bioguider 0.2.31__py3-none-any.whl → 0.2.32__py3-none-any.whl

bioguider/agents/agent_utils.py

@@ -27,6 +27,7 @@ from bioguider.utils.utils import clean_action_input
 from ..utils.gitignore_checker import GitignoreChecker
 from ..database.summarized_file_db import SummarizedFilesDb
 from bioguider.agents.common_conversation import CommonConversation
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -153,7 +154,9 @@ def read_directory(
         return None
     gitignore_checker = GitignoreChecker(
         directory=dir_path,
-        gitignore_path=gitignore_path
+        gitignore_path=gitignore_path,
+        exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+        exclude_file_patterns=configs["file_filters"]["excluded_files"],
     )
     files = gitignore_checker.check_files_and_folders(level=level)
     return files

bioguider/agents/evaluation_readme_task.py

@@ -28,6 +28,7 @@ from bioguider.utils.constants import (
     EvaluationREADMEResult,
 )
 from bioguider.utils.utils import increase_token_usage
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -638,7 +639,9 @@ class EvaluationREADMETask(EvaluationTask):
         repo_path = self.repo_path
         gitignore_path = Path(repo_path, ".gitignore")
         gitignore_checker = GitignoreChecker(
-            directory=repo_path, gitignore_path=gitignore_path
+            directory=repo_path, gitignore_path=gitignore_path,
+            exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+            exclude_file_patterns=configs["file_filters"]["excluded_files"],
         )
         found_readme_files = gitignore_checker.check_files_and_folders(
             check_file_cb=lambda root_dir, relative_path: Path(relative_path).name.lower() in possible_readme_files,

bioguider/managers/evaluation_manager.py

@@ -3,10 +3,8 @@ from pathlib import Path
 
 from bioguider.agents.evaluation_tutorial_task import EvaluationTutorialTask
 from bioguider.agents.evaluation_userguide_task import EvaluationUserGuideTask
-from bioguider.agents.prompt_utils import CollectionGoalItemEnum
 from bioguider.database.code_structure_db import CodeStructureDb
 from bioguider.utils.constants import ProjectMetadata
-from bioguider.utils.gitignore_checker import GitignoreChecker
 
 from ..agents.identification_task import IdentificationTask
 from ..rag.rag import RAG

bioguider/utils/code_structure_builder.py

@@ -6,6 +6,7 @@ from bioguider.utils.r_file_handler import RFileHandler
 from .gitignore_checker import GitignoreChecker
 from .python_file_handler import PythonFileHandler
 from ..database.code_structure_db import CodeStructureDb
+from ..rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -17,7 +18,12 @@ class CodeStructureBuilder:
         code_structure_db: CodeStructureDb,
     ):
         self.repo_path = str(repo_path)
-        self.gitignore_checker = GitignoreChecker(repo_path, str(gitignore_path))
+        self.gitignore_checker = GitignoreChecker(
+            directory=repo_path,
+            gitignore_path=str(gitignore_path),
+            exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+            exclude_file_patterns=configs["file_filters"]["excluded_files"],
+        )
         self.file_handler = PythonFileHandler(repo_path)
         self.code_structure_db = code_structure_db
 

bioguider/utils/r_file_handler.py

@@ -348,10 +348,12 @@ class RFileHandler:
             s = line.lstrip()
             if s.startswith("#'"):
                 buf.append(s[2:].lstrip())
-                line_idx -= 1
-                continue
-            # stop at first non-roxygen line (don’t cross blank + NULL padding blocks)
-            break
+            elif s.strip() == "":
+                pass
+            else:
+                # stop at first non-roxygen line (don’t cross blank + NULL padding blocks)
+                break
+            line_idx -= 1
         if not buf:
             return None
         buf.reverse()

{bioguider-0.2.31.dist-info → bioguider-0.2.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.31
+Version: 0.2.32
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.31.dist-info → bioguider-0.2.32.dist-info}/RECORD

