From 457d812f7084c8bae16728f8fc3f9d44359327d6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Dec 2025 11:55:08 +0000
Subject: [PATCH 1/3] Initial plan


From e5e549830be178e9510231b9fc52cb4c3837d211 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Dec 2025 12:03:05 +0000
Subject: [PATCH 2/3] Change skip options to single
 --skip-if-downloaded-already flag

Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com>
---
 README.md          |  4 ++--
 pridepy/pridepy.py | 26 +++++++++++++-------------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index 36030b0..6a8f38a 100644
--- a/README.md
+++ b/README.md
@@ -80,7 +80,7 @@ $ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Download
 
 Additional options: 
 
-- `--skip-if-downloaded-already` / `--no-skip-if-downloaded-already` flag is used to control whether to skip files that already exist in the output directory. By default, files are skipped if they already exist. Use `--no-skip-if-downloaded-already` to force re-download.
+- `--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.
 
@@ -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
 
diff --git a/pridepy/pridepy.py b/pridepy/pridepy.py
index 8e819d7..8821874 100644
--- a/pridepy/pridepy.py
+++ b/pridepy/pridepy.py
@@ -29,10 +29,10 @@ def main():
     help="output folder to download or copy raw files",
 )
 @click.option(
-    "--skip-if-downloaded-already/--no-skip-if-downloaded-already",
+    "--skip-if-downloaded-already",
     is_flag=True,
-    default=True,
-    help="Skip the download if the file has already been downloaded. Default is to skip.",
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 @click.option(
     "--aspera-maximum-bandwidth",
@@ -62,7 +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.
     """
@@ -102,10 +102,10 @@ def download_all_public_raw_files(
     help="output folder to download or copy raw files",
 )
 @click.option(
-    "--skip-if-downloaded-already/--no-skip-if-downloaded-already",
+    "--skip-if-downloaded-already",
     is_flag=True,
-    default=True,
-    help="Skip the download if the file has already been downloaded. Default is to skip.",
+    default=False,
+    help="Skip the download if the file has already been downloaded.",
 )
 @click.option(
     "--aspera-maximum-bandwidth",
@@ -186,10 +186,10 @@ def download_all_public_category_files(
     help="output folder to download or copy files",
 )
 @click.option(
-    "--skip-if-downloaded-already/--no-skip-if-downloaded-already",
+    "--skip-if-downloaded-already",
     is_flag=True,
-    default=True,
-    help="Skip the download if the file has already been downloaded. Default is to skip.",
+    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")
@@ -269,10 +269,10 @@ def download_file_by_name(
     help="output folder to download files",
 )
 @click.option(
-    "--skip-if-downloaded-already/--no-skip-if-downloaded-already",
+    "--skip-if-downloaded-already",
     is_flag=True,
-    default=True,
-    help="Skip the download if the file has already been downloaded. Default is to skip.",
+    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."""

From f34d523b770c3da45cf0ee834229c9d6c6296bd6 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Dec 2025 12:04:40 +0000
Subject: [PATCH 3/3] Update remaining docstrings with new default behavior

Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com>
---
 pridepy/pridepy.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pridepy/pridepy.py b/pridepy/pridepy.py
index 8821874..74afe55 100644
--- a/pridepy/pridepy.py
+++ b/pridepy/pridepy.py
@@ -143,7 +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.
@@ -223,7 +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