| name | papersmart-init |
| description | Initialize a PaperSmart scientific-manuscript workspace or a new PaperSmart project folder in English or Chinese, including the projects/shared directory model, required draft/reference/output/config/log templates, writing_samples, language profile, and companion skills. Use when the user asks to set up PaperSmart, create the base file system, choose English or Chinese workspace mode, scaffold a manuscript project, install dependencies, or prepare a reusable PaperSmart workspace for other users. |
PaperSmart-init
Overview
Set up the PaperSmart working environment before any manuscript writing. Preserve the separation between paper-specific project files and reusable cross-project resources.
Use scripts/init_papersmart.py for first-time filesystem setup. For routine new papers after the workspace exists, use PaperSmart-new-project.
Language Mode
Before running initialization, ask the user which workspace language to use:
- English folders and templates: default.
- 中文文件夹和模板：用户明确选择中文时使用。
Store the choice in shared/memory/papersmart_profile.md for English mode or 共享/记忆/papersmart_profile.md for Chinese mode. Later PaperSmart skills must read this profile first and answer in the configured output language.
Inputs
- Workspace root, defaulting to the current directory.
- Optional project slug, for example
paper_01_digital_doppelganger.
- Optional working title, target journal, manuscript language, and short research objective.
- Optional instruction to install companion skills immediately.
Directory Contract
Create this workspace shape:
projects/
README.md
shared/
README.md
docs/
prompts/
tools/
skills/
memory/
When a project slug is provided, create:
projects/<project_slug>/
README.md
config/project_config.md
logs/writing_log.md
logs/decision_log.md
01_draft/README.md
01_draft/data_inventory.md
01_draft/data/
01_draft/figures/
01_draft/tables/
01_draft/notes/
02_reference/README.md
02_reference/style_notes.md
02_reference/reference_index.md
02_reference/literature/
02_reference/target_journal/
02_reference/writing_samples/
03_output/README.md
03_output/manuscript/
03_output/tables/
03_output/figures/
03_output/supplement/
03_output/revision/change_log.md
03_output/revision/local_revision_tasks.md
03_output/translation/
03_output/submission/
Do not put project-specific drafts, data, outputs, revision records, or submission packages in shared/.
Chinese mode uses translated folder and template names, including 项目/, 共享/, 01_草稿/, 02_参考/写作样本/, and 03_输出/.
Workflow
- Confirm the workspace language. Use English if the user does not choose.
- Identify whether the task is workspace initialization or new-project scaffolding. If the user only asks for base setup, create the workspace roots without a project folder.
- If creating a project and multiple naming choices are possible, choose a short lowercase slug from the title. Use
paper_XX_short_slug when the user has not specified a naming convention.
- Run the script:
python shared/skills/papersmart-init/scripts/init_papersmart.py --workspace . --language en --project-slug paper_01_short_slug --project-title "Working title"
Add --install-skills when the user asks for dependency installation and network access is allowed:
python shared/skills/papersmart-init/scripts/init_papersmart.py --workspace . --language zh --install-skills
If the user's assistant stores skills in a known custom location, pass it explicitly:
python shared/skills/papersmart-init/scripts/init_papersmart.py --workspace . --language en --install-skills --skills-dir "<skills-dir>"
- Confirm that the script did not overwrite original user materials. Existing files should be preserved unless the user explicitly requested replacement.
- If companion skill installation fails, write the exact manual commands to the workspace memory folder.
Companion Skills
PaperSmart works best with these companion skills:
find-skills, used to choose the smallest useful skill set for a manuscript task.humanizer, used when the user wants writing to sound less machine-generated.- Nature-family academic skills, especially
nature-academic-search, nature-writing, nature-polishing, nature-figure, nature-citation, nature-response, nature-data, nature-reader, and nature-paper2ppt.
Installation sources used by the script:
find-skills: https://github.com/vercel-labs/skills/tree/main/skills/find-skillshumanizer: https://github.com/blader/humanizer- Nature skills:
https://github.com/Yuan1z0825/nature-skills
The script first checks whether those skill folders already exist under the local assistant skills directory. Skip installation for skills that are already present.
Project Templates
Use precise TODO: markers instead of guessing missing details. Template files should capture:
- Working title, article type, target journal, language, authors, study objective, research questions, methods, data sources, ethics, funding, conflicts, acknowledgements, and missing information in
config/project_config.md.
- Source materials, known datasets, table/figure inventories, known data-quality issues, and expected comparisons in
01_draft/data_inventory.md.
- Journal format, writing style, heading style, abstract length, citation style, table/figure rules, and submission constraints in
02_reference/style_notes.md or the Chinese equivalent.
- Literature anchors, target-journal files, writing samples, PDFs, citation files, and "style only, do not cite" notes in
02_reference/reference_index.md or the Chinese equivalent.
Handoff
After initialization, tell the user:
- The workspace or project path created.
- Which companion skills are installed, already present, or still missing.
- Where to place original materials:
01_draft/01_草稿 for user materials and 02_reference/02_参考 for style and literature context.
- That generated outputs must go to
03_output/03_输出.
- To use
PaperSmart-new-project for future papers instead of rerunning full initialization.