@@ -2,7 +2,7 @@ bioguider/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioguider/agents/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioguider/agents/agent_task.py,sha256=TL0Zx8zOmiAVslmNbfMPQ38qTQ73QospY6Dwrwf8POg,2890
 bioguider/agents/agent_tools.py,sha256=r21wHV6a-Ic2T0dk4YzA-_d7PodHPM3GzRxJqv-llSw,7286
-bioguider/agents/agent_utils.py,sha256=Mj6yr_2y4veWokXrXlAsaP38Ez9sdnZruM8ZnnpjxQ4,14825
+bioguider/agents/agent_utils.py,sha256=dA2xbS7ojeNyGBigyCGGCZOZGGUSUpPVfCYgWLqi0ZA,15011
 bioguider/agents/collection_execute_step.py,sha256=jE_oSQZI5WDaz0bJjUWoAfqWfVbGUqN--cvITSWCGiI,5614
 bioguider/agents/collection_observe_step.py,sha256=1xOw6N3uIoyh4h4_vcULAc5x5KZ9G-zZo42AhRidyn8,5373
 bioguider/agents/collection_plan_step.py,sha256=Nn0f8AOkEDCDtnhaqE7yCQoi7PVpsHmiUcsIqC0T0dQ,5956
@@ -23,7 +23,7 @@ bioguider/agents/dockergeneration_plan_step.py,sha256=SB8tQM9PkIKsD2o1DFD7bedcxz
 bioguider/agents/dockergeneration_task.py,sha256=mYmorLKnJ-Jku3Qq_Y_kcSTsbYIo3RiVdD0puxqXY5Q,6221
 bioguider/agents/dockergeneration_task_utils.py,sha256=v7emqrJlVW-A5ZdLmPSdiaMSKCR8uzy9UYzx_1cgzyo,9041
 bioguider/agents/evaluation_installation_task.py,sha256=0RNH5NV7YKwn_we_d3IjnFf_ee9IPCEQ_olebq2y8Ng,12130
-bioguider/agents/evaluation_readme_task.py,sha256=pi3oAGJgZhJgJG1xLgiobrk3Uy2a_JIarD5QSPBkmHA,30647
+bioguider/agents/evaluation_readme_task.py,sha256=GUrGZUK9Jvb82M0AooLRi7CeOpZ19t-YQfs-UxYKK2Q,30841
 bioguider/agents/evaluation_submission_requirements_task.py,sha256=J_6C-M2AfYue2C-gWBHl7KqGrTBuFBn9zmMV5vSRk-U,7834
 bioguider/agents/evaluation_task.py,sha256=uu0BjalctF9hQjGtT53whbeJHv2RVvs8_2woVUmOLRE,8132
 bioguider/agents/evaluation_tutorial_task.py,sha256=cxzXf5cXdZtYd8yCpffTlDGuZFx5NZ_iz9kkNXLLtns,10138
@@ -55,7 +55,7 @@ bioguider/generation/report_loader.py,sha256=bxajeTDxod36iFsbSZhXSQjotxqP7LuAg5M
 bioguider/generation/style_analyzer.py,sha256=Vn9FAK1qJBNLolLC1tz362k4UBaPl107BlvkQc8pV2I,983
 bioguider/generation/suggestion_extractor.py,sha256=kkPOYE6FXRtYlogV0GQdBraZZJm08I6Oux5YKGUF1UU,29442
 bioguider/generation/test_metrics.py,sha256=ACXmSZc2L_UkkmC5h2s4tG44MXW1d-hClFwPCD5_BFI,7505
-bioguider/managers/evaluation_manager.py,sha256=EoZ8V4rmx16zk1J3N9cNjeo0aCa7i32fLEQ3b2UolEQ,5917
+bioguider/managers/evaluation_manager.py,sha256=7WlshfnqFkk34dDlf50qAINK5sFTaoCFE0f0vGYyRdc,5789
 bioguider/managers/generation_manager.py,sha256=GqjCci2eWHnIcJ-SOn5-hEMi8p3Jk4Q5E4KSObKELPs,31945
 bioguider/managers/generation_test_manager.py,sha256=3mOBzQVpsLo_LpSspJcofn3CNtvgagS1DMr9Zuwkzq4,5307
 bioguider/rag/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -64,7 +64,7 @@ bioguider/rag/data_pipeline.py,sha256=hyBmjOpP1ka_y_4X0lUwlNKEBjmPNOmETEfQf-s86Z
 bioguider/rag/embedder.py,sha256=jofR8hOj3Aj2IyBQ9y6FeAc84tgq5agbIfCGyFxYpJ8,650
 bioguider/rag/rag.py,sha256=JFPwrJlKDSyd3U3Gce_NSxI5343eNUbqPG9Fs5Pfoq0,4696
 bioguider/settings.py,sha256=BD_iz9aYarxmWUl0XaKl4-D4oTXMhFzljsXLNn2phis,3143
-bioguider/utils/code_structure_builder.py,sha256=PVeooVKxkiBEkX_VEu8h1ACGs-ynrgk_ce2FKJfeeZc,1947
+bioguider/utils/code_structure_builder.py,sha256=t7Ao3r50v7c0JrS74J70mCOtaEFnKvam-bsA7OSvFQo,2192
 bioguider/utils/constants.py,sha256=NGmqEgxNDL1fe-htJbtHGcU94EVUK28YAupxGYOJO_c,9012
 bioguider/utils/default.gitignore,sha256=XjPdyO2KV8z8iyuqluaNR_70tBQftMpyKL8HboVNyeI,1605
 bioguider/utils/file_utils.py,sha256=DOWRluneNpGQ4uVwwX9Tp2VzmZ56wIqXKMyjcMH9Bpc,6229
@@ -72,9 +72,9 @@ bioguider/utils/gitignore_checker.py,sha256=pOYUwsS9D5014LxcZb0cj3s2CAYaD2uF_pYJ
 bioguider/utils/notebook_utils.py,sha256=SfU1iLuwgbDzNN-TUh_qbnfUSgn-PI6NrK6QfmdpMqQ,4009
 bioguider/utils/pyphen_utils.py,sha256=cdZc3qphkvMDeL5NiZ8Xou13M_uVNP7ifJ-FwxO-0BE,2680
 bioguider/utils/python_file_handler.py,sha256=BERiE2RHxpu3gAzv26jr8ZQetkrtnMZOv9SjpQ7WIdg,2650
-bioguider/utils/r_file_handler.py,sha256=8HpFaYKP8N1nItwr9tOx49m99pcLSt8EUtTNTJ7xNoE,19564
+bioguider/utils/r_file_handler.py,sha256=y57Y04wjgtFWve0lPg1EOrNNOccPfnNF0z2WnlFMX74,19616
 bioguider/utils/utils.py,sha256=h8OhCjzLpHkb3ndnjRBUOBHD7csbHdEVNXf75SRN8Zc,4413
-bioguider-0.2.31.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.31.dist-info/METADATA,sha256=k5RSl8D1JHB5mFSCWqcJjTLF1WDDhtBw2BbFfmg-Trw,1962
-bioguider-0.2.31.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.31.dist-info/RECORD,,
+bioguider-0.2.32.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.32.dist-info/METADATA,sha256=OTumO8NRGxVO5JZWKXb7ztoM_S7zh8bAuij2TUrABuA,1962
+bioguider-0.2.32.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.32.dist-info/RECORD,,