:
-    types: [published, created]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
-        with:
-          version: 1.7
+      - uses: julia-actions/cache@v2
       - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+        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 --project=docs/ docs/make.jl
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/pr-format.yml

@@ -0,0 +1,62 @@
+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@v4
+      - 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 "$GITHUB_ACTOR@users.noreply.github.com"
+            git commit -a -m "automatic formatting" -m "triggered by @$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