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sup table 1 #2

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sup table 1

sup table 1 #2

Workflow file for this run

.github/workflows/manubot.yaml at 0b304c3
name: Manubot
on:
push:
branches:
- main
- master
pull_request:
branches:
- main
- master
# NOTE: scheduled workflows are supported as of 2022-09-27 (example commented below)
# https://github.com/community/community/discussions/12269#discussioncomment-3747667
# scheduled:
# - cron: '40 10 1 * *' # https://crontab.guru/#40_10_1_*_*
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
permissions:
contents: write
env:
GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
# Set SPELLCHECK to true/false for whether to check spelling in this action.
# For workflow dispatch jobs, this SPELLCHECK setting will be overridden by the user input.
SPELLCHECK: true
defaults:
run:
shell: bash --login {0}
steps:
- name: Checkout Repository
uses: actions/checkout@v3
with:
# fetch entire commit history to support get_rootstock_commit
fetch-depth: 0
- name: Set Environment Variables (Workflow Dispatch)
if: github.event_name == 'workflow_dispatch'
run: |
echo "BUILD_PDF=${{ 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@v3
with:
path: ci/cache
key: ci-cache-${{ github.ref }}
restore-keys: |
ci-cache-${{ 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
miniforge-variant: Mambaforge
miniforge-version: 'latest'
use-mamba: true
- name: Install Spellcheck
if: env.SPELLCHECK == 'true'
run: bash ci/install-spellcheck.sh
- name: Build Manuscript
run: bash build/build.sh
- name: Upload Artifacts
uses: actions/upload-artifact@v3
with:
name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
path: output
- name: Deploy Manuscript
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 }}/actions/runs/${{ github.run_id }}
run: bash ci/deploy.sh