improve skip options

README.md

@@ -80,9 +80,9 @@ $ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Download
 
 Additional options: 
 
-- `-skip` flag is used to skip the download of files that already exist in the output directory.
-- `--aspera_maximum_bandwidth` flag is used to specify the maximum bandwidth for the Aspera download. The default value is 100M.
-- `--checksum_check` flag is used to check the checksum of the downloaded files. The default value is False.
+- `--skip-if-downloaded-already` flag is used to skip files that already exist in the output directory. By default, files are re-downloaded even if they already exist. Use this flag to avoid re-downloading existing files.
+- `--aspera-maximum-bandwidth` flag is used to specify the maximum bandwidth for the Aspera download. The default value is 100M.
+- `--checksum-check` flag is used to check the checksum of the downloaded files. The default value is False.
 
 ## Downloading raw files from ProteomeXchange (PX)
 
@@ -93,7 +93,7 @@ $ pridepy download-px-raw-files -a PXD039236 -o /Users/yourname/Downloads/folder
 ```
 
 - The tool resolves the ProteomeXchange XML and downloads via FTP when available, otherwise HTTP(S).
-- Resume and skip-if-already-downloaded are supported by default.
+- Resume is supported. Use `--skip-if-downloaded-already` flag to skip files that have already been downloaded.
 
 ## Download single file by name
 

pridepy/pridepy.py

@@ -24,25 +24,24 @@ def main():
 )
 @click.option(
     "-o",
-    "--output_folder",
+    "--output-folder",
     required=True,
     help="output folder to download or copy raw files",
 )
 @click.option(
-    "-skip",
-    "--skip_if_downloaded_already",
-    required=False,
-    default=True,
-    help="Boolean value to skip the download if the file has already been downloaded.",
+    "--skip-if-downloaded-already",
+    is_flag=True,
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 @click.option(
-    "--aspera_maximum_bandwidth",
+    "--aspera-maximum-bandwidth",
     required=False,
     help="Aspera maximum bandwidth (e.g 50M, 100M, 200M), depending on the user's network bandwidth, default is 100M",
     default="100M",
 )
 @click.option(
-    "--checksum_check",
+    "--checksum-check",
     required=False,
     help="Download checksum file for project",
     is_flag=True,
@@ -63,7 +62,7 @@ def download_all_public_raw_files(
         accession (str): PRIDE project accession.
         protocol (str): Protocol for downloading files (ftp, aspera, globus). Default is ftp.
         output_folder (str): Directory to save downloaded raw files.
-        skip_if_downloaded_already (bool): Skip download if files already exist. Default is True.
+        skip_if_downloaded_already (bool): Skip download if files already exist. Default is False.
         aspera_maximum_bandwidth (str): Maximum bandwidth for Aspera protocol. Default is 100M.
         checksum_check (bool): Flag to download checksum file for the project. Default is False.
     """
@@ -98,25 +97,24 @@ def download_all_public_raw_files(
 )
 @click.option(
     "-o",
-    "--output_folder",
+    "--output-folder",
     required=True,
     help="output folder to download or copy raw files",
 )
 @click.option(
-    "-skip",
-    "--skip_if_downloaded_already",
-    required=False,
-    default=True,
-    help="Boolean value to skip the download if the file has already been downloaded.",
+    "--skip-if-downloaded-already",
+    is_flag=True,
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 @click.option(
-    "--aspera_maximum_bandwidth",
+    "--aspera-maximum-bandwidth",
     required=False,
     help="Aspera maximum bandwidth (e.g 50M, 100M, 200M), depending on the user's network bandwidth, default is 100M",
     default="100M",
 )
 @click.option(
-    "--checksum_check",
+    "--checksum-check",
     required=False,
     help="Download checksum file for project",
     is_flag=True,
@@ -145,7 +143,7 @@ def download_all_public_category_files(
         accession (str): The PRIDE project accession identifier.
         protocol (str): The protocol to use for downloading files (ftp, aspera, globus).
         output_folder (str): The directory where the files will be downloaded.
-        skip_if_downloaded_already (bool): If True, skips downloading files that already exist.
