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Cross-cutting reference manager for medical manuscripts. Single entry point for citation-key validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, marker conversion (``[N]`` ↔ ``[@key]``), and native Zotero CWYW field-code injection. Replaces the inline reference-handling that previously lived in ``/write-paper`` Phase 7.6 and is reused by ``/revise``, ``/peer-review``, ``/sync-submission``, and any skill that produces a journal submission. Audit-only verification stays
One test taskI need to run an automated check to verify that all the [@citation_keys] referenced in my manuscript file actually exist in my BibTeX file so our build pipeline doesn't fail on missing keys. Please run the validation script for me.
Passed 20 of 22 test cases with the skill, and 3 of 22 without it.
and 17 more in the full report
17 fixed3 passed either way2 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
Pick what your agent runs on. You don't need a DecimalAI account.
No account or Python needed. Claude Code picks it up in its next session.
curl -fsSL --create-dirs -o .claude/skills/aperivue-manage-refs/SKILL.md https://app.decimal.ai/s/aperivue-manage-refs/SKILL.mdpip install "decimalai>=0.15"
decimalai skills add aperivue-manage-refs
claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"This gets SKILL.md only. The skill's 14 other files are not included. The other two ways bring them.
Type these in a Claude Code session. No account or API key. It writes the skill and any files it bundles, and asks first when its safety rating isn't Passed.
/plugin marketplace add decimal-labs/decimalai-claude-plugins
/plugin install decimalai@decimalai/decimalai:install aperivue-manage-refsThe plugin needs python3 and curl on your machine.
No tools at all. Claude Code picks it up in its next session.
.claude/skills/aperivue-manage-refs/SKILL.mdThis gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[claude-agent-sdk]"
decimalai skills add aperivue-manage-refsimport asyncio
from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
async def main():
question = "Hello!"
async with support.run(question) as run: # one user message, one run
async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[claude-agent-sdk]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import asyncio
from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
async def main():
question = "Hello!"
async with support.run(question) as run: # one user message, one run
async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdimport asyncio
from pathlib import Path
from claude_agent_sdk import ClaudeAgentOptions, query
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
options = ClaudeAgentOptions(system_prompt=f"You are a helpful agent.\n\n{skill}", max_turns=6)
async def main():
async for message in query(prompt="Hello!", options=options):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai-agents]"
decimalai skills add aperivue-manage-refsfrom agents import Agent, Runner
from decimalai.openai_agents import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
name=support.name,
instructions=support.instructions, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai-agents]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from agents import Agent, Runner
from decimalai.openai_agents import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
name=support.name,
instructions=support.instructions, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from agents import Agent, Runner
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = Agent(name="support", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai]"
decimalai skills add aperivue-manage-refsimport json
from openai import OpenAI
from decimalai.openai import agent_config
client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
# run.system is your prompt, then the skill list.
messages = [{"role": "system", "content": run.system}, run.message]
while True:
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=messages,
tools=[*TOOLS, *run.tools], # your tools, then load_skill
).choices[0].message
messages.append(reply)
if not reply.tool_calls:
break
for call in reply.tool_calls:
# load_skill is answered by the run; your own tools by FUNCTIONS.
function = FUNCTIONS.get(call.function.name)
messages.append(run.tool_result(call) or {
"role": "tool", "tool_call_id": call.id,
"content": function(**json.loads(call.function.arguments)) if function
else f"There is no tool named {call.function.name!r}.",
})
print(reply.content)
# The Responses API takes run.response_tools instead of run.tools.The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import json
from openai import OpenAI
from decimalai.openai import agent_config
client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
# run.system is your prompt, then the skill list.
messages = [{"role": "system", "content": run.system}, run.message]
while True:
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=messages,
tools=[*TOOLS, *run.tools], # your tools, then load_skill
).choices[0].message
messages.append(reply)
if not reply.tool_calls:
break
for call in reply.tool_calls:
# load_skill is answered by the run; your own tools by FUNCTIONS.
function = FUNCTIONS.get(call.function.name)
messages.append(run.tool_result(call) or {
"role": "tool", "tool_call_id": call.id,
"content": function(**json.loads(call.function.arguments)) if function
else f"There is no tool named {call.function.name!r}.",
})
print(reply.content)
# The Responses API takes run.response_tools instead of run.tools.No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from openai import OpenAI
client = OpenAI()
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=[
{"role": "system", "content": f"You are a helpful agent.\n\n{skill}"},
{"role": "user", "content": "Hello!"},
],
).choices[0].messageThis gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[anthropic]"
decimalai skills add aperivue-manage-refsimport anthropic
from decimalai.anthropic import agent_config
client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
question = "Hello!"
