feat(examples): add scientific writing examples (CAJAL re-implementation) (#1644)

Re-implements the CAJAL / scientific-paper functionality that was reverted
from the core SDK (PR #1611 / revert #1641) as proper examples per AGENTS.md:

- examples/scientific_writing/scientific_writer.py
  Single-agent pattern: regular Agent + @tool functions, no subclass.
  Uses the CAJAL-4B HuggingFace model via litellm.

- examples/scientific_writing/multi_agent_paper.py
  Multi-agent workflow: Literature Reviewer -> Methodologist -> Writer
  composed with AgentTeam + sequential Tasks (no custom Agent classes).

- examples/scientific_writing/agents.yaml
  YAML parity for the multi-agent workflow (AGENTS.md §7 '3-way' rule).

Why this location:
- AGENTS.md §4.1: core SDK has no heavy domain implementations.
- AGENTS.md §4.4: compose specialised Agents + tools, don't subclass Agent.
- AGENTS.md §6.1: domain-specific behaviour belongs in @tool functions.
- Wrapper / praisonai-tools were alternatives; examples/ keeps it
  discoverable and avoids bloating either package.

Co-authored-by: praisonai-bot <[email protected]>

examples/scientific_writing/agents.yaml

@@ -0,0 +1,40 @@
+# Scientific paper workflow — YAML equivalent of multi_agent_paper.py
+# Run with:
+#   praisonai agents run --file examples/scientific_writing/agents.yaml
+framework: praisonai
+topic: "Climate change effects on coral reef biodiversity"
+
+roles:
+  literature_reviewer:
+    role: "Literature Reviewer"
+    goal: "Survey recent academic work on {topic} and produce an APA review."
+    backstory: "Expert in academic literature surveying and citation hygiene."
+    llm: "gpt-4o-mini"
+    tasks:
+      review_literature:
+        description: "Produce a concise literature review with 5-8 APA citations."
+        expected_output: "APA-formatted literature review."
+
+  methodology_designer:
+    role: "Methodology Designer"
+    goal: "Design a reproducible research methodology for {topic}."
+    backstory: "Specialises in rigorous experimental design."
+    llm: "gpt-4o-mini"
+    tasks:
+      design_methodology:
+        description: "Write a reproducible methods section in LaTeX."
+        expected_output: "LaTeX methods section."
+
+  scientific_writer:
+    role: "Scientific Writer"
+    goal: "Assemble the final LaTeX paper on {topic}."
+    backstory: >-
+      Specialised in LaTeX-formatted academic papers, fine-tuned on
+      scientific literature (CAJAL-4B checkpoint).
+    llm: "huggingface/Agnuxo/CAJAL-4B-P2PCLAW"
+    tasks:
+      write_paper:
+        description: >-
+          Combine the literature review and methodology into a full
+          scientific paper on {topic}. Use LaTeX formatting.
+        expected_output: "Complete LaTeX paper."

examples/scientific_writing/multi_agent_paper.py

@@ -0,0 +1,73 @@
+"""Multi-agent scientific paper workflow (Researcher -> Methodologist -> Writer).
+
+Demonstrates the agent-centric pattern from AGENTS.md: compose specialised
+Agents with ``AgentTeam`` + sequential ``Task``s instead of creating custom
+Agent subclasses.  The writer uses the CAJAL-4B HuggingFace model; the
+reviewer and methodologist use general-purpose LLMs.
+
+Usage:
+    python examples/scientific_writing/multi_agent_paper.py
+"""
+from praisonaiagents import Agent, AgentTeam, Task
+
+from scientific_writer import (  # noqa: E402 — example imports a sibling file
+    build_scientific_writer,
+    format_citation,
+    format_latex_section,
+)
+
+
+literature_reviewer = Agent(
+    name="Literature Reviewer",
+    instructions=(
+        "You are an expert at surveying academic literature. "
+        "Produce a concise literature review with 5-8 key citations in APA."
+    ),
+    tools=[format_citation],
+)
+
+methodology_designer = Agent(
+    name="Methodology Designer",
+    instructions=(
+        "You design rigorous research methodologies. "
+        "Output a clear, reproducible methods section."
+    ),
+    tools=[format_latex_section],
+)
+
+scientific_writer = build_scientific_writer()
+
+
+def run(topic: str) -> str:
+    """Run the 3-agent workflow for a given research ``topic``."""
+    t1 = Task(
+        name="review_literature",
+        description=f"Review literature on: {topic}",
+        agent=literature_reviewer,
+        expected_output="APA literature review.",
+    )
+    t2 = Task(
+        name="design_methodology",
+        description=f"Design research methodology for: {topic}",
+        agent=methodology_designer,
+        expected_output="LaTeX methods section.",
+    )
+    t3 = Task(
+        name="write_paper",
+        description=(
+            f"Combine the literature review and methodology into a full "
+            f"scientific paper on: {topic}. Use LaTeX formatting."
+        ),
+        agent=scientific_writer,
+        expected_output="Complete LaTeX paper.",
+    )
+    team = AgentTeam(
+        agents=[literature_reviewer, methodology_designer, scientific_writer],
+        tasks=[t1, t2, t3],
+    )
+    return team.start()
+
+
+if __name__ == "__main__":
+    result = run("Transformer architectures for protein folding prediction")
+    print(result)

