Use Ruff linter and formatter

.gitignore

@@ -1,7 +1,6 @@
-# pycache
+# Subdirectories
 __pycache__/
-
-# vscode
+sample_data/
 .vscode/
 
 # python bytecode

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.6
+  hooks:
+    - id: ruff  # run the linter
+      args: [ --fix ]
+    - id: ruff-format  # run the formatter

docs/conf.py

@@ -8,25 +8,27 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../pygem/'))
 
-project = 'PyGEM'
-copyright = '2023, David Rounce'
-author = 'David Rounce'
-release = '1.0.1'
+sys.path.insert(0, os.path.abspath("../pygem/"))
+
+project = "PyGEM"
+copyright = "2023, David Rounce"
+author = "David Rounce"
+release = "1.0.1"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ['sphinx_book_theme',
-              'myst_parser',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.intersphinx',
-              'numpydoc',
-              'sphinx.ext.viewcode',
-              'sphinx_togglebutton',
-              ]
+extensions = [
+    "sphinx_book_theme",
+    "myst_parser",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "numpydoc",
+    "sphinx.ext.viewcode",
+    "sphinx_togglebutton",
+]
 
 myst_enable_extensions = [
     "amsmath",
@@ -39,21 +41,20 @@
     "html_image",
 ]
 
-#templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
+# templates_path = ['_templates']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 
-html_theme = 'sphinx_book_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
 
 html_theme_options = {
     "repository_url": "https://github.com/PyGEM-Community/PyGEM",
     "use_repository_button": True,
-    "show_nav_level":2,
-    "navigation_depth":3,
-    }
+    "show_nav_level": 2,
+    "navigation_depth": 3,
+}

pygem/__init__.py

@@ -5,8 +5,10 @@
 
 Distrubted under the MIT lisence
 """
+
 from importlib.metadata import version
+
 try:
     __version__ = version(__name__)
 except:
-    __version__ = None
+    __version__ = None

pygem/bin/op/duplicate_gdirs.py

@@ -7,43 +7,64 @@
 
 duplicate OGGM glacier directories
 """
+
 import argparse
 import os
 import shutil
+
 # pygem imports
 import pygem.setup.config as config
+
 # check for config
 config.ensure_config()
 # read the config
 pygem_prms = config.read_config()
 
+
 def main():
-    parser = argparse.ArgumentParser(description="Script to make duplicate oggm glacier directories - primarily to avoid corruption if parellelizing runs on a single glacier")
+    parser = argparse.ArgumentParser(
+        description="Script to make duplicate oggm glacier directories - primarily to avoid corruption if parellelizing runs on a single glacier"
+    )
     # add arguments
-    parser.add_argument('-rgi_glac_number', type=str, default=None,
-                        help='Randoph Glacier Inventory region')
-    parser.add_argument('-num_copies', type=int, default=1,
-                        help='Number of copies to create of the glacier directory data')
+    parser.add_argument(
+        "-rgi_glac_number",
+        type=str,
+        default=None,
+        help="Randoph Glacier Inventory region",
+    )
+    parser.add_argument(
+        "-num_copies",
+        type=int,
+        default=1,
+        help="Number of copies to create of the glacier directory data",
+    )
     args = parser.parse_args()
     num_copies = args.num_copies
     glac_num = args.rgi_glac_number
 
-    if (glac_num is not None) and (num_copies)>1:
-        reg,id = glac_num.split('.')
+    if (glac_num is not None) and (num_copies) > 1:
+        reg, id = glac_num.split(".")
         reg = reg.zfill(2)
         thous = id[:2]
-
-        root = pygem_prms['root'] + '/' + pygem_prms['oggm']['oggm_gdir_relpath']
-        sfix = '/per_glacier/' + f'RGI60-{reg}/' + f'RGI60-{reg}.{thous}/'
+
+        root = (
+            pygem_prms["root"] + "/" + pygem_prms["oggm"]["oggm_gdir_relpath"]
+        )
+        sfix = "/per_glacier/" + f"RGI60-{reg}/" + f"RGI60-{reg}.{thous}/"
 
         for n in range(num_copies):
-            nroot = os.path.abspath(root.replace('gdirs',f'gdirs_{n+1}'))
+            nroot = os.path.abspath(root.replace("gdirs", f"gdirs_{n + 1}"))
             # duplicate structure
-            os.makedirs(nroot + sfix + f'RGI60-{reg}.{id}', exist_ok=True)
+            os.makedirs(nroot + sfix + f"RGI60-{reg}.{id}", exist_ok=True)
             # copy directory data
-            shutil.copytree(root + sfix + f'RGI60-{reg}.{id}', nroot + sfix + f'RGI60-{reg}.{id}', dirs_exist_ok=True)
+            shutil.copytree(
+                root + sfix + f"RGI60-{reg}.{id}",
+                nroot + sfix + f"RGI60-{reg}.{id}",
+                dirs_exist_ok=True,
+            )
 
     return
 
-if __name__ == '__main__':
-    main()
+
+if __name__ == "__main__":
+    main()

pygem/bin/op/initialize.py

@@ -7,49 +7,57 @@
 
 initialization script (ensure config.yaml and get sample datasets)
 """
-import requests
-import zipfile
-import os,sys
+
+import os
 import shutil
+import zipfile
+
+import requests
 from ruamel.yaml import YAML
+
 # set up config.yaml
 import pygem.setup.config as config
+
 config.ensure_config(overwrite=True)
 
