scientify 1.2.2 → 1.3.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "scientify",
-  "version": "1.2.2",
+  "version": "1.3.0",
   "description": "Scientify - AI-powered research workflow automation for OpenClaw. Includes idea generation, literature review, research pipeline skills, and arxiv tool.",
   "type": "module",
   "main": "dist/index.js",

package/skills/_shared/workspace-spec.md

@@ -0,0 +1,129 @@
+# Workspace Directory Specification
+
+All Scientify skills share a unified project-based workspace structure.
+
+## Base Path
+
+```
+~/.openclaw/workspace/projects/
+├── .active                      # Current project ID (plain text)
+├── {project-id}/                # Each research topic has its own project
+│   └── ...
+└── {another-project}/
+```
+
+## Project Structure
+
+```
+~/.openclaw/workspace/projects/{project-id}/
+├── project.json                 # Project metadata
+├── task.json                    # Research task definition
+│
+├── survey/                      # /literature-survey outputs
+│   ├── search_terms.json        # Generated search keywords
+│   ├── raw_results.json         # All search results
+│   ├── filtered_papers.json     # Papers with relevance scores
+│   ├── clusters.json            # Clustered by research direction
+│   └── report.md                # Final survey report
+│
+├── papers/                      # Downloaded paper sources
+│   ├── {direction-1}/           # Organized by cluster
+│   │   ├── paper_list.md
+│   │   └── {arxiv_id}/          # .tex source files
+│   ├── {direction-2}/
+│   └── uncategorized/
+│
+├── repos/                       # Cloned reference repositories
+│   ├── {repo-name-1}/
+│   └── {repo-name-2}/
+│
+├── ideas/                       # /idea-generation outputs
+│   ├── gaps.md                  # Identified research gaps
+│   ├── idea_1.md ... idea_5.md  # Generated ideas
+│   ├── selected_idea.md         # Enhanced best idea
+│   ├── implementation_report.md # Code mapping
+│   └── summary.md               # Final summary
+│
+├── review/                      # /write-review-paper outputs
+│   ├── reading_plan.md          # Prioritized reading list
+│   ├── notes/                   # Per-paper reading notes
+│   │   └── {paper_id}.md
+│   ├── comparison.md            # Method comparison table
+│   ├── timeline.md              # Research timeline
+│   ├── taxonomy.md              # Classification system
+│   ├── draft.md                 # Survey paper draft
+│   └── bibliography.bib         # References
+│
+├── plan_res.md                  # /research-pipeline: implementation plan
+├── project/                     # /research-pipeline: code implementation
+│   ├── model/
+│   ├── data/
+│   ├── training/
+│   ├── testing/
+│   ├── run.py
+│   └── requirements.txt
+├── iterations/                  # Review iterations
+│   ├── judge_v1.md
+│   └── judge_v2.md
+└── experiment_res.md            # Final results
+```
+
+## Conventions
+
+### File Existence = Step Completion
+
+Check output file before executing any step. If exists, skip.
+
+Enables:
+- **Crash recovery**: resume from last completed step
+- **Incremental progress**: rerunning skips completed work
+- **Transparency**: inspect progress by listing directory
+
+### Project Metadata
+
+**project.json:**
+```json
+{
+  "id": "battery-rul-prediction",
+  "name": "Battery RUL Prediction",
+  "created": "2024-01-15T10:00:00Z",
+  "topics": ["battery", "remaining useful life", "prediction"]
+}
+```
+
+**task.json:**
+```json
+{
+  "domain": "battery health",
+  "focus": "RUL prediction using transformer",
+  "date_limit": "2024-01-01",
+  "created": "2024-01-15"
+}
+```
+
+### Immutability
+
+Once written, do NOT modify outputs unless user explicitly asks.
+Exception: `project/` is mutable during implement-review-iterate loop.
+
+### Active Project
+
+```bash
+# Read active project
+cat ~/.openclaw/workspace/projects/.active
+
+# Set active project
+echo "battery-rul-prediction" > ~/.openclaw/workspace/projects/.active
+
+# Set $WORKSPACE variable
+WORKSPACE=~/.openclaw/workspace/projects/$(cat ~/.openclaw/workspace/projects/.active)
+```
+
+## Skill Outputs Summary
+
+| Skill | Primary Outputs |
+|-------|-----------------|
+| `/literature-survey` | `survey/`, `papers/` |
+| `/idea-generation` | `ideas/` |
+| `/write-review-paper` | `review/` |
+| `/research-pipeline` | `project/`, `iterations/`, `experiment_res.md` |

package/skills/idea-generation/SKILL.md

@@ -17,6 +17,8 @@ Generate innovative research ideas grounded in literature analysis. This skill r
 
 **Core principle:** Ideas MUST be grounded in actual papers, not generated from model knowledge.
 
+**Workspace:** See `../_shared/workspace-spec.md` for directory structure. Outputs go to `$WORKSPACE/ideas/`.
+
 ---
 
 ## Step 1: Check Workspace Resources

package/skills/literature-survey/SKILL.md

@@ -14,6 +14,8 @@ metadata:
 
 Comprehensive literature discovery workflow for a research domain. This skill searches broadly, filters by relevance, clusters by direction, and iterates to ensure complete coverage.
 
