Use google-style docstrings

geofetch/cli.py

@@ -8,13 +8,25 @@
 
 
 def _safe_echo(var):
-    """Returns an environment variable if it exists, or an empty string if not"""
+    """Return an environment variable if it exists, or an empty string if not.
+
+    Args:
+        var: Environment variable name.
+
+    Returns:
+        Environment variable value or empty string.
+    """
     return os.getenv(var, "")
 
 
 def _parse_cmdl(cmdl):
-    """
-    parser
+    """Parse command line arguments.
+
+    Args:
+        cmdl: Command line arguments.
+
+    Returns:
+        Parsed arguments.
     """
     parser = VersionInHelpParser(
         description="Automatic GEO and SRA data downloader",
@@ -207,7 +219,7 @@ def _parse_cmdl(cmdl):
         help="""Optional: Filter size for processed files
                 that are stored as sample repository [Default: None].
                 Works only for sample data.
-                Supported input formats : 12B, 12KB, 12MB, 12GB. 
+                Supported input formats : 12B, 12KB, 12MB, 12GB.
                 Ignored unless 'processed' flag is set.""",
     )
 

geofetch/finder.py

@@ -27,72 +27,88 @@
 
 
 class Finder:
-    """
-    Class for finding GSE accessions in special period of time.
+    """Class for finding GSE accessions in special period of time.
+
     Additionally, user can add specific filters for the search,
-    while initialization of the class
+    while initialization of the class.
     """
 
     def __init__(self, filters: str = None, retmax: int = RETMAX):
-        """
-        :param filters: filters that have to be added to the query.
-            Filter Patterns can be found here:
-            https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Using_the_Advanced_Search_Pag
-        :param retmax: maximum number of retrieved accessions.
+        """Initialize Finder.
+
+        Args:
+            filters: Filters that have to be added to the query.
+                Filter Patterns can be found here:
+                https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Using_the_Advanced_Search_Pag.
+            retmax: Maximum number of retrieved accessions.
         """
         self.query_customized_ending = ETOOLS_ENDING.format(retmax=retmax)
         self.query_filter_str = self._create_filter_str(filters)
         self.last_result = []
 
     def get_gse_all(self) -> list:
-        """
-        Get list of all gse accession available in GEO
-        :return: list of gse accession
+        """Get list of all gse accession available in GEO.
+
+        Returns:
+            List of gse accession.
         """
         return self.get_gse_id_by_query(url=self._compose_url())
 
     def get_gse_last_3_month(self) -> list:
-        """
-        Get list of gse accession that were uploaded or updated in last 3 month
-        :return: list of gse accession
+        """Get list of gse accession that were uploaded or updated in last 3 month.
+
+        Returns:
+            List of gse accession.
         """
         return self.get_gse_id_by_query(url=self._compose_url(THREE_MONTH_FILTER))
 
     def get_gse_last_week(self) -> list:
-        """
-        Get list of gse accession that were uploaded or updated in last week
-        :return: list of gse accession
+        """Get list of gse accession that were uploaded or updated in last week.
+
+        Returns:
+            List of gse accession.
         """
         return self.get_gse_by_day_count(7)
 
     def get_gse_by_day_count(self, n_days: int = 1) -> list:
-        """
-        Get list of gse accessions that were uploaded or updated in last X days
-        :param n_days: number of days from now [e.g. 5]
-        :return: list of gse accession
+        """Get list of gse accessions that were uploaded or updated in last X days.
+
+        Args:
+            n_days: Number of days from now [e.g. 5].
+
+        Returns:
+            List of gse accession.
         """
         today = datetime.today()
         start_date = today - timedelta(days=n_days)
         start_date_str = start_date.strftime("%Y/%m/%d")
         return self.get_gse_by_date(start_date_str)
 
