fix: cleanup workflow section code

- Fix critical variable shadowing bug in CommandExecutor.py where loop
  variable `i` was overwritten inside the loop, causing incorrect file
  indexing when processing multiple input files
- Remove redundant if/else in FileManager._set_dir() that called the
  same function in both branches
- Remove commented-out dead code in StreamlitUI.py and Logger.py
- Fix docstring typo in Logger.py ("input_widgetThis" -> "This")
- Remove unnecessary empty markdown heading used for checkbox spacing
- Fix bare except clause in ParameterManager.py to catch specific
  exceptions (JSONDecodeError, IOError, OSError)

https://claude.ai/code/session_01LaYLob1uWygBXmUS2JRKmH

Author: claude

src/workflow/CommandExecutor.py

@@ -273,14 +273,14 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
                 # get value from input_output dictionary
                 value = input_output[k]
                 # when multiple input/output files exist (e.g., multiple mzMLs and featureXMLs), but only one additional input file (e.g., one input database file)
-                if len(value) == 1:
-                    i = 0
+                # use index 0 for single-item lists, otherwise use the loop index
+                idx = 0 if len(value) == 1 else i
                 # when the entry is a list of collected files to be passed as one [["sample1", "sample2"]]
-                if isinstance(value[i], list):
-                    command += value[i]
+                if isinstance(value[idx], list):
+                    command += value[idx]
                 # standard case, files was a list of strings, take the file name at index
                 else:
-                    command += [value[i]]
+                    command += [value[idx]]
             # Add non-default TOPP tool parameters
             if tool in params.keys():
                 for k, v in params[tool].items():

src/workflow/FileManager.py

@@ -123,10 +123,7 @@ def _set_dir(self, files: List[str], subdir_name: str) -> List[str]:
         Returns:
             List[str]: The files list with new directory.
         """
-        if not subdir_name:
-            subdir_name = self._create_results_sub_dir(subdir_name)
-        else:
-            subdir_name = self._create_results_sub_dir(subdir_name)
+        subdir_name = self._create_results_sub_dir(subdir_name)
 
         def change_subdir(file_path, subdir):
             return Path(subdir, Path(file_path).name)

src/workflow/Logger.py

@@ -2,7 +2,7 @@
 
 class Logger:
     """
-    A simple logging class for writing messages to a log file. input_widgetThis class is designed
+    A simple logging class for writing messages to a log file. This class is designed
     to append messages to a log file in the current workflow directory, facilitating
     easy tracking of events, errors, or other significant occurrences in processes called
     during workflow execution.
@@ -35,8 +35,4 @@ def log(self, message: str, level: int = 0) -> None:
                 f.write(f"{message}\n\n")
         if level <= 2:
             with open(Path(log_dir, "all.log"), "a", encoding="utf-8") as f:
-                f.write(f"{message}\n\n")
-        # log_types = ["minimal", "commands and run times", "tool outputs", "all"]
-        # for i, log_type in enumerate(log_types):
-        #     with open(Path(log_dir, f"{log_type.replace(" ", "-")}.log"), "a", encoding="utf-8") as f:
-        #         f.write(f"{message}\n\n")
+                f.write(f"{message}\n\n")

src/workflow/ParameterManager.py

@@ -126,7 +126,7 @@ def get_parameters_from_json(self) -> dict:
             try:
                 with open(self.params_file, "r", encoding="utf-8") as f:
                     return json.load(f)
-            except:
+            except (json.JSONDecodeError, IOError, OSError):
                 st.error("**ERROR**: Attempting to load an invalid JSON parameter file. Reset to defaults.")
                 return {}
 

src/workflow/StreamlitUI.py

@@ -163,9 +163,6 @@ def upload_widget(
 
         # Local file upload option: via directory path
         if st.session_state.location == "local":
-            # c2_text, c2_checkbox = c2.columns([1.5, 1], gap="large")
-            # c2_text.markdown("**OR add files from local folder**")
-            # use_copy = c2_checkbox.checkbox("Make a copy of files", key=f"{key}-copy_files", value=True, help="Create a copy of files in workspace.")
             with c2.container(border=True):
                 st_cols = st.columns([0.05, 0.55], gap="small")
                 with st_cols[0]:
@@ -812,7 +809,6 @@ def display_TOPP_params(params: dict, num_cols):
                         p["value"] = p["value"].split("\n")
                     # bools
                     if isinstance(p["value"], bool):
-                        cols[i].markdown("##")
                         cols[i].checkbox(
                             name,
                             value=(