with support.run(question) as run: # one user message, one run
answer = client.beta.messages.tool_runner(
model="claude-haiku-5-5",
max_tokens=4096,
system=run.system, # your prompt, then the skill list
tools=[*run.tools], # your tools, then load_skill
messages=[{"role": "user", "content": question}],
).until_done()The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[anthropic]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import anthropic
from decimalai.anthropic import agent_config
client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
question = "Hello!"
with support.run(question) as run: # one user message, one run
answer = client.beta.messages.tool_runner(
model="claude-haiku-5-5",
max_tokens=4096,
system=run.system, # your prompt, then the skill list
tools=[*run.tools], # your tools, then load_skill
messages=[{"role": "user", "content": question}],
).until_done()No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
import anthropic
client = anthropic.Anthropic()
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
reply = client.messages.create(
model="claude-haiku-5-5",
max_tokens=4096,
system=f"You are a helpful agent.\n\n{skill}",
messages=[{"role": "user", "content": "Hello!"}],
)This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[google-genai]"
decimalai skills add aperivue-manage-refsfrom google import genai
from google.genai import types
from decimalai.google_genai import agent_config
client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
config = types.GenerateContentConfig(
system_instruction=run.system, # your prompt, then the skill list
tools=[*TOOLS, *run.tool_params], # your functions, then load_skill
)
contents = [{"role": "user", "parts": [{"text": run.message}]}]
while True:
response = client.models.generate_content(
model="gemini-3.5-flash", contents=contents, config=config,
)
if not response.function_calls:
break
contents.append(response.candidates[0].content)
parts = []
for call in response.function_calls:
# load_skill is answered by the run; your own functions by FUNCTIONS.
# A loop of your own rather than automatic function calling, which
# raises KeyError when the model asks for a function you did not pass.
function = FUNCTIONS.get(call.name)
parts.append(run.tool_result(call) or {"function_response": {
"name": call.name, "id": call.id,
"response": {"result": function(**(call.args or {})) if function
else f"There is no function named {call.name!r}."},
}})
contents.append({"role": "user", "parts": parts})
print(response.text)The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[google-genai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from google import genai
from google.genai import types
from decimalai.google_genai import agent_config
client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
config = types.GenerateContentConfig(
system_instruction=run.system, # your prompt, then the skill list
tools=[*TOOLS, *run.tool_params], # your functions, then load_skill
)
contents = [{"role": "user", "parts": [{"text": run.message}]}]
while True:
response = client.models.generate_content(
model="gemini-3.5-flash", contents=contents, config=config,
)
if not response.function_calls:
break
contents.append(response.candidates[0].content)
parts = []
for call in response.function_calls:
# load_skill is answered by the run; your own functions by FUNCTIONS.
# A loop of your own rather than automatic function calling, which
# raises KeyError when the model asks for a function you did not pass.
function = FUNCTIONS.get(call.name)
parts.append(run.tool_result(call) or {"function_response": {
"name": call.name, "id": call.id,
"response": {"result": function(**(call.args or {})) if function
else f"There is no function named {call.name!r}."},
}})
contents.append({"role": "user", "parts": parts})
print(response.text)No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from google import genai
from google.genai import types
client = genai.Client()
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
response = client.models.generate_content(
model="gemini-3.5-flash",
contents="Hello!",
config=types.GenerateContentConfig(system_instruction=f"You are a helpful agent.\n\n{skill}"),
)This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[langchain]" langchain-openai
decimalai skills add aperivue-manage-refsfrom langchain.agents import create_agent
from decimalai.langchain import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = create_agent(
"openai:gpt-5.4-mini",
tools=[], # your tools; the middleware adds load_skill
middleware=[support.middleware], # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[langchain]" langchain-openaifrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from langchain.agents import create_agent
from decimalai.langchain import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = create_agent(
"openai:gpt-5.4-mini",
tools=[], # your tools; the middleware adds load_skill
middleware=[support.middleware], # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from langchain.agents import create_agent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = create_agent("openai:gpt-5.4-mini", tools=[], system_prompt=f"You are a helpful agent.\n\n{skill}")
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})This gets SKILL.md only. The skill's 14 other files are not included.
CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" "crewai>=1.15.27"
decimalai skills add aperivue-manage-refsimport decimalai.crewai
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=decimalai.crewai.skills(), # the installed folder
tools=decimalai.crewai.skill_tools(), # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()The same install from Python, for a notebook or a setup script. CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" "crewai>=1.15.27"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import decimalai.crewai
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=decimalai.crewai.skills(), # the installed folder
tools=decimalai.crewai.skill_tools(), # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()No DecimalAI package. CrewAI's own loader reads the folder, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=[Path(".agents/skills")],
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[adk]"
decimalai skills add aperivue-manage-refsfrom decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = LlmAgent(
name="support", # ADK needs a Python identifier
model="gemini-3.5-flash",
instruction=support.instruction, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[adk]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = LlmAgent(
name="support", # ADK needs a Python identifier
model="gemini-3.5-flash",
instruction=support.instruction, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from google.adk.agents import LlmAgent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = LlmAgent(
name="support",
model="gemini-3.5-flash",
instruction=lambda context: f"You are a helpful agent.\n\n{skill}",
)This gets SKILL.md only. The skill's 14 other files are not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[pydantic-ai]"
decimalai skills add aperivue-manage-refsfrom pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
"openai:gpt-4o-mini",
name=support.name,
tools=[], # your tools; the capability adds load_skill
capabilities=[support], # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[pydantic-ai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
"openai:gpt-4o-mini",
name=support.name,
tools=[], # your tools; the capability adds load_skill
capabilities=[support], # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from pydantic_ai import Agent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = Agent("openai:gpt-4o-mini", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")This gets SKILL.md only. The skill's 14 other files are not included.
Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" deepagents
decimalai skills add aperivue-manage-refsimport decimalai.deepagents
from deepagents import create_deep_agent
agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).
The same install from Python, for a notebook or a setup script. Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" deepagentsfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import decimalai.deepagents
from deepagents import create_deep_agent
agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from deepagents import create_deep_agent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = create_deep_agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})This gets SKILL.md only. The skill's 14 other files are not included.
Its own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" agent-framework
decimalai skills add aperivue-manage-refsimport asyncio
from agent_framework import Agent
from decimalai.agent_framework import skills
agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))It caches skills by default, so restart the process after decimalai skills update.
The same install from Python, for a notebook or a setup script. Its own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" agent-frameworkfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
import asyncio
from agent_framework import Agent
from decimalai.agent_framework import skills
agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))It caches skills by default, so restart the process after decimalai skills update.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdimport asyncio
from pathlib import Path
from agent_framework import Agent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = Agent(client=client, instructions=f"You are a helpful agent.\n\n{skill}")
asyncio.run(agent.run("Hello!"))This gets SKILL.md only. The skill's 14 other files are not included.
Strands' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" strands-agents
decimalai skills add aperivue-manage-refsfrom decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell
agent = Agent(
model=model, # always pass one: the default is Amazon Bedrock
system_prompt="You are a helpful agent.",
tools=[file_editor, shell],
plugins=[skills()],
)
agent("Hello!")Strands loads an agent's skills once, so build the agent again after decimalai skills update.
The same install from Python, for a notebook or a setup script. Strands' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" strands-agentsfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-manage-refs")
if result.exit_code:
raise SystemExit(result.problems)
from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell
agent = Agent(
model=model, # always pass one: the default is Amazon Bedrock
system_prompt="You are a helpful agent.",
tools=[file_editor, shell],
plugins=[skills()],
)
agent("Hello!")Strands loads an agent's skills once, so build the agent again after decimalai skills update.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/aperivue-manage-refs/SKILL.mdfrom pathlib import Path
from strands import Agent
skill = Path(".agents/skills/aperivue-manage-refs/SKILL.md").read_text()
agent = Agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent("Hello!")This gets SKILL.md only. The skill's 14 other files are not included.
No account or Python needed. Cursor, Copilot, Cline and Warp read this folder by themselves.
curl -fsSL --create-dirs -o .agents/skills/aperivue-manage-refs/SKILL.md https://app.decimal.ai/s/aperivue-manage-refs/SKILL.mdpip install "decimalai>=0.15"
decimalai skills add aperivue-manage-refsThis gets SKILL.md only. The skill's 14 other files are not included. The pinned install brings them.
No tools at all. Cursor, Copilot, Cline and Warp read this folder by themselves.
.agents/skills/aperivue-manage-refs/SKILL.mdThis gets SKILL.md only. The skill's 14 other files are not included.
Give its text to your model as instructions. No account or package needed.
This gets SKILL.md only. The skill's 14 other files are not included.
Raw files: /s/aperivue-manage-refs/SKILL.md · /s/aperivue-manage-refs.json
Fetch the file and give its text to your model as instructions. No account or package needed.
curl -fsSL https://app.decimal.ai/s/aperivue-manage-refs/SKILL.mdcurl -fsSL https://app.decimal.ai/s/aperivue-manage-refs.jsonThis gets SKILL.md only. The skill's 14 other files are not included.
Give your agent this task. In testing, the model failed it without the skill and passed it with the skill.
I need to run an automated check to verify that all the [@citation_keys] referenced in my manuscript file actually exist in my BibTeX file so our build pipeline doesn't fail on missing keys. Please run the validation script for me.
What to look for
Saved prompts and skills, pinned versions, and traces of this skill in your runs. DecimalAI does not run your agent.
Claude Code reads files from your project, so DecimalAI config does not apply there.
On Claude Agent SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On OpenAI Agents: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On OpenAI SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Anthropic: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Gemini API: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On LangChain: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On CrewAI: set DECIMAL_API_KEY and add decimalai.init(crewai=True) to record runs and skill use. The skill version stays in your repo.
On Google ADK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Pydantic AI: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Deep Agents: set DECIMAL_API_KEY and add decimalai.init(langchain=True) to record runs and skill use. The skill version stays in your repo.
On Microsoft Agent Framework: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.
On Strands: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.
Editors read files from your project, so DecimalAI config does not apply there.
Anywhere else: record a use with decimalai.log_skill_activation() inside a trace.
One of 17 test cases the skill fixed. Same model, same prompt, with and without the skill.
I need to run an automated check to verify that all the [@citation_keys] referenced in my manuscript file actually exist in my BibTeX file so our build pipeline doesn't fail on missing keys. Please run the validation script for me.
| Checked | Without skill | With skill |
|---|---|---|
| Prescribes scripts/check_citation_keys.py rather than generic python scripts or custom regex search | Missed | Passed |
The instructions your model reads when the skill loads.
Pick the tool from the Decision Tree; do not invent a parallel pipeline. References are never
hand-typed: the list is always rendered by pandoc citeproc + journal CSL or by the Zotero Word
plugin (CWYW). This skill writes (renders, injects, converts); bibliographic correctness against
PubMed/CrossRef stays in /verify-refs — one read-only audit, one writer.
