Fixed bug in run folder naming and added link to FutureHouse trajectory in all output files

.gitignore

@@ -100,6 +100,7 @@ coverage.xml
 .hypothesis/
 .tox/
 htmlcov/
+scratchpad.ipynb
 
 # Documentation
 docs/_build/

robin/configuration.py

@@ -59,10 +59,6 @@ def get_default_llm_config():
     return copy.deepcopy(_DEFAULT_LLM_CONFIG_DATA)
 
 
-DEFAULT_DISEASE_NAME = "dry age-related macular degeneration"
-DEFAULT_FOLDER_NAME = f"{DEFAULT_DISEASE_NAME[:70].replace(" ", "_")}_{datetime.now().strftime("%Y-%m-%d_%H-%M")}"
-
-
 def _get_prompt_args(template_string: str) -> set[str]:
     """
     Extracts root variable names from f-string like placeholders (e.g., {variable})
@@ -276,20 +272,31 @@ class Config:
         default=5, description="Number of candidates to generate for each query."
     )
     disease_name: str = Field(
-        default=DEFAULT_DISEASE_NAME, description="Name of the disease to focus on."
+        default="input_disease", description="Name of the disease to focus on."
     )
-    run_folder_name: str = Field(
-        default=DEFAULT_FOLDER_NAME,
-        description="Name of the folder where results will be stored.",
+    run_folder_name: str | None = Field(
+        default=None,
+        description=(
+            "Name of the folder where results will be stored. "
+            "If not provided or None, it will be auto-generated "
+            "using the disease_name and the timestamp."
+        ),
     )
-
     futurehouse_api_key: str = "insert_futurehouse_api_key_here"
     llm_name: str = "o4-mini"
     llm_config: dict | None = Field(default_factory=get_default_llm_config)
     agent_settings: AgentConfig = Field(default_factory=AgentConfig)
     _fh_client: FutureHouseClient | None = PrivateAttr(default=None)
     _llm_client: LiteLLMModel | None = PrivateAttr(default=None)
 
+    @model_validator(mode="after")
+    def set_run_folder_name_default(self) -> "RobinConfiguration":
+        if self.run_folder_name is None:
+            disease_part = self.disease_name[:70].replace(" ", "_")
+            timestamp_part = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+            self.run_folder_name = f"{disease_part}_{timestamp_part}"
+        return self
+
     @property
     def fh_client(self) -> FutureHouseClient:
         if self._fh_client is None:

robin/utils.py

@@ -251,6 +251,7 @@ def save_crow_files(
         query_text = item.get("query", "").strip()
         answer_text = item.get("answer", "").strip()
         sources_text = item.get("sources", "").strip()
+        task_id_text = item.get("task_run_id", "").strip()
 
         file_number = i + 1
 
@@ -274,6 +275,7 @@ def save_crow_files(
             content = f"Hypothesis: {hypothesis_text}\n\n"
         content += f"Query: {query_text}\n\n"
         content += f"{answer_text}\n\n"
+        content += f"Full trajectory link: https://platform.futurehouse.org/trajectories/{task_id_text}\n\n"
         content += f"References:\n{sources_text}\n"
 
         try:
@@ -297,6 +299,7 @@ def save_falcon_files(
     for i, item in enumerate(data_list):
         hypothesis_text = item.get("hypothesis", "").strip()
         formatted_output_text = item.get("formatted_output", "").strip()
+        task_id_text = item.get("task_run_id", "").strip()
 
         file_number = i + 1
 
@@ -316,7 +319,8 @@ def save_falcon_files(
         filepath = run_dir_path / filename
 
         content = f"Proposal for {hypothesis_text}\n\n"
-        content += f"{formatted_output_text}"
+        content += f"{formatted_output_text}\n\n"
+        content += f"Full trajectory link: https://platform.futurehouse.org/trajectories/{task_id_text}\n"
 
         try:
             filepath.write_text(content, encoding="utf-8")