+
 def update_config_root(conf_path, datapath):
     yaml = YAML()
     yaml.preserve_quotes = True  # Preserve quotes around string values
-    
+
     # Read the YAML file
-    with open(conf_path, 'r') as file:
+    with open(conf_path, "r") as file:
         config = yaml.load(file)
 
     # Update the key with the new value
-    config['root'] = datapath
+    config["root"] = datapath
 
     # Save the updated configuration back to the file
-    with open(conf_path, 'w') as file:
+    with open(conf_path, "w") as file:
         yaml.dump(config, file)
 
+
 def print_file_tree(start_path, indent=""):
     # Loop through all files and directories in the current directory
     for item in os.listdir(start_path):
         path = os.path.join(start_path, item)
-        
+
         # Print the current item with indentation
         print(indent + "|-- " + item)
-        
+
         # Recursively call this function if the item is a directory
         if os.path.isdir(path):
             print_file_tree(path, indent + "    ")
-
+
+
 def get_confirm_token(response):
     """Extract confirmation token for Google Drive large file download."""
     for key, value in response.cookies.items():
         if key.startswith("download_warning"):
             return value
     return None
 
+
 def save_response_content(response, destination):
     """Save the response content to a file."""
     chunk_size = 32768
@@ -58,6 +66,7 @@ def save_response_content(response, destination):
             if chunk:  # Filter out keep-alive chunks
                 file.write(chunk)
 
+
 def get_unique_folder_name(dir):
     """Generate a unique folder name by appending a suffix if the folder already exists."""
     counter = 1
@@ -67,14 +76,15 @@ def get_unique_folder_name(dir):
         counter += 1
     return unique_dir
 
+
 def download_and_unzip_from_google_drive(file_id, output_dir):
     """
     Download a ZIP file from Google Drive and extract its contents.
-    
+
     Args:
         file_id (str): The Google Drive file ID.
         output_dir (str): The directory to save and extract the contents of the ZIP file.
-    
+
     Returns:
         int: 1 if the ZIP file was successfully downloaded and extracted, 0 otherwise.
     """
@@ -90,19 +100,29 @@ def download_and_unzip_from_google_drive(file_id, output_dir):
     try:
         # Start the download process
         with requests.Session() as session:
-            response = session.get(base_url, params={"id": file_id}, stream=True)
+            response = session.get(
+                base_url, params={"id": file_id}, stream=True
+            )
             token = get_confirm_token(response)
             if token:
-                response = session.get(base_url, params={"id": file_id, "confirm": token}, stream=True)
+                response = session.get(
+                    base_url,
+                    params={"id": file_id, "confirm": token},
+                    stream=True,
+                )
             save_response_content(response, zip_path)
 
         # Unzip the file
-        tmppath = os.path.join(output_dir, 'tmp')
-        with zipfile.ZipFile(zip_path, 'r') as zip_ref:
+        tmppath = os.path.join(output_dir, "tmp")
+        with zipfile.ZipFile(zip_path, "r") as zip_ref:
             zip_ref.extractall(tmppath)
 
         # get root dir name of zipped files
-        dir = [item for item in os.listdir(tmppath) if os.path.isdir(os.path.join(tmppath, item))][0]
+        dir = [
+            item
+            for item in os.listdir(tmppath)
+            if os.path.isdir(os.path.join(tmppath, item))
+        ][0]
         unzip_dir = os.path.join(tmppath, dir)
         # get unique name if root dir name already exists in output_dir
         output_dir = get_unique_folder_name(os.path.join(output_dir, dir))
@@ -112,33 +132,35 @@ def download_and_unzip_from_google_drive(file_id, output_dir):
         os.remove(zip_path)
         return output_dir  # Success
 
-    except (requests.RequestException, zipfile.BadZipFile, Exception) as e:
+    except (requests.RequestException, zipfile.BadZipFile, Exception):
         return None  # Failure
-
+
+
 def main():
     # Define the base directory
-    basedir = os.path.join(os.path.expanduser('~'), 'PyGEM')
+    basedir = os.path.join(os.path.expanduser("~"), "PyGEM")
     # Google Drive file id for sample dataset
     file_id = "1Wu4ZqpOKxnc4EYhcRHQbwGq95FoOxMfZ"
     # download and unzip
     out = download_and_unzip_from_google_drive(file_id, basedir)
 
     if out:
-        print(f"Downloaded PyGEM sample dataset:")
+        print("Downloaded PyGEM sample dataset:")
         print(os.path.abspath(out))
         try:
             print_file_tree(out)
         except:
             pass
 
     else:
-        print(f'Error downloading PyGEM sample dataset.')
+        print("Error downloading PyGEM sample dataset.")
 
     # update root path in config.yaml
     try:
-        update_config_root(config.config_file, out+'/sample_data/')
+        update_config_root(config.config_file, out + "/sample_data/")
     except:
         pass
-
+
+
 if __name__ == "__main__":
-    main()
+    main()