CI-1012 - Fix upload when given an s3 path, add include archived flag in process (#186)

* remove expand user from upload

* include archived

* bump

Author: nathanthorpe

cirro/file_utils.py

@@ -151,9 +151,9 @@ def upload_directory(directory: PathLike,
 
     for file in files:
         if isinstance(file, str):
-            file_path = Path(directory, file).expanduser()
+            file_path = Path(directory, file)
         else:
-            file_path = file.expanduser()
+            file_path = file
 
         # Check if is present in the file_path_map
         # if it is, use the mapped value as the destination path

cirro/services/process.py

@@ -15,14 +15,15 @@ class ProcessService(BaseService):
     """
     Service for interacting with the Process endpoints
     """
-    def list(self, process_type: Executor = None) -> List[Process]:
+    def list(self, process_type: Executor = None, include_archived=False) -> List[Process]:
         """
         Retrieves a list of available processes
 
         Args:
             process_type (`cirro_api_client.v1.models.Executor`): Optional process type (INGEST, CROMWELL, or NEXTFLOW)
+            include_archived: Whether to include archived processes in the list (default False)
         """
-        processes = get_processes.sync(client=self._api_client)
+        processes = get_processes.sync(client=self._api_client, include_archived=include_archived)
         return [p for p in processes if not process_type or process_type == p.executor]
 
     def get(self, process_id: str) -> ProcessDetail:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cirro"
-version = "1.9.4"
+version = "1.9.5"
 description = "CLI tool and SDK for interacting with the Cirro platform"
 authors = ["Cirro Bio <[email protected]>"]
 license = "MIT"