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Add punctuation to docstrings

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This commit is contained in:
Julian Stirling 2025-07-10 02:03:02 +01:00
parent 4dc41bb008
commit 80beeea07b
34 changed files with 232 additions and 235 deletions
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56
src/openflexure_microscope_server/scan_directories.py
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@ -20,7 +20,7 @@ class NotEnoughFreeSpaceError(IOError):
class ScanInfo(BaseModel):
"""Summary information about a scan folder"""
"""Summary information about a scan folder."""
name: str
created: float
@ -31,7 +31,7 @@ class ScanInfo(BaseModel):
class ScanDirectoryManager:
"""A class for managing interactions with scan directories"""
"""A class for managing interactions with scan directories."""
_base_scan_dir: str
@ -42,22 +42,22 @@ class ScanDirectoryManager:
@property
def base_dir(self) -> str:
"""The base directory scans are saved to"""
"""The base directory scans are saved to."""
return self._base_scan_dir
def exists(self, scan_name: str) -> bool:
"""Return True if scan of this name exists on disk"""
"""Return True if scan of this name exists on disk."""
return os.path.isdir(self.path_for(scan_name))
def path_for(self, scan_name: str) -> str:
"""Return the path for a given scan name
"""Return the path for a given scan name.
Returns the path even if it doesn't exist
"""
return os.path.join(self._base_scan_dir, scan_name)
def img_dir_for(self, scan_name: str) -> str:
"""Return the path for the image dir for a given scan name
"""Return the path for the image dir for a given scan name.
Returns the path even if it doesn't exist
"""
@ -66,7 +66,7 @@ class ScanDirectoryManager:
def get_file_path_from(
self, scan_name: str, filename: str, check_exists: bool = False
) -> Optional[str]:
"""Return the full file path for the file within a scan directory
"""Return the full file path for the file within a scan directory.
If check_exists is True then None will be returned if the file does
not exist.
@ -80,7 +80,7 @@ class ScanDirectoryManager:
def get_file_path_from_img_dir(
self, scan_name: str, filename: str, check_exists: bool = False
) -> Optional[str]:
"""Return the full file path for the file within a scan directory
"""Return the full file path for the file within a scan directory.
If check_exists is True, None is returned if the file does not exist. If False
then the path is returned anyway
@ -103,18 +103,18 @@ class ScanDirectoryManager:
@property
def all_scans(self) -> list[str]:
"""Return a list of the scan names in the base directory"""
"""Return a list of the scan names in the base directory."""
return [f.name for f in os.scandir(self._base_scan_dir) if f.is_dir()]
def all_scans_info(self) -> list[ScanInfo]:
"""Return a lists of ScanInfo objects for each scan"""
"""Return a lists of ScanInfo objects for each scan."""
all_info: list[ScanInfo] = []
for scan_name in self.all_scans:
all_info.append(ScanDirectory(scan_name, self.base_dir).scan_info())
return all_info
def _unique_scan_name(self, scan_name: str) -> str:
"""Get the next unique scan name starting with the given name
"""Get the next unique scan name starting with the given name.
For more explanation on the scan naming see `new_scan_dir`
"""
@ -143,7 +143,7 @@ class ScanDirectoryManager:
return f"{scan_name}_{scan_num:0{SCAN_ZERO_PAD_DIGITS}d}"
def new_scan_dir(self, scan_name: str) -> "ScanDirectory":
"""Get a unique name for this scan and create a directory for it
"""Get a unique name for this scan and create a directory for it.
The scan will be named ``{scan_name}_0001`` where the number is
zero-padded to be SCAN_ZERO_PAD_DIGITS digits long (to allow correct sorting if the
@ -165,11 +165,11 @@ class ScanDirectoryManager:
return ScanDirectory(full_scan_name, self.base_dir)
def delete_scan(self, scan_name: str) -> None:
"""Delete a scan"""
"""Delete a scan."""
shutil.rmtree(self.path_for(scan_name))
def zip_scan(self, scan_name: str, final_version: bool = False) -> "ScanDirectory":
"""Zips any images from the scan not yet zipped, return full path to zip
"""Zips any images from the scan not yet zipped, return full path to zip.
