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Commit 0318a5b

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psui3905psui3905
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Minor fix
1 parent 0945718 commit 0318a5b
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15 files changed

+46-382Lines changed: 46 additions & 382 deletions
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‎README.md‎

Copy file name to clipboardExpand all lines: README.md
+5-5Lines changed: 5 additions & 5 deletions
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Original file line numberDiff line numberDiff line change
@@ -140,7 +140,7 @@ from medea import medea, AgentLLM, LLMConfig
140140
from medea import ResearchPlanning, Analysis, LiteratureReasoning
141141
from medea import (
142142
ResearchPlanDraft, ContextVerification, IntegrityVerification,
143-
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQulityChecker,
143+
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQualityChecker,
144144
LiteratureSearch, PaperJudge, OpenScholarReasoning
145145
)
146146

@@ -162,7 +162,7 @@ analysis_actions = [
162162
CodeGenerator(tmp=0.4, llm_provider=backbone_llm),
163163
AnalysisExecution(),
164164
CodeDebug(tmp=0.4, llm_provider=backbone_llm),
165-
AnalysisQulityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
165+
AnalysisQualityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
166166
]
167167

168168
literature_actions = [
@@ -203,7 +203,7 @@ from medea import experiment_analysis, AgentLLM, LLMConfig
203203
from medea import ResearchPlanning, Analysis
204204
from medea import (
205205
ResearchPlanDraft, ContextVerification, IntegrityVerification,
206-
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQulityChecker
206+
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQualityChecker
207207
)
208208

209209
# Step 1: Initialize LLMs
@@ -223,7 +223,7 @@ analysis_actions = [
223223
CodeGenerator(tmp=0.4, llm_provider=backbone_llm),
224224
AnalysisExecution(),
225225
CodeDebug(tmp=0.4, llm_provider=backbone_llm),
226-
AnalysisQulityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
226+
AnalysisQualityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
227227
]
228228

229229
# Step 3: Create modules
@@ -349,7 +349,7 @@ python main.py --task immune_response --patient-tpm-root /path/to/tpm/data
349349
# Custom temperature (LLM temperature for all modules)
350350
python main.py --temperature 0.7
351351

352-
# Custom quality iterations (3 max iteration for IntegrityVerification, 3 max iteration for AnalysisQulityChecker)
352+
# Custom quality iterations (3 max iteration for IntegrityVerification, 3 max iteration for AnalysisQualityChecker)
353353
python main.py --quality-max-iter 3 --code-quality-max-iter 3
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355355
# Custom debate rounds
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‎examples/README.md‎

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+2-2Lines changed: 2 additions & 2 deletions
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@@ -91,10 +91,10 @@ analysis_llm = AgentLLM(LLMConfig({"temperature": 0.5}), llm_name="claude")
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9292
**Max iterations**:
9393
```python
94-
from medea import IntegrityVerification, AnalysisQulityChecker
94+
from medea import IntegrityVerification, AnalysisQualityChecker
9595

9696
IntegrityVerification(max_iter=3) # Research plan quality
97-
AnalysisQulityChecker(max_iter=2) # Code quality
97+
AnalysisQualityChecker(max_iter=2) # Code quality
9898
```
9999

100100
## Troubleshooting
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‎examples/custom_workflow.py‎

Copy file name to clipboardExpand all lines: examples/custom_workflow.py
+3-3Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@
2828
CodeGenerator,
2929
AnalysisExecution,
3030
CodeDebug,
31-
AnalysisQulityChecker,
31+
AnalysisQualityChecker,
3232
# Literature reasoning actions
3333
LiteratureSearch,
3434
PaperJudge,
@@ -100,7 +100,7 @@ def example_2_experiment_analysis_system():
100100
CodeGenerator(tmp=0.4, llm_provider="gpt-4o"),
101101
AnalysisExecution(),
102102
CodeDebug(tmp=0.4, llm_provider="gpt-4o"),
103-
AnalysisQulityChecker(tmp=0.4, llm_provider="gpt-4o", max_iter=2),
103+
AnalysisQualityChecker(tmp=0.4, llm_provider="gpt-4o", max_iter=2),
104104
]
105105

106106
# Initialize agents
@@ -182,7 +182,7 @@ def example_4_custom_temperature():
182182
CodeGenerator(tmp=0.5, llm_provider="gpt-4o"),
183183
AnalysisExecution(),
184184
CodeDebug(tmp=0.5, llm_provider="gpt-4o"),
185-
AnalysisQulityChecker(tmp=0.5, llm_provider="gpt-4o", max_iter=1),
185+
AnalysisQualityChecker(tmp=0.5, llm_provider="gpt-4o", max_iter=1),
186186
]
187187

188188
# Initialize agents
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‎examples/quickstart.py‎

Copy file name to clipboardExpand all lines: examples/quickstart.py
+2-2Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
CodeGenerator,
2727
AnalysisExecution,
2828
CodeDebug,
29-
AnalysisQulityChecker,
29+
AnalysisQualityChecker,
3030
# Literature reasoning actions
3131
LiteratureSearch,
3232
PaperJudge,
@@ -85,7 +85,7 @@ def main():
8585
CodeGenerator(tmp=temperature, llm_provider=os.getenv("BACKBONE_LLM", "gpt-4o")),
8686
AnalysisExecution(),
8787
CodeDebug(tmp=temperature, llm_provider=os.getenv("BACKBONE_LLM", "gpt-4o")),
88-
AnalysisQulityChecker(tmp=temperature, llm_provider=os.getenv("BACKBONE_LLM", "gpt-4o"), max_iter=2),
88+
AnalysisQualityChecker(tmp=temperature, llm_provider=os.getenv("BACKBONE_LLM", "gpt-4o"), max_iter=2),
8989
]
9090

9191
# Literature reasoning actions
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‎main.py‎

Copy file name to clipboardExpand all lines: main.py
+3-3Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -44,7 +44,7 @@
4444
from medea.modules.agent_llms import LLMConfig, AgentLLM
4545

4646
# Agent implementations
47-
from medea.modules.experiment_analysis import Analysis, CodeDebug, AnalysisExecution, CodeGenerator, AnalysisQulityChecker
47+
from medea.modules.experiment_analysis import Analysis, CodeDebug, AnalysisExecution, CodeGenerator, AnalysisQualityChecker
4848
from medea.modules.discussion import multi_round_discussion
4949
from medea.modules.literature_reasoning import LiteratureSearch, OpenScholarReasoning, PaperJudge, LiteratureReasoning
5050
from medea.modules.research_planning import ContextVerification, ResearchPlanDraft, IntegrityVerification, ResearchPlanning
@@ -401,7 +401,7 @@ def parse_arguments():
401401

402402
# Iteration limits
403403
QUALITY_MAX_ITER = args.quality_max_iter
404-
CODE_QAULITY_MAX_ITER = args.code_quality_max_iter
404+
CODE_QUALITY_MAX_ITER = args.code_quality_max_iter
405405

406406
# Panel discussion settings
407407
DEBATE_ROUND = args.debate_rounds
@@ -472,7 +472,7 @@ def medea_unittest(df, user_template=None, agent_template=None):
472472
CodeGenerator(tmp=analysis_act_tmp, llm_provider=backbone_llm),
473473
AnalysisExecution(),
474474
CodeDebug(tmp=analysis_act_tmp, llm_provider=backbone_llm),
475-
AnalysisQulityChecker(tmp=analysis_act_tmp, llm_provider=backbone_llm, max_iter=CODE_QAULITY_MAX_ITER),
475+
AnalysisQualityChecker(tmp=analysis_act_tmp, llm_provider=backbone_llm, max_iter=CODE_QUALITY_MAX_ITER),
476476
]
477477

478478
print("=== Init Literature Reasoning Actions ===", flush=True)
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‎medea.egg-info/PKG-INFO‎

Copy file name to clipboardExpand all lines: medea.egg-info/PKG-INFO
+5-5Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -254,7 +254,7 @@ from medea import medea, AgentLLM, LLMConfig
254254
from medea import ResearchPlanning, Analysis, LiteratureReasoning
255255
from medea import (
256256
ResearchPlanDraft, ContextVerification, IntegrityVerification,
257-
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQulityChecker,
257+
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQualityChecker,
258258
LiteratureSearch, PaperJudge, OpenScholarReasoning
259259
)
260260

@@ -276,7 +276,7 @@ analysis_actions = [
276276
CodeGenerator(tmp=0.4, llm_provider=backbone_llm),
277277
AnalysisExecution(),
278278
CodeDebug(tmp=0.4, llm_provider=backbone_llm),
279-
AnalysisQulityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
279+
AnalysisQualityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
280280
]
281281

282282
literature_actions = [
@@ -317,7 +317,7 @@ from medea import experiment_analysis, AgentLLM, LLMConfig
317317
from medea import ResearchPlanning, Analysis
318318
from medea import (
319319
ResearchPlanDraft, ContextVerification, IntegrityVerification,
320-
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQulityChecker
320+
CodeGenerator, AnalysisExecution, CodeDebug, AnalysisQualityChecker
321321
)
322322

323323
# Step 1: Initialize LLMs
@@ -337,7 +337,7 @@ analysis_actions = [
337337
CodeGenerator(tmp=0.4, llm_provider=backbone_llm),
338338
AnalysisExecution(),
339339
CodeDebug(tmp=0.4, llm_provider=backbone_llm),
340-
AnalysisQulityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
340+
AnalysisQualityChecker(tmp=0.4, llm_provider=backbone_llm, max_iter=2)
341341
]
342342

343343
# Step 3: Create modules
@@ -463,7 +463,7 @@ python main.py --task immune_response --patient-tpm-root /path/to/tpm/data
463463
# Custom temperature (LLM temperature for all modules)
464464
python main.py --temperature 0.7
465465

466-
# Custom quality iterations (3 max iteration for IntegrityVerification, 3 max iteration for AnalysisQulityChecker)
466+
# Custom quality iterations (3 max iteration for IntegrityVerification, 3 max iteration for AnalysisQualityChecker)
467467
python main.py --quality-max-iter 3 --code-quality-max-iter 3
468468

469469
# Custom debate rounds
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‎medea/__init__.py‎

Copy file name to clipboardExpand all lines: medea/__init__.py
+2-2Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
CodeGenerator,
3232
AnalysisExecution,
3333
CodeDebug,
34-
AnalysisQulityChecker
34+
AnalysisQualityChecker
3535
)
3636

3737
from .modules.literature_reasoning import (
@@ -68,7 +68,7 @@
6868
'CodeGenerator',
6969
'AnalysisExecution',
7070
'CodeDebug',
71-
'AnalysisQulityChecker',
71+
'AnalysisQualityChecker',
7272

7373
# Literature reasoning actions
7474
'LiteratureSearch',
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‎medea/modules/agent_llms.py‎

Copy file name to clipboardExpand all lines: medea/modules/agent_llms.py
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,7 @@ def run(
121121
temperature=self.temperature,
122122
model=self.model,
123123
mod='chat', # Already in message format
124-
attemps=max_attempts,
124+
attempts=max_attempts,
125125
use_openrouter=self.use_openrouter
126126
)
127127
return response
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‎medea/modules/experiment_analysis.py‎

Copy file name to clipboardExpand all lines: medea/modules/experiment_analysis.py
+3-3Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -429,7 +429,7 @@ def __call__(self, code_snippet: CodeSnippet):
429429
return f"{code_snippet}: debugged, call AnalysisExecution next."
430430

431431

432-
class AnalysisQulityChecker(BaseAction):
432+
class AnalysisQualityChecker(BaseAction):
433433
"""Checks code quality and provides feedback for improvement."""
434434

435435
def __init__(self, llm_provider: str = None, tmp: float = 0.4, max_iter: int = 3) -> None:
@@ -554,7 +554,7 @@ def __init__(
554554
CodeGenerator(llm_provider=os.getenv("BACKBONE_LLM")),
555555
AnalysisExecution(),
556556
CodeDebug(llm_provider=os.getenv("BACKBONE_LLM")),
557-
AnalysisQulityChecker(llm_provider=os.getenv("BACKBONE_LLM")),
557+
AnalysisQualityChecker(llm_provider=os.getenv("BACKBONE_LLM")),
558558
]
559559

560560
name = "analysis_agent"
@@ -783,5 +783,5 @@ def forward(self, task: TaskPackage, agent_act: AgentAct) -> str:
783783
return observation
784784
if param_parse_flag:
785785
return WRONG_ACTION_PARAM
786-
return ACION_NOT_FOUND_MESS
786+
return ACTION_NOT_FOUND_MESS
787787

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‎medea/modules/literature_reasoning.py‎

Copy file name to clipboardExpand all lines: medea/modules/literature_reasoning.py
+2-2Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
from agentlite.agents import ABCAgent, BaseAgent
44
from agentlite.commons import AgentAct, TaskPackage
55
from agentlite.commons.AgentAct import ActObsChainType
6-
from agentlite.agents.agent_utils import act_match, ACION_NOT_FOUND_MESS
6+
from agentlite.agents.agent_utils import act_match, ACTION_NOT_FOUND_MESS
77
from typing import List, Dict, Any
88
import os
99
import torch
@@ -544,7 +544,7 @@ def forward(self, task: TaskPackage, agent_act: AgentAct):
544544
return observation
545545
if param_parse_flag:
546546
return WRONG_ACTION_PARAM
547-
return ACION_NOT_FOUND_MESS
547+
return ACTION_NOT_FOUND_MESS
548548

549549
def __add_inner_actions__(self):
550550
"""Add inner action types based on reasoning type."""

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