few bug solving

utils/convert_to_hdf5.py

@@ -1,8 +1,28 @@
 # coding: utf-8
 
+import argparse
+import os
 from snapshotprocessor import SnapshotProcessor
 
 
 def convert_to_hdf5(path, snap_num, path_out=".", filename=None, **kwargs):
     snap = SnapshotProcessor(path=path, num=snap_num, path_out=path_out, **kwargs)
     snap.convert_hdf5(filename)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Convert Ramses output into a list of cells"
+    )
+    parser.add_argument(
+        "snapshots", help="path to the snapshots", nargs="+", default=[]
+    )
+    parser.add_argument("-o", "--out", help="path to the output", default=".")
+
+    args = parser.parse_args()
+
+    for snap in args.snapshots:
+        path = os.path.dirname(snap)
+        numstem = os.path.basename(snap)
+        snap_num = int(numstem.split("_")[1])
+        convert_to_hdf5(path, snap_num, args.out)

utils/runselector.py

@@ -40,7 +40,7 @@ class NamelistRecursive:
 class RunSelector:
     def __init__(
         self,
-        path_in,
+        path_in=".",
         in_runs=None,
         in_nums="all",
         nml_filename="run.nml",
@@ -93,7 +93,7 @@ class RunSelector:
             sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
 
         """
-        
+
         # Initialize logger
         self.logger = logging.getLogger("run_self")
         self.logger.propagate = False
@@ -450,7 +450,9 @@ class RunSelector:
 
         # Be sure we have a namelist
         if self.fallback_nml and run not in self.namelist:
-            self.logger.warning(f"Used fallback namelist for run {run} from output {nums[0]}")
+            self.logger.warning(
+                f"Used fallback namelist for run {run} from output {nums[0]}"
+            )
             path = f"{self.path_in}/{run}/output_{nums[0]:05}/namelist.txt"
             self.namelist[run] = self.load_namelist(run, path=path)