+        skip_if_downloaded_already (bool): If True, skips downloading files that already exist. Default is False.
         aspera_maximum_bandwidth (str): Maximum bandwidth for Aspera transfers.
         checksum_check (bool): If True, downloads the checksum file for the project.
         category (str): The category of files to download.
@@ -180,30 +178,29 @@ def download_all_public_category_files(
     default="ftp",
     help="Protocol to be used to download files either by ftp or aspera or from globus. Default is ftp",
 )
-@click.option("-f", "--file_name", required=True, help="fileName to be downloaded")
+@click.option("-f", "--file-name", required=True, help="fileName to be downloaded")
 @click.option(
     "-o",
-    "--output_folder",
+    "--output-folder",
     required=True,
     help="output folder to download or copy files",
 )
 @click.option(
-    "-skip",
-    "--skip_if_downloaded_already",
-    required=False,
-    default=True,
-    help="Boolean value to skip the download if the file has already been downloaded.",
+    "--skip-if-downloaded-already",
+    is_flag=True,
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 @click.option("--username", required=False, help="PRIDE login username for private files")
 @click.option("--password", required=False, help="PRIDE login password for private files")
 @click.option(
-    "--aspera_maximum_bandwidth",
+    "--aspera-maximum-bandwidth",
     required=False,
     help="Aspera maximum bandwidth (e.g 50M, 100M, 200M), depending on the user's network bandwidth, default is 100M",
     default="100M",
 )
 @click.option(
-    "--checksum_check",
+    "--checksum-check",
     required=False,
     help="Download checksum file for project",
     is_flag=True,
@@ -226,7 +223,7 @@ def download_file_by_name(
     :param protocol: Protocol to be used to download files either by ftp or aspera or from globus. Default is ftp
     :param file_name: fileName to be downloaded
     :param output_folder: output folder to download or copy files
-    :param skip_if_downloaded_already: Boolean value to skip the download if the file has already been downloaded.
+    :param skip_if_downloaded_already: Boolean value to skip the download if the file has already been downloaded. Default is False.
     :param username: PRIDE login username for private files
     :param password: PRIDE login password for private files
     :param aspera_maximum_bandwidth: Aspera maximum bandwidth (e.g 50M, 100M, 200M), depending on the user's network bandwidth, default is 100M
@@ -267,16 +264,15 @@ def download_file_by_name(
 )
 @click.option(
     "-o",
-    "--output_folder",
+    "--output-folder",
     required=True,
     help="output folder to download files",
 )
 @click.option(
-    "-skip",
-    "--skip_if_downloaded_already",
-    required=False,
-    default=True,
-    help="Boolean to skip a file if it already exists",
+    "--skip-if-downloaded-already",
+    is_flag=True,
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 def download_px_raw_files(accession: str, output_folder: str, skip_if_downloaded_already: bool):
     """CLI wrapper to download raw files via ProteomeXchange XML."""
@@ -308,7 +304,7 @@ def list_private_files(accession, user, password):
 @main.command()
 @click.option(
     "-o",
-    "--output_file",
+    "--output-file",
     required=True,
     help="output file to save all the projects metadata",
 )
@@ -324,7 +320,7 @@ def stream_projects_metadata(output_file):
 @main.command()
 @click.option(
     "-o",
-    "--output_file",
+    "--output-file",
     required=True,
     help="output file to save all the files metadata",
 )
@@ -360,7 +356,7 @@ def stream_files_metadata(accession, output_file):
 )
 @click.option(
     "-ps",
-    "--page_size",
+    "--page-size",
     required=False,
     default=100,
     type=click.IntRange(min=1, max=1000),
@@ -376,14 +372,14 @@ def stream_files_metadata(accession, output_file):
 )
 @click.option(
     "-sd",
-    "--sort_direction",
+    "--sort-direction",
     required=False,
     default="DESC",
     help="Sorting direction: ASC or DESC",
 )
 @click.option(
     "-sf",
-    "--sort_fields",
+    "--sort-fields",
     required=False,
     default=["submission_date"],
     multiple=True,