Merge pull request #1214 from greenelab/rootstock-2024-01-14

Update rootstock on 2024-01-14

.appveyor.yml

@@ -20,7 +20,7 @@ only_commits:
     - ci/install.sh
     - content/
 
-image: ubuntu
+image: ubuntu2204
 services:
   - docker
 

.github/workflows/ai-revision.yaml

@@ -0,0 +1,75 @@
+name: ai-revision
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: 'Branch to revise'
+        required: true
+        type: string
+        default: 'main'
+      file_names:
+        description: 'File names to revise'
+        required: false
+        type: string
+        default: ''
+      model:
+        description: 'Language model'
+        required: true
+        type: string
+        default: 'text-davinci-003'
+      custom_prompt:
+        description: 'Custom prompt'
+        required: false
+        type: string
+        default: ''
+      branch_name:
+        description: 'Output branch'
+        required: true
+        type: string
+        default: 'ai-revision-davinci'
+
+jobs:
+  ai-revise:
+    name: AI Revise
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    defaults:
+      run:
+        shell: bash --login {0}
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+        with: 
+          ref: ${{ inputs.branch }} 
+      - name: Install environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install Manubot AI revision dependencies
+        run: |
+          # install using the same URL used for manubot in build/environment.yml
+          manubot_line=$(grep "github.com/manubot/manubot" build/environment.yml)
+          manubot_url=$(echo "$manubot_line" | awk -F"- " '{print $2}')
+
+          pip install ${manubot_url}#egg=manubot[ai-rev]
+      - name: Revise manuscript
+        env:
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          AI_EDITOR_LANGUAGE_MODEL: ${{ inputs.model }}
+          AI_EDITOR_FILENAMES_TO_REVISE: ${{ inputs.file_names }}
+          AI_EDITOR_CUSTOM_PROMPT: ${{ inputs.custom_prompt }}
+          # More variables can be specified to control the behavior of the model:
+          #  https://github.com/manubot/manubot-ai-editor/blob/main/libs/manubot_ai_editor/env_vars.py
+        run: manubot ai-revision --content-directory content/
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v4
+        with:
+          commit-message: 'revise using AI model\n\nUsing the OpenAI model ${{ inputs.model }}'
+          title: 'AI-based revision using ${{ inputs.model }}'
+          author: OpenAI model ${{ inputs.model }} <support@openai.com>
+          add-paths: |
+            content/*.md
+          branch: ${{ inputs.branch_name }}
+          draft: true

.github/workflows/manubot.yaml

@@ -42,6 +42,8 @@ jobs:
   manubot:
     name: Manubot
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     env:
       GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }}
       LITSEARCH: false
@@ -91,7 +93,9 @@ 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

@@ -271,6 +271,8 @@ name: Daniel S. Himmelstein  # mandatory
 initials: DSH  # optional
 orcid: 0000-0002-3012-7446  # mandatory
 twitter: dhimmel  # optional
+mastodon: dhimmel  # optional: mastodon username
+mastodon-server: genomic.social  # optional: mastodon server (instance)
 email: daniel.himmelstein@gmail.com  # suggested
 corresponding: true  # optional, if set to true displays author's email for correspondence (not used in this project)
 affiliations:  # as a list, at least one line with institution, city, and country required
@@ -349,13 +351,55 @@ 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.
 Potential spelling errors will be printed in the continuous integration log along with the files and line numbers in which they appeared.
 Words in `build/assets/custom-dictionary.txt` are ignored during spellchecking.
 Spellchecking is currently only supported for English language manuscripts.
 
