various fixes (#161)

.env.example

@@ -5,7 +5,5 @@
 # OpenAI API Key
 OPENAI_API_KEY=YOUR_OPENAI_API_KEY_GOES_HERE  # pragma: allowlist secret
 
-# PQA API Key to use LiteratureSearch tool (optional) -- it also requires OpenAI key
-PQA_API_KEY=YOUR_PQA_API_KEY_GOES_HERE # pragma: allowlist secret
 
 # Optional: add TogetherAI, Fireworks, or Anthropic API key here to use their models

.pre-commit-config.yaml

@@ -10,28 +10,28 @@ repos:
       - id: mixed-line-ending
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.270"
+    rev: "v0.7.1"
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
   - repo: https://github.com/psf/black
-    rev: "23.3.0"
+    rev: "24.10.0"
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.3.0"
+    rev: "v1.13.0"
     hooks:
       - id: mypy
         args: [--pretty, --ignore-missing-imports]
         additional_dependencies: [types-requests]
   - repo: https://github.com/PyCQA/isort
-    rev: "5.12.0"
+    rev: "5.13.2"
     hooks:
       - id: isort
         args: [--profile=black]
   - repo: https://github.com/Yelp/detect-secrets
-    rev: v1.0.3
+    rev: v1.5.0
     hooks:
       - id: detect-secrets
         args: [--exclude-files, ".github/workflows/"]

mdagent/tools/base_tools/analysis_tools/plot_tools.py

@@ -124,7 +124,7 @@ def _run(self, file_id: str) -> str:
             plotting_tools._find_file(file_id)
             plotting_tools.process_csv()
             plot_result = plotting_tools.plot_data()
-            if type(plot_result) == str:
+            if isinstance(plot_result, str):
                 return "Succeeded. IDs of figures created: " + plot_result
             else:
                 return "Failed. No figures created."

mdagent/tools/base_tools/analysis_tools/rdf_tool.py

@@ -159,7 +159,7 @@ def validate_input(self, input):
             )
 
         if stride:
-            if type(stride) != int:
+            if not isinstance(stride, int):
                 try:
                     stride = int(stride)
                     if stride <= 0:

mdagent/tools/base_tools/preprocess_tools/uniprot.py

@@ -693,9 +693,11 @@ def get_ids(
         if include_uniprotkbids:
             all_ids + [entry["uniProtkbId"] for entry in ids_] if ids_ else []
         accession = self.get_data(query, desired_field="accession")
-        all_ids + [
-            entry["primaryAccession"] for entry in accession
-        ] if accession else []
+        (
+            all_ids + [entry["primaryAccession"] for entry in accession]
+            if accession
+            else []
+        )
         if single_id:
             return [all_ids[0]] if all_ids else []
         return list(set(all_ids))

mdagent/tools/base_tools/simulation_tools/setup_and_run.py

@@ -273,14 +273,22 @@ def setup_system(self):
             PME,
         ]:
             if self.sim_params["Ensemble"] == "NPT":
-                self.system.addForce(
-                    MonteCarloBarostat(
-                        self.int_params["Pressure"],
-                        self.int_params["Temperature"],
-                        self.sim_params.get("barostatInterval", 25),
-                    )
+                pressure = self.int_params.get("Pressure", 1.0)
+
+            if "Pressure" not in self.int_params:
+                print(
+                    "Warning: 'Pressure' not provided. ",
+                    "Using default pressure of 1.0 atm.",
                 )
 
+            self.system.addForce(
+                MonteCarloBarostat(
+                    pressure,
+                    self.int_params["Temperature"],
+                    self.sim_params.get("barostatInterval", 25),
+                )
+            )
+
     def setup_integrator(self):
         print("Setting up integrator...")
         int_params = self.int_params
@@ -1219,7 +1227,7 @@ def _process_parameters(self, user_params, param_type="system_params"):
                         )
                 if key == "constraints":
                     try:
-                        if type(value) == str:
+                        if isinstance(value, str):
                             if value == "None":
                                 processed_params[key] = None
                             elif value == "HBonds":
@@ -1243,7 +1251,7 @@ def _process_parameters(self, user_params, param_type="system_params"):
                             "part of the parameters.\n"
                         )
                 if key == "rigidWater" or key == "rigidwater":
-                    if type(value) == bool:
+                    if isinstance(value, bool):
                         processed_params[key] = value
                     elif value == "True":
                         processed_params[key] = True
@@ -1268,7 +1276,7 @@ def _process_parameters(self, user_params, param_type="system_params"):
                         )
                 if key == "solvate":
                     try:
-                        if type(value) == bool:
+                        if isinstance(value, bool):
                             processed_params[key] = value
                         elif value == "True":
                             processed_params[key] = True
@@ -1480,7 +1488,7 @@ def check_system_params(cls, values):
 
         # forcefield
         forcefield_files = values.get("forcefield_files")
-        if forcefield_files is None or forcefield_files is []:
+        if forcefield_files is None or forcefield_files == []:
             print("Setting default forcefields")
             forcefield_files = ["amber14-all.xml", "amber14/tip3pfb.xml"]
         elif len(forcefield_files) == 0:
@@ -1492,7 +1500,7 @@ def check_system_params(cls, values):
                     error_msg += "The forcefield file is not present"
 
         save = values.get("save", True)
-        if type(save) != bool:
+        if not isinstance(save, bool):
             error_msg += "save must be a boolean value"
 
         if error_msg != "":

mdagent/tools/maketools.py

@@ -74,7 +74,7 @@ def make_all_tools(
         all_tools += [
             ModifyBaseSimulationScriptTool(path_registry=path_instance, llm=llm),
         ]
-        if "OPENAI_API_KEY" in os.environ and "PQA_API_KEY" in os.environ:
+        if path_instance.ckpt_papers:
             all_tools += [Scholar2ResultLLM(llm=llm, path_registry=path_instance)]
         if human:
             all_tools += [agents.load_tools(["human"], llm)[0]]