Fixes for unix passin for --inlist when using --inlist {cmd}

Author: nkphysics

autonicer/__init__.py

@@ -54,8 +54,8 @@ def run(args=None):
         "-inlist",
         "--inlist",
         help="Input .csv list with path to OBSID dirs or mpu7_cl.evt files for use with --reprocess and/or --checkcal",
-        type=str,
         default=None,
+        nargs="+",
     )
 
     argp = p.parse_args(args)

autonicer/reprocess.py

@@ -165,16 +165,21 @@ def inlist(argp):
     cwd = os.getcwd()
     curr_cals = autonicer.get_caldb_ver()
     try:
-        df = pd.read_csv(f"{argp.inlist}")
-        for i in df["Input"]:
-            path_sep = i.split("/xti/event_cl/")
-            os.chdir(path_sep[0])
-            if argp.checkcal is True or argp.reprocess is True:
-                reprocess_check(argp, curr_cals)
-            os.chdir(cwd)
+        if len(argp.inlist) == 1:
+            df = pd.read_csv(f"{argp.inlist[0]}")
+            for i in df["Input"]:
+                path_sep = i.split("/xti/event_cl/")
+                os.chdir(path_sep[0])
+                if argp.checkcal is True or argp.reprocess is True:
+                    reprocess_check(argp, curr_cals)
+                os.chdir(cwd)
+        else:
+            raise FileNotFoundError
 
     except FileNotFoundError:
-        dirs = glob.glob(f"{argp.inlist}")
+        dirs = argp.inlist
+        if len(argp.inlist) == 1:
+            dirs = glob.glob(f"{argp.inlist[0]}")
         if len(dirs) != 0:
             for i in dirs:
                 try:
@@ -188,7 +193,7 @@ def inlist(argp):
         else:
             print(colored(f"DATASETS NOT FOUND", "red"))
     except pd.errors.ParserError:
-        print(colored(f"Unable to resolve --inlist {argp.inlist}", "red"))
+        print(colored(f"Unable to resolve --inlist {argp.inlist[0]}", "red"))
     except KeyError:
-        print(colored(f"{argp.inlist} format not readable", "red"))
+        print(colored(f"{argp.inlist[0]} format not readable", "red"))
         print("Format must be csv with Input column for inlist files...")

tests/test_autonicer.py

@@ -286,7 +286,7 @@ def test_inlist_readin(capsys):
     os.chdir(f"{base_dir}")
     files = ["requirements.txt", "README.md"]
     for i in files:
-        autonicer.run(["--checkcal", f"--inlist={i}"])
+        autonicer.run(["--checkcal", "--inlist", f"{i}"])
     out, err = capsys.readouterr()
     pd_err = "Unable to resolve --inlist README.md"
     key_err = "requirements.txt format not readable"