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‎USAGE.md‎
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‎build/environment.yml‎
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@@ -0,0 +1,66 @@
+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'
+      branch_name:
+        description: 'Output branch'
+        required: true
+        type: string
+        default: 'ai-revision-davinci'
+
+jobs:
+  ai-revise:
+    name: AI Revise
+    runs-on: ubuntu-latest
+    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 }}
+          # 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
@@ -329,6 +329,32 @@ Potential spelling errors will be printed in the continuous integration log alon
 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, fixing spelling and grammar errors, and improving 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."
+
+By default, the tool uses the model `text-davinci-003`.
+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).
@@ -344,6 +370,14 @@ 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.
 
@@ -20,7 +20,7 @@ dependencies:
   - pip:
     - cffi==1.15.0
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@82f25cb8d698a12d69e533686867a8a4afd35c4c
+    - git+https://github.com/manubot/manubot@d4242ffa4194e4a13a68c5f6466feff559d3f9d5
     - isbnlib==3.10.10
     - opentimestamps-client==0.7.1
     - opentimestamps==0.4.3