``final_version`` Set true to stitch all files not just the scan images
this should only be done at the end as it is not possible to update a file
@ -178,7 +178,7 @@ class ScanDirectoryManager:
return ScanDirectory(scan_name, self.base_dir).zip_files(final_version)
def check_free_disk_space(self, min_space: int = 500000000) -> None:
"""Raise an exception if there is not enough free disk space to continue scanning
"""Raise an exception if there is not enough free disk space to continue scanning.
:param min_space: the minimum space required in bytes.
Default = 500,000,000 (500MB)
@ -194,7 +194,7 @@ class ScanDirectoryManager:
class ScanDirectory:
"""A class for handling interactions with scan directories
"""A class for handling interactions with scan directories.
Initalisation parameters:
name: the name of the scan (the scan directory basename)
@ -214,12 +214,12 @@ class ScanDirectory:
@property
def name(self) -> str:
"""The name of the scan"""
"""The name of the scan."""
return self._name
@property
def dir_path(self) -> str:
"""The full path to the scan directory"""
"""The full path to the scan directory."""
return os.path.join(self._base_scan_dir, self._name)
@property
@ -235,17 +235,17 @@ class ScanDirectory:
@property
def created_time(self) -> float:
"""The time the directory was created on disk"""
"""The time the directory was created on disk."""
return os.path.getctime(self.dir_path)
def get_scan_files(self):
"""Return a list of the files in the images dir"""
"""Return a list of the files in the images dir."""
if self.images_dir is None:
return []
return os.listdir(self.images_dir)
def _extract_scan_images(self, file_list: list[str]):
"""Extract files which match the naming convention for scan images
"""Extract files which match the naming convention for scan images.
:param file_list: The list of files to search. Normally this would be
``self.get_scan_files()``
@ -255,7 +255,7 @@ class ScanDirectory:
return [i for i in file_list if IMAGE_REGEX.search(i)]
def _extract_final_stitches(self, file_list: list[str]):
"""Extract files which match the naming convention for final stitches
"""Extract files which match the naming convention for final stitches.
:param file_list: The list of files to search.
@ -264,7 +264,7 @@ class ScanDirectory:
return [i for i in file_list if STITCH_REGEX.search(i)]
def _extract_dzi_files(self, file_list: list[str]):
"""Extract files which match the naming convention for dzi_files
"""Extract files which match the naming convention for dzi_files.
:param file_list: The list of files to search.
@ -273,7 +273,7 @@ class ScanDirectory:
return [i for i in file_list if i.endswith("dzi")]
def get_final_stitch_name(self) -> Optional[str]:
"""Return the filename for the final stitch (in the images dir)
"""Return the filename for the final stitch (in the images dir).
If no final stitch is found, return None
"""
@ -283,11 +283,11 @@ class ScanDirectory:
return stitches[0]
def get_modified_time(self) -> float:
"""Return the modified time of the directory"""
"""Return the modified time of the directory."""
return max(os.stat(root).st_mtime for root, _, _ in os.walk(self.dir_path))
def scan_info(self) -> ScanInfo:
"""Return the information for the scan directory as a ScanInfo object"""
"""Return the information for the scan directory as a ScanInfo object."""
scan_files = self.get_scan_files()
scan_images = self._extract_scan_images(scan_files)
stitches = self._extract_final_stitches(scan_files)
@ -325,7 +325,7 @@ class ScanDirectory:
return files
def zip_files(self, final_version: bool = False) -> str:
"""Zips any images from the scan not yet zipped, return full path to zip
"""Zips any images from the scan not yet zipped, return full path to zip.
``final_version`` Set true to stitch all files not just the scan images
this should only be done at the end as it is not possible to update a file
@ -357,6 +357,6 @@ class ScanDirectory:
def get_files_in_zip(zip_path):
"""List the relative paths of all files and folders in the zip folder specified"""
"""List the relative paths of all files and folders in the zip folder specified."""
scan_zip = zipfile.ZipFile(zip_path)
return [os.path.normpath(i) for i in scan_zip.namelist()]