| Situation | Tool | Why |
|---|---|---|
Validate [@bibkey] ↔ refs.bib (UNDEFINED / UNUSED keys) | scripts/check_citation_keys.py | Hard build gate, runs in seconds |
| Single-author submission lockdown, frozen output | scripts/render_pandoc.sh -j <journal> | Reproducible, CI-friendly |
| Cascade rejection (e.g., ER → JVIR → CVIR) | render_pandoc.sh with new -j | CSL swap reformats references in seconds |
| Verify a journal CSL renders the in-text format / DOI / journal-name style the author guide actually requires | scripts/check_csl_render.py --csl <x>.csl --bib refs.bib --journal <key> --md manuscript.md | A stub/"dependent" CSL inherits its parent's format, which may differ from the guide (parenthetical vs superscript, DOI kept, full journal names). --md judges only the keys pandoc reads as cited (nocite: '@*' = whole bib); a preprint server named as the journal (journal = {arXiv}) is exempt from the abbreviation check; with no --journal/--expect-* the run is NOT_ASSESSED (exit 2), never PASS. Spec keys and what is not checked: references/REFERENCE_STYLE_SPECS.md. Run BEFORE submission, not after the proof PDF |
| Reference list prints FULL journal names but the journal wants NLM abbreviations | scripts/fill_journal_abbrev.py --bib refs.bib --out refs_abbrev.bib | Writes shortjournal from PubMed (PMID, else DOI → PMID), then CrossRef short-container-title, named per entry (often ISO 4 with periods, not NLM: check those). Inserts after the journal field in the entry's own indentation, never overwrites, re-parses before writing; exit 1 = some lookups failed. In a Better BibTeX-managed bib, fill Zotero's "Journal Abbr" instead |
| Reviewer revision: add 1–2 refs to a Word doc with co-authors live | Zotero Word plugin (user GUI) | Minimal disruption to track-changes flow |
| Reviewer revision: bulk reference change | Edit markdown SSOT, re-run render_pandoc.sh | Consistency, no cherry-pick risk |
Migrate [N] numeric markers → [@key] for pandoc | scripts/md_marker_convert.py --to-keys | Mapping-driven, partial conversion safe |
Convert [@key] → [N] for round-trip / debug | scripts/md_marker_convert.py --to-numbers | Same map, opposite direction |
| Wire native Zotero CWYW field codes into a .docx (live Refresh in Word) | scripts/inject_zotero_cwyw.py | Co-author Word workflow, post-circulation editability |
| Manuscript ↔ rendered DOCX cross-reference QC | scripts/check_xref.py --strict | Submission gate (P0 blocker on mismatch) |
| Figures/tables submitted as separate attachments (radiology, most medical journals) | check_xref.py --strict --allow-separate-attachments | Downgrades MISSING_DOCX to WARN; MISSING_BODY/MISMATCH remain P0 |
| v_(N+1) docx build-time regeneration check | check_xref.py --vN-docx-md5 <prev>.docx [--vN-md <prev>.md] | Identity = unmodified seed copy; missing diff lines = body not regenerated |
| Duplicate bibliography in the built artifact | scripts/check_reference_duplication.py --docx <built>.docx (or --text <rendered>.md) | DUP_REF_HEADING / REF_NUMBER_RESTART / REF_SIGNATURE_DUP (Major). Catches a hand-typed ## References list plus the pandoc --citeproc auto-bibliography, which renders two lists (the second often after the legends). Run after any citeproc build |
Publisher markup in a .bib title (renders as garbage) | scripts/check_bib_title_markup.py --bib refs.bib --strict | CrossRef titles carry <scp>WHO</scp> / <i>IDH</i>; BBT escapes them ({$<$}scp{$>$}) or strips them without restoring the space (andTERTPromoter). verify_refs proves the reference is true; this proves it will print. TITLE_MARKUP / TITLE_FUSION (Major) |
| Master pre-submission gate (recommended before any submission) | scripts/pre_submission_gate.sh | Chains check_citation_keys → check_bib_title_markup → verify_refs --strict → render_pandoc (optional) → check_xref --strict; single artifact qc/pre_submission_gate.json |
| Direct render with a built-in reference audit | scripts/render_pandoc.sh (audits the .bib via /verify-refs first; blocks on FABRICATED/MISMATCH/duplicates; reports UNVERIFIED rows as not clean, without blocking; after the render, warns about cited journal entries without shortjournal, which the style prints in full) | Best-effort (skips with a warning if /verify-refs is not alongside); opt out with -S. The master gate passes -S because it runs verify_refs in its stage 3 |
| Bibliographic audit against PubMed / CrossRef | delegate to /verify-refs | Audit-only — keep writer/auditor separation |
User provides manuscript.md with [@bibkey] citations + refs.bib.
python3 "${CLAUDE_SKILL_DIR}/scripts/check_citation_keys.py" manuscript.md refs.bib
— exits non-zero on UNDEFINED keys. Fix and re-run. A [@NEW:topic_slug] drafting
placeholder from /write-paper is reported as UNDEFINED too: resolve each by adding the
citation to Zotero (/lit-sync then refreshes refs.bib) and replacing the placeholder with
the real [@bibkey]. Never let a [@NEW:...] reach a rendered DOCX.More skills from the same source and nearby in the registry, with their headline benchmark lift.