Added remove_directory function to replace use of shutil

species/data/isochrone_data/iso_linder2019.py

@@ -1,5 +1,3 @@
-import shutil
-
 from pathlib import Path
 
 import h5py
@@ -9,7 +7,7 @@
 from typeguard import typechecked
 
 from species.core import constants
-from species.util.data_util import extract_tarfile
+from species.util.data_util import extract_tarfile, remove_directory
 
 
 @typechecked
@@ -79,7 +77,7 @@ def add_linder2019(database: h5py._hl.files.File, input_path: str) -> None:
         # unpacked because the file permissions are set to read-only
         # such that the extract_tarfile will cause an error if the
         # files need to be overwritten
-        shutil.rmtree(data_folder)
+        remove_directory(data_folder)
 
     data_folder.mkdir()
 

species/data/spec_data/spec_allers2013.py

@@ -6,8 +6,6 @@
 <https://github.com/aburgasser/splat>`_.
 """
 
-import shutil
-
 from pathlib import Path
 
 import h5py
@@ -19,7 +17,7 @@
 from astroquery.simbad import Simbad
 from typeguard import typechecked
 
-from species.util.data_util import extract_tarfile
+from species.util.data_util import extract_tarfile, remove_directory
 from species.util.query_util import get_simbad
 
 
@@ -87,7 +85,7 @@ def add_allers2013(input_path: str, database: h5py._hl.files.File) -> None:
         )
 
     if data_folder.exists():
-        shutil.rmtree(data_folder)
+        remove_directory(data_folder)
 
     print(f"\nUnpacking {print_text} (173 kB)...", end="", flush=True)
     extract_tarfile(str(data_file), str(data_folder))

species/data/spec_data/spec_bonnefoy2014.py

@@ -5,7 +5,6 @@
 """
 
 import gzip
-import shutil
 
 from pathlib import Path
 
@@ -16,7 +15,7 @@
 from astropy.io import fits
 from typeguard import typechecked
 
-from species.util.data_util import extract_tarfile
+from species.util.data_util import extract_tarfile, remove_directory
 
 
 @typechecked
@@ -58,7 +57,7 @@ def add_bonnefoy2014(input_path: str, database: h5py._hl.files.File) -> None:
         )
 
     if data_folder.exists():
-        shutil.rmtree(data_folder)
+        remove_directory(data_folder)
 
     print(f"\nUnpacking {print_text} (2.3 MB)...", end="", flush=True)
     extract_tarfile(str(data_file), str(data_folder))

species/data/spec_data/spec_kesseli2017.py

@@ -3,8 +3,6 @@
 Kesseli et al. (2017) to the database.
 """
 
-import shutil
-
 from pathlib import Path
 
 import h5py
@@ -14,7 +12,7 @@
 from astropy.io import fits
 from typeguard import typechecked
 
-from species.util.data_util import extract_tarfile
+from species.util.data_util import extract_tarfile, remove_directory
 
 
 @typechecked
@@ -53,7 +51,7 @@ def add_kesseli2017(input_path: str, database: h5py._hl.files.File) -> None:
         )
 
     if data_folder.exists():
-        shutil.rmtree(data_folder)
+        remove_directory(data_folder)
 
     print(
         "\nUnpacking SDSS spectra from Kesseli et al. 2017 (145 MB)...",

species/util/data_util.py

@@ -1065,3 +1065,30 @@ def convert_units(
         )
 
     return flux_out
+
+
+@typechecked
+def remove_directory(dir_in: Path) -> None:
+    """
+    Function for removing all files and directories within a
+    specified input directory.
+
+    Parameters
+    ----------
+    dir_in : Path
+        Directory that should be recursively removed, that is,
+        including all the files and directories within ``dir_in``.
+
+    Returns
+    -------
+    NoneType
+        None
+    """
+
+    for path_item in dir_in.iterdir():
+        if path_item.is_dir():
+            remove_directory(path_item)
+        else:
+            path_item.unlink()
+
+    dir_in.rmdir()

species/util/fit_util.py

@@ -309,12 +309,14 @@ def get_residuals(
         else:
             n_fixed = 0
 
-            warnings.warn("The 'fixed_param' group is not found in "
-                          f"the results of {tag}. Probably the "
-                          "results were obtained with an older "
-                          "version of the package. Please rerun "
-                          "FitModel to update the results. Setting "
-                          "the number of fixed parameters to zero.")
+            warnings.warn(
+                "The 'fixed_param' group is not found in "
+                f"the results of {tag}. Probably the "
+                "results were obtained with an older "
+                "version of the package. Please rerun "
+                "FitModel to update the results. Setting "
+                "the number of fixed parameters to zero."
+            )
 
         print("\nModel parameters:")
         for param_idx in range(n_param):