     def get_gse_by_date(self, start_date: str, end_date: str = None) -> list:
-        """
-        Search gse accessions by providing start date and end date. By default, the last date is today.
-        :param start_date: the oldest date of update (from YYYY/MM/DD to now) [input format: 'YYYY/MM/DD']
-        :param end_date: the nearest date of update (from __ to YYYY/MM/DD) [input format: 'YYYY/MM/DD']
-        :return: list of gse accessions
+        """Search gse accessions by providing start date and end date.
+
+        By default, the last date is today.
+
+        Args:
+            start_date: The oldest date of update (from YYYY/MM/DD to now) [input format: 'YYYY/MM/DD'].
+            end_date: The nearest date of update (from __ to YYYY/MM/DD) [input format: 'YYYY/MM/DD'].
+
+        Returns:
+            List of gse accessions.
         """
         if end_date is None:
             end_date = TODAY_DATE
         new_date_filter = DATE_FILTER.format(start_date=start_date, end_date=end_date)
         return self.get_gse_id_by_query(url=self._compose_url(new_date_filter))
 
     def get_gse_id_by_query(self, url: str) -> list:
-        """
-        Run esearch (ncbi search tool) by specifying URL and retrieve gse list result
-        :param url: url of the query
-        :return: list of gse ids
+        """Run esearch (ncbi search tool) by specifying URL and retrieve gse list result.
+
+        Args:
+            url: Url of the query.
+
+        Returns:
+            List of gse ids.
         """
         uids_list = self._run_search_query(url)
         gse_id_list = [self.uid_to_gse(d) for d in uids_list]
@@ -101,30 +117,39 @@ def get_gse_id_by_query(self, url: str) -> list:
 
     @staticmethod
     def uid_to_gse(uid: str) -> str:
-        """
-        UID to GES accession converter
-        :param uid: uid string (Unique Identifier Number in GEO)
-        :return: GSE id string
+        """Convert UID to GSE accession.
+
+        Args:
+            uid: Uid string (Unique Identifier Number in GEO).
+
+        Returns:
+            GSE id string.
         """
         uid_regex = re.compile(r"[1-9]+0+([1-9]+[0-9]*)")
         return "GSE" + uid_regex.match(uid).group(1)
 
     @staticmethod
     def find_differences(old_list: list, new_list: list) -> list:
-        """
-        Compare 2 lists and search for elements that are not in old list
-        :param old_list: old list of elements
-        :param new_list: new list of elements
-        :return: list of elements that are not in old list but are in new_list
+        """Compare 2 lists and search for elements that are not in old list.
+
+        Args:
+            old_list: Old list of elements.
+            new_list: New list of elements.
+
+        Returns:
+            List of elements that are not in old list but are in new_list.
         """
         return list(set(new_list) - set(old_list))
 
     @staticmethod
     def _run_search_query(url: str) -> list:
-        """
-        Run get request and return list of uids found
-        :param url: url of the query
-        :return: list of UIDs
+        """Run get request and return list of uids found.
+
+        Args:
+            url: Url of the query.
+
+        Returns:
+            List of UIDs.
         """
         x = requests.get(url)
         if x.status_code != 200:
@@ -143,32 +168,38 @@ def _run_search_query(url: str) -> list:
 
     @staticmethod
     def _create_filter_str(filters: str = None) -> str:
-        """
-        Tune filter for url request
-        :param filters: filter should look like here: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Using_the_Advanced_Search_Pag
-        :return: tuned filter string
+        """Tune filter for url request.
+
+        Args:
+            filters: Filter should look like here: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Using_the_Advanced_Search_Pag.
+
+        Returns:
+            Tuned filter string.
         """
         if filters == "" or filters is None:
             return ""
         return f"+(AND+{filters})"
 
     def _compose_url(self, date_filter: str = None) -> str:
-        """
-        Compose final url by adding date filter
-        :param date_filter: date filter that has to be used in the query
-        :return: string of final url
+        """Compose final url by adding date filter.
+
+        Args:
+            date_filter: Date filter that has to be used in the query.
+
+        Returns:
+            String of final url.
         """
         if date_filter is None:
             date_filter = ""
 
         return f"{ETOOLS_GEO_GSE_BASE}{self.query_filter_str}{date_filter}{self.query_customized_ending}"
 
     def generate_file(self, file_path: str, gse_list: list = None):
-        """
-        Save the list of GSE accessions stored in this Finder object to a given file
-        :param file_path: root to the file where gse accessions have to be saved
-        :param gse_list: list of gse accessions
-        :return: NoReturn
+        """Save the list of GSE accessions stored in this Finder object to a given file.
+
+        Args:
+            file_path: Root to the file where gse accessions have to be saved.
+            gse_list: List of gse accessions.
         """
         if gse_list is None:
             gse_list = self.last_result