examples/scientific_writing/scientific_writer.py

@@ -0,0 +1,85 @@
+"""Scientific Paper Writer — single-agent example using the CAJAL model.
+
+CAJAL (``Agnuxo/CAJAL-4B-P2PCLAW``) is a 4B-parameter HuggingFace model
+specialised for LaTeX-formatted academic writing.  This example shows how
+to use it with a regular ``Agent`` and ``@tool`` functions — no new Agent
+subclass is needed.  Run 3 ways: Python (this file), CLI, or YAML.
+
+Requirements:
+    pip install "praisonaiagents[llm]"          # for litellm / HuggingFace
+    export HUGGINGFACE_API_KEY=...              # or run a local inference server
+
+Usage:
+    python examples/scientific_writing/scientific_writer.py
+"""
+from praisonaiagents import Agent, tool
+
+
+@tool
+def format_latex_section(title: str, content: str) -> str:
+    """Wrap prose content in a LaTeX ``\\section{}`` block.
+
+    Args:
+        title: Section heading (e.g. ``"Introduction"``).
+        content: The body text.
+
+    Returns:
+        LaTeX-formatted section string.
+    """
+    return f"\\section{{{title}}}\n{content}\n"
+
+
+@tool
+def format_citation(authors: str, year: int, title: str, venue: str) -> str:
+    """Render a single APA-style citation line.
+
+    Args:
+        authors: ``"Smith, J. & Jones, A."``
+        year: Publication year.
+        title: Paper title.
+        venue: Journal / conference name.
+
+    Returns:
+        One APA-formatted citation string.
+    """
+    return f"{authors} ({year}). {title}. *{venue}*."
+
+
+SCIENTIFIC_INSTRUCTIONS = """You are a specialised scientific paper writer.
+
+Produce high-quality academic content with:
+- Clear structure (Abstract, Introduction, Methodology, Results, Discussion,
+  Conclusion, References)
+- Rigorous methodology and precise language
+- Proper APA citations and LaTeX formatting
+- Honest limitations and future work sections
+
+Use ``format_latex_section`` to wrap each section in LaTeX, and
+``format_citation`` to build the References list.
+"""
+
+
+def build_scientific_writer(
+    model: str = "huggingface/Agnuxo/CAJAL-4B-P2PCLAW",
+) -> Agent:
+    """Construct a scientific-writing Agent.
+
+    Override ``model`` for any HuggingFace / local / API model — the default
+    targets the CAJAL-4B checkpoint for LaTeX-style academic output.
+    """
+    return Agent(
+        name="Scientific Writer",
+        instructions=SCIENTIFIC_INSTRUCTIONS,
+        llm=model,
+        tools=[format_latex_section, format_citation],
+    )
+
+
+if __name__ == "__main__":
+    agent = build_scientific_writer()
+    paper = agent.start(
+        "Write a short scientific paper (Abstract + Introduction + Conclusion) "
+        "on 'Climate change effects on coral reef biodiversity'. "
+        "Use LaTeX formatting and include at least 3 APA citations."
+    )
+    print(paper)