+**Workspace:** See `../_shared/workspace-spec.md` for directory structure. Outputs go to `$WORKSPACE/survey/` and `$WORKSPACE/papers/`.
+
 ## Architecture: Isolated Sub-agent
 
 This survey runs in an **isolated sub-session** to avoid context pollution. The main session only receives the final report.

package/skills/research-pipeline/SKILL.md

@@ -13,44 +13,22 @@ metadata:
 
 # Research Pipeline
 
-Automate an end-to-end ML research workflow: idea -> literature search -> survey -> plan -> implement -> review -> iterate.
+Automate an end-to-end ML research workflow: idea → literature → survey → plan → implement → review → iterate.
 
-All intermediate results live in a project-based workspace directory. **File existence = step completion.** If a step's output file already exists, skip that step and move on. This enables crash recovery and incremental progress.
+**Workspace:** See `../_shared/workspace-spec.md` for directory structure. Outputs go to `$WORKSPACE/project/`, `$WORKSPACE/iterations/`.
 
----
+**File existence = step completion.** Skip steps whose output already exists.
 
-## Workspace Convention (Project-based)
+---
 
-**IMPORTANT**: This skill uses the same project-based workspace as `idea-generation`. Check or set the active project first.
+## Step 0: Check Active Project
 
-### Check Active Project
 ```bash
 cat ~/.openclaw/workspace/projects/.active 2>/dev/null
 ```
 
-If a project is active, set `$WORKSPACE = ~/.openclaw/workspace/projects/{project_id}/`.
-
-If no active project exists, create one based on the research idea (see Step 1).
-
-### Directory Structure
-```
-$WORKSPACE/
-├── project.json          # Project metadata
-├── task.json             # Research task/idea definition
-├── search_results.md     # Search results (Step 2)
-├── prepare_res.md        # Selected repos (Step 3)
-├── papers/               # Downloaded papers (Step 4)
-├── repos/                # Cloned repositories (Step 3)
-├── notes/                # Paper notes (Step 5)
-├── survey_res.md         # Literature survey (Step 5)
-├── plan_res.md           # Implementation plan (Step 6)
-├── project/              # Code implementation (Step 7)
-├── ml_res.md             # Implementation report (Step 7)
-├── iterations/           # Review iterations (Step 8-9)
-│   ├── judge_v1.md
-│   └── ...
-└── experiment_res.md     # Final results (Step 10)
-```
+If active, set `$WORKSPACE = ~/.openclaw/workspace/projects/{project_id}/`.
+If none, create based on research idea in Step 1.
 
 ---
 

package/skills/research-pipeline/references/workspace-spec.md

@@ -1,81 +1,5 @@
-# Workspace Directory Specification
+# Workspace Specification
 
-All research pipeline artifacts live in a `workspace/` directory. The location is either specified by the user or defaults to the current working directory plus `workspace/`.
+**This file has moved to the shared location.**
 
-## Directory Layout
-
-```
-workspace/
-  task.json                 # Input: research task definition
-  search_results.md         # Step 2: arxiv + github search results
-  prepare_res.md            # Step 3: selected repos and rationale
-  survey_res.md             # Step 5: synthesized literature survey
-  plan_res.md               # Step 6: four-part implementation plan
-  ml_res.md                 # Step 7: implementation report
-  experiment_res.md         # Step 10: full training results
-
-  repos/                    # Step 3: cloned reference repositories
-    repo-name-1/
-    repo-name-2/
-
-  papers/                   # Step 4: downloaded paper sources
-    2401.12345.tex
-    2401.67890.tex
-
-  notes/                    # Step 5: per-paper survey notes
-    paper_001.md
-    paper_002.md
-
-  iterations/               # Steps 8-9: review history
-    judge_v1.md
-    judge_v2.md
-
-  project/                  # Step 7: implementation code
-    model/
-    data/
-    training/
-    testing/
-    utils/
-    run.py
-    requirements.txt
-```
-
-## Conventions
-
-### File Existence = Step Completion
-
-The research pipeline uses file existence as the checkpoint mechanism. Before executing any step, check whether its output file already exists. If it does, skip the step.
-
-This enables:
-- **Crash recovery**: resume from the last completed step.
-- **Incremental progress**: re-running the pipeline skips completed work.
-- **Transparency**: a human can inspect progress by listing the directory.
-
-### Naming Rules
-
-- Markdown files (`.md`) for human-readable outputs.
-- JSON files (`.json`) for structured data (task definition).
-- Paper notes use sequential numbering: `paper_001.md`, `paper_002.md`.
-- Review iterations use version numbering: `judge_v1.md`, `judge_v2.md`.
-
-### Immutability
-
-Once a step's output is written, do NOT modify it unless the user explicitly asks. If a step needs to be re-done, delete the output file first, then re-execute.
-
-Exception: `workspace/project/` is mutable during the implement-review-iterate loop (Steps 7-9).
-
-### task.json Schema
-
-```json
-{
-  "idea": "A 1-3 sentence description of the research idea",
-  "references": ["2401.12345", "paper title string"],
-  "domain": "recommendation systems",
-  "date_limit": "2024-01-01"
-}
-```
-
-- `idea` (required): The core research idea to implement.
-- `references` (optional): ArXiv IDs or paper titles as starting points.
-- `domain` (optional): Research domain for focused searching.
-- `date_limit` (optional): Only consider papers published after this date.
+See: `../../_shared/workspace-spec.md` for the unified workspace specification used by all Scientify skills.

package/skills/write-review-paper/SKILL.md

@@ -14,6 +14,8 @@ metadata:
 
 Guide for writing a structured literature review or survey paper from papers you've already collected. This skill helps with reading strategy, note organization, and academic writing.
 
+**Workspace:** See `../_shared/workspace-spec.md` for directory structure. Outputs go to `$WORKSPACE/review/`.
+
 ## Prerequisites
 
 Before starting, ensure you have: