Updates from local regarding shell and subprocess

Author: santibravocmcc

main.py

@@ -367,8 +367,8 @@ def run_medslik_sim(self, simdir, simname, separate_slicks=False):
             # Compile and start running (replacing `cd` with `cwd`)
             compile_script = "MODEL_SRC/compile.sh"
             run_script = "RUN.sh"
-            subprocess.run(["sh", compile_script], check=True, cwd=os.path.join(model_dir, "RUN")) # nosec
-            subprocess.run(["./" + run_script], check=True, cwd=os.path.join(model_dir, "RUN")) # nosec
+            subprocess.run(["sh", compile_script], check=True, cwd=os.path.join(model_dir, "RUN"))
+            subprocess.run(["./" + run_script], check=True, cwd=os.path.join(model_dir, "RUN"))
 
         else:
             # Handle separate slicks
@@ -391,8 +391,8 @@ def run_medslik_sim(self, simdir, simname, separate_slicks=False):
                 # Compile and start running
                 compile_script = "MODEL_SRC/compile.sh"
                 run_script = "RUN.sh"
-                subprocess.run(["sh", compile_script], check=True, cwd=os.path.join(model_dir, "RUN")) # nosec
-                subprocess.run(["./" + run_script], check=True, cwd=os.path.join(model_dir, "RUN")) # nosec
+                subprocess.run(["sh", compile_script], check=True, cwd=os.path.join(model_dir, "RUN"))
+                subprocess.run(["./" + run_script], check=True, cwd=os.path.join(model_dir, "RUN"))
 
         # Copy output files (replacing `cp -r`)
         output_dest = os.path.join(simdir, simname, "out_files")

src/download/download_copernicus_parser.py

@@ -289,8 +289,8 @@ def download_copernicus(
                 # saves the daily current or temperature netcdf in the case dir
                 ds.to_netcdf(output_name)
 
-                # remove the temporary files
-                temp_files = [os.path.join(output_path, "curr.nc"), os.path.join(output_path, "temp.nc")]
-                for temp_file in temp_files:
-                    if os.path.exists(temp_file):
-                        os.remove(temp_file)
+        # remove the temporary files
+        temp_files = [os.path.join(output_path, "curr.nc"), os.path.join(output_path, "temp.nc")]
+        for temp_file in temp_files:
+            if os.path.exists(temp_file):
+                os.remove(temp_file)

src/plot/plot_mdk3.py

@@ -330,6 +330,7 @@ def plot_pyngl(
                                 {plot_lat[0]} {plot_lat[1]}"
             ],
             # shell=True,
+            # shell=True,
             check=True,
         ) # nosec