Update rootstock on 2020-11-10

greenelab · Nov 10, 2020 · 3d73f75 · 3d73f75
2 parents cfa2a35 + 97b2948
commit 3d73f75
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Showing 24 changed files with 517 additions and 178 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -23,20 +23,33 @@ image: ubuntu
 services:
   - docker
 
+# Set SPELLCHECK to true to enable Pandoc spellchecking
+environment:
+  SPELLCHECK: true
+
 install:
   # Create the message with the triggering commit before install so it is
   # available if the build fails
   - TRIGGERING_COMMIT=${APPVEYOR_PULL_REQUEST_HEAD_COMMIT:-APPVEYOR_REPO_COMMIT}
-  - appveyor AddMessage "commit $TRIGGERING_COMMIT"
+  - JOB_MESSAGE=" for commit $TRIGGERING_COMMIT "
   - source ci/install.sh
-    
+
 test_script:
   - bash build/build.sh
   - MANUSCRIPT_FILENAME=manuscript-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}
   - cp output/manuscript.html $MANUSCRIPT_FILENAME.html
   - cp output/manuscript.pdf $MANUSCRIPT_FILENAME.pdf
   - appveyor PushArtifact $MANUSCRIPT_FILENAME.html
   - appveyor PushArtifact $MANUSCRIPT_FILENAME.pdf
+  - |
+      if [ "${SPELLCHECK:-}" = "true" ]; then
+        SPELLING_ERRORS_FILENAME=spelling-errors-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt
+        cp output/spelling-errors.txt $SPELLING_ERRORS_FILENAME
+        appveyor PushArtifact $SPELLING_ERRORS_FILENAME
+        SPELLING_ERROR_LOCATIONS_FILENAME=spelling-error-locations-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt
+        cp output/spelling-error-locations.txt $SPELLING_ERROR_LOCATIONS_FILENAME
+        appveyor PushArtifact $SPELLING_ERROR_LOCATIONS_FILENAME
+      fi
 
 build: off
 
@@ -46,6 +59,16 @@ cache:
 on_success:
   - echo "Artifacts available from $APPVEYOR_URL/project/$APPVEYOR_ACCOUNT_NAME/$APPVEYOR_PROJECT_SLUG/builds/$APPVEYOR_BUILD_ID/artifacts"
   - echo "Updated PDF available from $APPVEYOR_URL/api/buildjobs/$APPVEYOR_JOB_ID/artifacts/$MANUSCRIPT_FILENAME.pdf"
+  - appveyor AddMessage "$JOB_MESSAGE is now complete."
+  - |
+      if [ "${SPELLCHECK:-}" = "true" ]; then
+        SPELLING_ERROR_COUNT=($(wc -l $SPELLING_ERROR_LOCATIONS_FILENAME))
+        appveyor AddMessage " <details><summary>Found $SPELLING_ERROR_COUNT potential spelling error(s). Preview:</summary>$(head -n 100 $SPELLING_ERROR_LOCATIONS_FILENAME)"
+        appveyor AddMessage "... </details>"
+      fi
+
+on_failure:
+  - appveyor AddMessage "$JOB_MESSAGE failed."
 
 # The following lines can be safely deleted, which will disable AppVeyorBot
 # notifications in GitHub pull requests
@@ -55,7 +78,6 @@ on_success:
 notifications:
   - provider: GitHubPullRequest
     template: "AppVeyor [build {{buildVersion}}]({{buildUrl}})
-      {{#jobs}}{{#messages}} for {{message}} by @{{&commitAuthorUsername}}{{/messages}}{{/jobs}}
-      {{#passed}} is now complete. The rendered manuscript from this build is temporarily available for download at:\n\n{{/passed}}
-      {{#failed}} failed.{{/failed}}
-      {{#jobs}}{{#artifacts}}- [`{{fileName}}`]({{permalink}})\n{{/artifacts}}{{/jobs}}"
+      {{#jobs}}{{#messages}}{{{message}}}{{/messages}}{{/jobs}}
+      {{#passed}}The rendered manuscript from this build is temporarily available for download at:\n\n
+      {{#jobs}}{{#artifacts}}- [`{{fileName}}`]({{permalink}})\n{{/artifacts}}{{/jobs}}{{/passed}}"
diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
@@ -12,25 +12,38 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
+      SPELLCHECK: true
     steps:
       - name: Set Environment Variables
         run: |
           TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
-          TRIGGERING_SHA_7=${TRIGGERING_SHA::7}
-          echo "::set-env name=TRIGGERING_SHA_7::$TRIGGERING_SHA_7"
+          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
           echo "TRIGGERING_SHA: $TRIGGERING_SHA"
       - name: Checkout Repository
         uses: actions/checkout@v2
         with:
           # fetch entire commit history to support get_rootstock_commit
           fetch-depth: 0
+      - name: Cache
+        uses: actions/cache@v1
+        with:
+          path: ci/cache
+          key: ci-cache-${{ github.ref }}
+          restore-keys: |
+            ci-cache-refs/heads/master
       - name: Install Environment
-        uses: goanpeca/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: manubot
           environment-file: build/environment.yml
           auto-activate-base: false
           miniconda-version: 'latest'
+      - name: Install Spellcheck
+        shell: bash --login {0}
+        run: |
+          if [ "${SPELLCHECK:-}" = "true" ]; then
+            bash ci/install-spellcheck.sh
+          fi
       - name: Build Manuscript
         shell: bash --login {0}
         run: bash build/build.sh

diff --git a/.gitignore b/.gitignore
@@ -11,6 +11,9 @@ webpage/v
 # Manubot cache directory
 ci/cache
 
+# Pandoc filters downloaded during continuous integration setup
+build/pandoc/filters/spellcheck.lua
+
 # Python
 __pycache__/
 *.pyc