Merge branch 'main' into neuroconv_aws

catalystneuro · Dec 6, 2024 · cfe9ade · cfe9ade
2 parents 253855b + 54e6ea9
commit cfe9ade
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,8 +14,10 @@
 * Added the `rclone_transfer_batch_job` helper function for executing Rclone data transfers in AWS Batch jobs. [PR #1085](https://github.com/catalystneuro/neuroconv/pull/1085)
 * Added the `deploy_neuroconv_batch_job` helper function for deploying NeuroConv AWS Batch jobs. [PR #1086](https://github.com/catalystneuro/neuroconv/pull/1086)
 
+
 ## Improvements
 * Use mixing tests for ecephy's mocks [PR #1136](https://github.com/catalystneuro/neuroconv/pull/1136)
+* Use pytest format for dandi tests to avoid window permission error on teardown [PR #1151](https://github.com/catalystneuro/neuroconv/pull/1151)
 
 # v0.6.5 (November 1, 2024)
 

diff --git a/tests/test_minimal/test_tools/dandi_transfer_tools.py b/tests/test_minimal/test_tools/dandi_transfer_tools.py
@@ -1,13 +1,9 @@
 import os
 import sys
 from datetime import datetime
-from pathlib import Path
 from platform import python_version as get_python_version
-from shutil import rmtree
-from tempfile import mkdtemp
 
 import pytest
-from hdmf.testing import TestCase
 from pynwb import NWBHDF5IO
 
 from neuroconv.tools.data_transfers import automatic_dandi_upload
@@ -24,80 +20,63 @@
     not HAVE_DANDI_KEY,
     reason="You must set your DANDI_API_KEY to run this test!",
 )
-class TestAutomaticDANDIUpload(TestCase):
-    def setUp(self):
-        self.tmpdir = Path(mkdtemp())
-        self.nwb_folder_path = self.tmpdir / "test_nwb"
-        self.nwb_folder_path.mkdir()
-        metadata = get_default_nwbfile_metadata()
-        metadata["NWBFile"].update(
-            session_start_time=datetime.now().astimezone(),
-            session_id=f"test-automatic-upload-{sys.platform}-{get_python_version().replace('.', '-')}",
-        )
-        metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
-        with NWBHDF5IO(path=self.nwb_folder_path / "test_nwb_1.nwb", mode="w") as io:
-            io.write(make_nwbfile_from_metadata(metadata=metadata))
+def test_automatic_dandi_upload(tmp_path):
+    nwb_folder_path = tmp_path / "test_nwb"
+    nwb_folder_path.mkdir()
+    metadata = get_default_nwbfile_metadata()
+    metadata["NWBFile"].update(
+        session_start_time=datetime.now().astimezone(),
+        session_id=f"test-automatic-upload-{sys.platform}-{get_python_version().replace('.', '-')}",
+    )
+    metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
+    with NWBHDF5IO(path=nwb_folder_path / "test_nwb_1.nwb", mode="w") as io:
+        io.write(make_nwbfile_from_metadata(metadata=metadata))
 
-    def tearDown(self):
-        rmtree(self.tmpdir)
-
-    def test_automatic_dandi_upload(self):
-        automatic_dandi_upload(dandiset_id="200560", nwb_folder_path=self.nwb_folder_path, staging=True)
+    automatic_dandi_upload(dandiset_id="200560", nwb_folder_path=nwb_folder_path, staging=True)
 