+## AI-assisted authoring
+
+The workflow [`ai-revision`](.github/workflows/ai-revision.yaml) is available to assist authors in writing their manuscripts.
+It uses large language models to revise the manuscript text, fix spelling and grammar errors, and improve the sentence structure and the writing style with section-specific prompts.
+It is manually triggered by the user (it never runs automatically), and it generates a pull request with suggested revisions.
+Then the user can review these changes and merge the pull request if they are acceptable.
+More information about this tool is available in [this manuscript](https://greenelab.github.io/manubot-gpt-manuscript/).
+
+You need to change your repository settings to 1) provide a secret with name `OPENAI_API_KEY` containing your OpenAI API token, and 2) allow workflows to create pull requests.
+For 1), go to the settings page and, within "Secrets and variables," select "Actions."
+Next, create a repository secret with the name `OPENAI_API_KEY` and the value of the API token (you can also do this using "Organization secrets" if available).
+For 2), go to "Actions", "General", "Workflow permissions", and activate the checkbox "Allow GitHub Actions to create and approve pull requests."
+
+Additionally, you also need to decide which type of prompts you want to use.
+"Prompts" are the instructions given to the language model to revise your manuscript.
+Basically, you can select 1) the default set of section-specific prompts already provided by the tool, or 2) a custom prompt that you provide.
+For 1), you can check [this manuscript](https://greenelab.github.io/manubot-gpt-manuscript/) for a more detailed description of the section-specific prompts.
+These prompts are already provided, but they need to know the section of each of your Markdown files (for instance, if it is the abstract, or the introduction, etc.).
+For this, the tool will try to infer them from the file names automatically, and if this fails, the tool might not revise all of your files.
+In this case, you need to indicate the section of each file using the "section mapping" environment variable that is described [here](https://github.com/manubot/manubot-ai-editor/blob/main/libs/manubot_ai_editor/env_vars.py) (read the header of the file for more instructions).
+For 2), you can provide your own custom prompt, which will be used for all the files regardless of their section.
+For example, instead of the more complex section-specific prompts in 1), you might just want to perform simpler revision tasks.
+An example of a custom prompt is "proofread the following paragraph".
+You can provide your custom prompt when you manually trigger the workflow by using the "Custom prompt" field.
+This could be more appropriate if you are testing different prompts.
+To set a fixed prompt for all runs, read the documentation [here](https://github.com/manubot/manubot-ai-editor/blob/main/libs/manubot_ai_editor/env_vars.py) to set the "custom prompt" environment variable.
+
+By default, the tool uses the model `text-davinci-003`, but you are encouraged to check the [OpenAI documentation](https://platform.openai.com/docs/models) to see which models are available, which one is the most suitable for your manuscript, and [whether our tool supports it](https://github.com/manubot/manubot-ai-editor).
+Make sure to check the [pricing](https://openai.com/api/pricing/) of the OpenAI API.
+With $0.02 per 1000 tokens using the most powerful AI models, the cost for a revision of a standard manuscript (around 35 paragraphs) should be around $0.50.
+The workflow allows specifying the branch and file names (in the `content/` directory) to revise, the language model to use, and the output branch name.
+Internally, the workflow uses the tool [Manubot AI Editor](https://github.com/manubot/manubot-ai-editor) to revise the manuscript.
+For more advanced users, the behavior of the Manubot AI Editor or the parameters used for the language model can be changed using environment variables.
+These variables can be changed in the workflow file (`ai-revision.yaml`).
+
+It is important to note that using language models in scientific writing is a matter of debate among researchers and journal editors.
+Therefore, it's advisable to follow the guidelines that journals and the research community propose.
+For example, the *Nature* journal has published [rules about using language models in scholarly writing](https://www.nature.com/articles/d41586-023-00191-1), such as not listing the tools as authors and documenting how they were used.
+Since a Manubot-based manuscript uses GitHub, one approach consists of linking the AI-generated pull request, which will transparently show the changes suggested by the AI tool.
+
 ## Manubot feedback
 
 If you experience any issues with the Manubot or would like to contribute to its source code, please visit [`manubot/manubot`](https://github.com/manubot/manubot) or [`manubot/rootstock`](https://github.com/manubot/rootstock).
@@ -371,6 +415,14 @@ DOI: [10.1371/journal.pcbi.1007128](https://doi.org/10.1371/journal.pcbi.1007128
 
 The Manubot version of this manuscript is available at <https://greenelab.github.io/meta-review/>.
 
+To cite the Manubot AI Editor or for more information on its design, see `@doi:10.1101/2023.01.21.525030`:
+
+> **A publishing infrastructure for AI-assisted academic authoring**<br>
+Milton Pividori, Casey S. Greene<br>
+*bioRxiv* (2023) <https://doi.org/grpf8m><br>
+DOI: [10.1101/2023.01.21.525030](https://doi.org/10.1101/2023.01.21.525030)
+
+
 ## Acknowledgments
 
 We would like to thank the contributors and funders whose support makes the Manubot project possible.

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).
@@ -24,12 +35,17 @@ The individual manuscripts to build are specified in the file `content/individua
 
 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:
@@ -42,6 +58,9 @@ 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
   - pandas=1.5.2
   - pandoc=2.19.2
   - pango=1.48.10
@@ -21,7 +22,7 @@ dependencies:
   - pip:
     - cffi==1.15.0
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@82f25cb8d698a12d69e533686867a8a4afd35c4c
+    - git+https://github.com/manubot/manubot@6e6f6a5aac381120faf3ef02e594b5babc77da2b
     - isbnlib==3.10.10
     - opentimestamps-client==0.7.1
     - opentimestamps==0.4.3

ci/install.sh

@@ -7,16 +7,16 @@
 set -o errexit \
     -o pipefail
 
-wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-$(uname)-$(uname -m).sh \
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh \
   --output-document miniforge.sh
 bash miniforge.sh -b -p $HOME/miniconda
 source $HOME/miniconda/etc/profile.d/conda.sh
 hash -r
 conda config \
   --set always_yes yes \
   --set changeps1 no
-conda env create --quiet --file build/environment.yml
-conda list --name manubot
+mamba env create --quiet --file build/environment.yml
+mamba list --name manubot
 conda activate manubot
 
 # Install Spellcheck filter for Pandoc