From 9dfa5148f8a7c84cb34a50d6cb0a661128877a00 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Jun 2026 08:34:19 +0000
Subject: [PATCH 1/2] fix: use is_file() to avoid treating study-ID directories
 as CSV paths

---
 pridepy/pdc/client.py            |  4 ++--
 pridepy/tests/test_pdc_client.py | 11 +++++++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/pridepy/pdc/client.py b/pridepy/pdc/client.py
index 3e217ed..275267f 100644
--- a/pridepy/pdc/client.py
+++ b/pridepy/pdc/client.py
@@ -139,7 +139,7 @@ def parse_accessions(accession: str) -> List[str]:
         raise ValueError("--accession must not be empty")
 
     source_path = Path(accession).expanduser()
-    if source_path.exists():
+    if source_path.is_file():
         if source_path.suffix.lower() != ".csv":
             raise ValueError(f"Only CSV accession files are supported: {source_path}")
         return _read_accessions_from_csv(source_path)
@@ -168,7 +168,7 @@ def parse_download_requests(accession: str, file_type: Optional[str] = None) ->
     command_file_type = normalize_file_type(file_type) if file_type else None
     source_path = Path(accession).expanduser()
 
-    if source_path.exists():
+    if source_path.is_file():
         if source_path.suffix.lower() != ".csv":
             raise ValueError(f"Only CSV accession files are supported: {source_path}")
 
diff --git a/pridepy/tests/test_pdc_client.py b/pridepy/tests/test_pdc_client.py
index 472cc0b..5edfe68 100644
--- a/pridepy/tests/test_pdc_client.py
+++ b/pridepy/tests/test_pdc_client.py
@@ -60,6 +60,17 @@ class TestPDCAccessions(TestCase):
     def test_single_accession(self):
         assert parse_accessions("PDC000109") == ["PDC000109"]
 
+    def test_accession_not_confused_with_same_named_directory(self):
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            old_cwd = os.getcwd()
+            os.chdir(tmp_dir)
+            try:
+                os.makedirs("PDC000714")
+                assert parse_accessions("PDC000714") == ["PDC000714"]
+                assert parse_download_requests("PDC000714") == [PDCDownloadRequest("PDC000714", None)]
+            finally:
+                os.chdir(old_cwd)
+
     def test_comma_accessions_are_deduped(self):
         assert parse_accessions("PDC000109,PDC000110,PDC000109") == [
             "PDC000109",

From 629a1d163bd8afafbda9bd2ca732d117d0a9e529 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Jun 2026 08:38:08 +0000
Subject: [PATCH 2/2] chore: bump version to 0.0.17

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b94d076..e557eec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "pridepy"
-version = "0.0.16"
+version = "0.0.17"
 description = "Python Client library for PRIDE Rest API"
 readme = "README.md"
 requires-python = ">=3.9"