format numpydoc (#306)

- add hook
- format numpydoc

Author: njzjz

.pre-commit-config.yaml

@@ -20,6 +20,12 @@ repos:
     rev: 22.12.0
     hooks:
     -   id: black-jupyter
+# numpydoc
+-   repo: https://github.com/Carreau/velin
+    rev: 0.0.12
+    hooks:
+    - id: velin
+      args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
     rev: 1.13.0

dpdispatcher/ssh_context.py

@@ -673,9 +673,9 @@ def block_checkcall(self, cmd, asynchronously=False, stderr_whitelist=None):
 
         Parameters
         ----------
-        cmd: str
+        cmd : str
             The command to run.
-        asynchronously: bool, optional, default=False
+        asynchronously : bool, optional, default=False
             Run command asynchronously. If True, `nohup` will be used to run the command.
         """
         assert self.remote_root is not None
@@ -795,16 +795,16 @@ def _put_files(
 
         Parameters
         ----------
-        files: list
+        files : list
             uploaded files
-        dereference: bool, default: True
+        dereference : bool, default: True
             If dereference is False, add symbolic and hard links to the archive.
             If it is True, add the content of the target files to the archive.
             This has no effect on systems that do not support symbolic links.
-        directories: list, default: None
+        directories : list, default: None
             uploaded directories non-recursively. Use `files` for uploading
             recursively
-        tar_compress: bool, default: True
+        tar_compress : bool, default: True
             If tar_compress is True, compress the archive using gzip
             It it is False, then it is uncompressed
         """

dpdispatcher/utils.py

@@ -14,7 +14,7 @@ def get_sha256(filename):
 
     Parameters
     ----------
-    filename: str
+    filename : str
         The filename.
 
     Returns
@@ -49,12 +49,12 @@ def generate_totp(secret: str, period: int = 30, token_length: int = 6) -> str:
 
     Parameters
     ----------
-    secret: str
+    secret : str
         The encoded secret provided by the HPC. It's usually extracted
         from a 2D code and base32 encoded.
-    period: int, default=30
+    period : int, default=30
         Time period where the code is valid in seconds.
-    token_length: int, default=6
+    token_length : int, default=6
         The token length.
 
     Returns
@@ -90,9 +90,9 @@ def rsync(
 
     Parameters
     ----------
-    from_file: str
+    from_file : str
         SRC
-    to_file: str
+    to_file : str
         DEST
     port : int, default=22
         port for ssh
@@ -149,11 +149,11 @@ def retry(
 
     Parameters
     ----------
-    max_retry: int, default=3
+    max_retry : int, default=3
         The maximum retry times. If None, it will retry forever.
-    sleep: int or float, default=60
+    sleep : int or float, default=60
         The sleep time in seconds.
-    catch_exception: Exception, default=Exception
+    catch_exception : Exception, default=Exception
         The exception to catch.
 
     Returns