Merge pull request #14 from quinlan-lab/rootstock-2023-09-06

Merge upstream changes from rootstock repo

.github/workflows/ai-revision.yaml

@@ -27,6 +27,9 @@ jobs:
   ai-revise:
     name: AI Revise
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     defaults:
       run:
         shell: bash --login {0}

.github/workflows/manubot.yaml

@@ -38,6 +38,8 @@ 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.
@@ -82,7 +84,9 @@ jobs:
           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

USAGE.md

@@ -322,6 +322,8 @@ metadata:
   csl: https://github.com/citation-style-language/styles/raw/906cd6d43d0c136190ecfbb12f6af0ca794e3c5b/peerj.csl
 ```
 
+Instructions for generating additional manuscript output formats such as DOCX can be found in [`build/README.md`](build/README.md).
+
 ## Spellchecking
 
 When the `SPELLCHECK` environment variable is `true`, the pandoc [spellcheck filter](https://github.com/pandoc/lua-filters/tree/master/spellcheck) is run.

build/README.md

@@ -7,8 +7,19 @@ However, setting the `BUILD_PDF` environment variable to `false` will suppress P
 For example, run local builds using the command `BUILD_PDF=false bash build/build.sh`.
 
 To build a DOCX file of the manuscript, set the `BUILD_DOCX` environment variable to `true`.
-For example, use the command `BUILD_DOCX=true bash build/build.sh`.
-To export DOCX for all CI builds, set an environment variable (see docs for [GitHub Actions](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/using-environment-variables)).
+For example, use the command `BUILD_DOCX=true bash build/build.sh` locally.
+To export DOCX for all CI builds, set an environment variable in the CI configuration file.
+For GitHub Actions, set the variable in `.github\workflows\manubot.yaml` (see [docs](https://help.github.com/en/actions/automating-your-workflow-with-github-actions/using-environment-variables)):
+
+```yaml
+name: Manubot
+env:
+  BUILD_DOCX: true
+```
+
+To generate a single DOCX output of the latest manuscript with GitHub Actions, click the "Actions" tab at the top of the repository.
+Select the "Manubot" workflow, then the "Run workflow" button and check "generate DOCX output" before clicking the green "Run workflow" button.
+
 Currently, equation numbers via `pandoc-eqnos` are not supported for DOCX output.
 
 Format conversion is done using [Pandoc](https://pandoc.org/MANUAL.html).
@@ -20,12 +31,17 @@ To change the options, either edit the YAML files directly or add additional `--
 
 Note: currently, **Windows is not supported**.
 
-Install the [conda](https://conda.io) environment specified in [`environment.yml`](environment.yml) by running the following commands
+The Manubot environment is managed with [conda](https://conda.io).
+If you do not have `conda` installed, we recommend using the Miniforge3 (includes `conda`) or Mambaforge (includes `conda` and `mamba`) installers from [miniforge](https://github.com/conda-forge/miniforge).
+Install the environment from [`environment.yml`](environment.yml) by running one of following commands
 (from the repository's root directory):
 
 ```sh
-# Install the environment
+# Install the environment using conda
 conda env create --file build/environment.yml
+
+# Install the environment using mamba (faster)
+mamba env create --file build/environment.yml
 ```
 
 If the `manubot` environment is already installed, but needs to be updated to reflect changes to `environment.yml`, use one of the following options:
@@ -38,6 +54,9 @@ conda env update --file build/environment.yml
 # Slower than option 1, but guarantees a fresh environment.
 conda env remove --name manubot
 conda env create --file build/environment.yml
+
+# option 3: reinstall the manubot environment faster using mamba.
+mamba env create --force --file build/environment.yml
 ```
 
 Activate with `conda activate manubot` (assumes `conda` version of [at least](https://github.com/conda/conda/blob/9d759d8edeb86569c25f6eb82053f09581013a2a/CHANGELOG.md#440-2017-12-20) 4.4).

build/environment.yml

@@ -7,6 +7,7 @@ dependencies:
   - ghp-import=2.1.0
   - jinja2=3.1.2
   - jsonschema=4.17.0
+  - librsvg=2.52.5
   - pandoc=2.19.2
   - pango=1.48.10
   - pip=22.3.1

content/00.front-matter.md

@@ -52,7 +52,7 @@ Published: {{manubot.date_long}}
   {%- endif %}
   {%- if author.mastodon is defined and author.mastodon is not none and author["mastodon-server"] is defined and author["mastodon-server"] is not none %}
     {%- set has_ids = true %}
-    · ![Mastodon icon](images/mastodon.svg){.inline_icon}
+    · ![Mastodon icon](images/mastodon.svg){.inline_icon width=16 height=16}
     [\@{{author.mastodon}}@{{author["mastodon-server"]}}](https://{{author["mastodon-server"]}}/@{{author.mastodon}})
   {%- endif %}
   {%- if has_ids %}

setup.bash

@@ -15,7 +15,7 @@ echo "OWNER and REPO refer to the details of your manuscript repo location:"
 echo "i.e. https://github.com/OWNER/REPO."
 echo
 echo "Options:"
-echo "  -o --owner   GitHub user or organisation name."
+echo "  -o --owner   GitHub user or organization name."
 echo "  -r --repo    Name of the repository for your new manuscript."
 echo "  -y --yes     Non-interactive mode. Continue script without asking for confirmation that the repo exists."
 echo "  -s --ssh     Use SSH to authenticate GitHub account. HTTPS is used by default."
@@ -104,7 +104,7 @@ if [ -z "${OWNER}" ] || [ -z "${REPO}" ]; then
   echo "First, we need to specify where to create the GitHub repo for your manuscript."
   echo
   echo "The URL will take this format: https://github.com/OWNER/REPO."
-  echo "OWNER is your username or organisation"
+  echo "OWNER is your username or organization"
   echo "REPO is the name of your repository"
   echo
   read -r -p "Type in the OWNER now:" input
@@ -188,13 +188,13 @@ fi
 case $AUTH in
   0)
   echo
-  echo "Seting origin URL using its https web address"
+  echo "Setting origin URL using its https web address"
   echo
   git remote set-url origin https://github.com/${OWNER}/${REPO}.git
   ;;
   1)
   echo
-  echo "Seting origin URL using SSH"
+  echo "Setting origin URL using SSH"
   echo
   git remote set-url origin git@github.com:$OWNER/$REPO.git
   ;;