Merge pull request #306 from jashapiro/jashapiro/rootstock-2022-08-11

Update rootstock

.appveyor.yml

@@ -8,10 +8,11 @@ skip_branch_with_pr: true
 # to only build commits from pull requests
 branches:
   only:
+    - main
     - master
 
 # Only run AppVeyor on commits that modify at least one of the following files
-# Delete these lines to run AppVeyor on all master branch commits
+# Delete these lines to run AppVeyor on all main/master branch commits
 only_commits:
   files:
     - .appveyor.yml

.github/workflows/manubot.yaml

@@ -2,62 +2,100 @@ name: Manubot
 on:
   push:
     branches:
+      - main
       - master
   pull_request:
     branches:
+      - main
       - master
+  # NOTE: scheduled workflows aren't supported
+  # https://github.jparrowsec.cnmunity/t/github-event-repository-fork-context-does-detect-forks-in-scheduled-jobs/185925
+  workflow_dispatch:
+    inputs:
+      BUILD_PDF:
+        type: boolean
+        description: generate PDF output
+        default: true
+      BUILD_DOCX:
+        type: boolean
+        description: generate DOCX output
+        default: true
+      BUILD_LATEX:
+        type: boolean
+        description: generate LaTeX output
+        default: false
+      SPELLCHECK:
+        type: boolean
+        description: Check spelling
+        default: true
+      MANUBOT_USE_DOCKER:
+        type: boolean
+        description: Use Docker to generate PDF
+        default: true
 jobs:
   manubot:
     name: Manubot
     runs-on: ubuntu-latest
     env:
       GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
+      # Set SPELLCHECK to true/false for whether to check spelling in this action.
+      # For workflow dispatch jobs, this SPELLCHECK setting will be overridden by the user input.
       SPELLCHECK: true
+    defaults:
+      run:
+        shell: bash --login {0}
     steps:
-      - name: Set Environment Variables
-        run: |
-          TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
-          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
-          echo "TRIGGERING_SHA: $TRIGGERING_SHA"
       - name: Checkout Repository
         uses: actions/checkout@v2
         with:
           # fetch entire commit history to support get_rootstock_commit
           fetch-depth: 0
+      - name: Set Environment Variables (Workflow Dispatch)
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          echo "BUILD_PDF=${{ github.event.inputs.BUILD_PDF }}" >> $GITHUB_ENV
+          echo "BUILD_DOCX=${{ github.event.inputs.BUILD_DOCX }}" >> $GITHUB_ENV
+          echo "BUILD_LATEX=${{ github.event.inputs.BUILD_LATEX }}" >> $GITHUB_ENV
+          echo "SPELLCHECK=${{ github.event.inputs.SPELLCHECK }}" >> $GITHUB_ENV
+          echo "MANUBOT_USE_DOCKER=${{ github.event.inputs.MANUBOT_USE_DOCKER }}" >> $GITHUB_ENV
+      - name: Set Environment Variables
+        run: |
+          TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
+          echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
+          echo "TRIGGERING_SHA: $TRIGGERING_SHA"
+          DEFAULT_BRANCH=${{ github.event.repository.default_branch }}
+          echo "DEFAULT_BRANCH=${DEFAULT_BRANCH}" >> $GITHUB_ENV
+          echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV
+          echo "DEFAULT_BRANCH=$DEFAULT_BRANCH"
       - name: Cache
         uses: actions/cache@v1
         with:
           path: ci/cache
           key: ci-cache-${{ github.ref }}
           restore-keys: |
-            ci-cache-refs/heads/master
+            ci-cache-${{ env.DEFAULT_BRANCH_REF }}
       - name: Install Environment
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: manubot
           environment-file: build/environment.yml
           auto-activate-base: false
-          miniconda-version: 'latest'
+          miniforge-version: 'latest'
       - name: Install Spellcheck
-        shell: bash --login {0}
-        run: |
-          if [ "${SPELLCHECK:-}" = "true" ]; then
-            bash ci/install-spellcheck.sh
-          fi
+        if: env.SPELLCHECK == 'true'
+        run: bash ci/install-spellcheck.sh
       - name: Build Manuscript
-        shell: bash --login {0}
         run: BUILD_DOCX=true bash build/build.sh
       - name: Upload Artifacts
         uses: actions/upload-artifact@v1
         with:
           name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
           path: output
       - name: Deploy Manuscript
-        if: github.ref == 'refs/heads/master' && github.event_name == 'push' && !github.event.repository.fork
+        if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name != 'pull_request' && !github.event.repository.fork
         env:
           MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}
           CI_BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks
-          CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/runs/${{ github.run_id }}
-        shell: bash --login {0}
+          CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
         run: bash ci/deploy.sh

README.md

@@ -2,9 +2,9 @@
 
 <!-- usage note: edit the H1 title above to personalize the manuscript -->
 
-[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://AlexsLemonade.github.io/OpenPBTA-manuscript/)
-[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://AlexsLemonade.github.io/OpenPBTA-manuscript/manuscript.pdf)
-[![GitHub Actions Status](https://github.com/AlexsLemonade/OpenPBTA-manuscript/workflows/Manubot/badge.svg)](https://github.com/AlexsLemonade/OpenPBTA-manuscript/actions)
+[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/)
+[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf)
+[![GitHub Actions Status](https://github.com/manubot/rootstock/workflows/Manubot/badge.svg)](https://github.com/manubot/rootstock/actions)
 
 ## Manuscript description
 
@@ -81,13 +81,13 @@ Whenever a pull request is opened, CI (continuous integration) will test whether
 The build process aims to detect common errors, such as invalid citations.
 If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.
 
-When a commit to the `master` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches.
+When a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches.
 The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:
 
 + **HTML manuscript** at https://AlexsLemonade.github.io/OpenPBTA-manuscript/
 + **PDF manuscript** at https://AlexsLemonade.github.io/OpenPBTA-manuscript/manuscript.pdf
 
-For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml) if using GitHub Actions or [`.travis.yml`](.travis.yml) if using Travis CI.
+For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml).
 
 ## License