 
 @pytest.mark.skipif(
     not HAVE_DANDI_KEY,
     reason="You must set your DANDI_API_KEY to run this test!",
 )
-class TestAutomaticDANDIUploadNonParallel(TestCase):
-    def setUp(self):
-        self.tmpdir = Path(mkdtemp())
-        self.nwb_folder_path = self.tmpdir / "test_nwb"
-        self.nwb_folder_path.mkdir()
-        metadata = get_default_nwbfile_metadata()
-        metadata["NWBFile"].update(
-            session_start_time=datetime.now().astimezone(),
-            session_id=f"test-automatic-upload-{sys.platform}-{get_python_version().replace('.', '-')}-non-parallel",
-        )
-        metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
-        with NWBHDF5IO(path=self.nwb_folder_path / "test_nwb_2.nwb", mode="w") as io:
-            io.write(make_nwbfile_from_metadata(metadata=metadata))
-
-    def tearDown(self):
-        rmtree(self.tmpdir)
+def test_automatic_dandi_upload_non_parallel(tmp_path):
+    nwb_folder_path = tmp_path / "test_nwb"
+    nwb_folder_path.mkdir()
+    metadata = get_default_nwbfile_metadata()
+    metadata["NWBFile"].update(
+        session_start_time=datetime.now().astimezone(),
+        session_id=(f"test-automatic-upload-{sys.platform}-" f"{get_python_version().replace('.', '-')}-non-parallel"),
+    )
+    metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
+    with NWBHDF5IO(path=nwb_folder_path / "test_nwb_2.nwb", mode="w") as io:
+        io.write(make_nwbfile_from_metadata(metadata=metadata))
 
-    def test_automatic_dandi_upload_non_parallel(self):
-        automatic_dandi_upload(
-            dandiset_id="200560", nwb_folder_path=self.nwb_folder_path, staging=True, number_of_jobs=1
-        )
+    automatic_dandi_upload(dandiset_id="200560", nwb_folder_path=nwb_folder_path, staging=True, number_of_jobs=1)
 
 
 @pytest.mark.skipif(
     not HAVE_DANDI_KEY,
     reason="You must set your DANDI_API_KEY to run this test!",
 )
-class TestAutomaticDANDIUploadNonParallelNonThreaded(TestCase):
-    def setUp(self):
-        self.tmpdir = Path(mkdtemp())
-        self.nwb_folder_path = self.tmpdir / "test_nwb"
-        self.nwb_folder_path.mkdir()
-        metadata = get_default_nwbfile_metadata()
-        metadata["NWBFile"].update(
-            session_start_time=datetime.now().astimezone(),
-            session_id=f"test-automatic-upload-{sys.platform}-{get_python_version().replace('.', '-')}-non-parallel-non-threaded",
-        )
-        metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
-        with NWBHDF5IO(path=self.nwb_folder_path / "test_nwb_3.nwb", mode="w") as io:
-            io.write(make_nwbfile_from_metadata(metadata=metadata))
-
-    def tearDown(self):
-        rmtree(self.tmpdir)
+def test_automatic_dandi_upload_non_parallel_non_threaded(tmp_path):
+    nwb_folder_path = tmp_path / "test_nwb"
+    nwb_folder_path.mkdir()
+    metadata = get_default_nwbfile_metadata()
+    metadata["NWBFile"].update(
+        session_start_time=datetime.now().astimezone(),
+        session_id=(
+            f"test-automatic-upload-{sys.platform}-"
+            f"{get_python_version().replace('.', '-')}-non-parallel-non-threaded"
+        ),
+    )
+    metadata.update(Subject=dict(subject_id="foo", species="Mus musculus", age="P1D", sex="U"))
+    with NWBHDF5IO(path=nwb_folder_path / "test_nwb_3.nwb", mode="w") as io:
+        io.write(make_nwbfile_from_metadata(metadata=metadata))
 
-    def test_automatic_dandi_upload_non_parallel_non_threaded(self):
-        automatic_dandi_upload(
-            dandiset_id="200560",
-            nwb_folder_path=self.nwb_folder_path,
-            staging=True,
-            number_of_jobs=1,
-            number_of_threads=1,
-        )
+    automatic_dandi_upload(
+        dandiset_id="200560",
+        nwb_folder_path=nwb_folder_path,
+        staging=True,
+        number_of_jobs=1,
+        number_of_threads=1,
+    )