From c9790f8075696a9a185b6395bcfe5b5b5a5ba3c6 Mon Sep 17 00:00:00 2001
From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Date: Fri, 14 Apr 2023 17:25:01 -0700
Subject: [PATCH 1/2] pin iohub version to 0.1.0.dev3 from PyPI

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index e3030f3d..8bf83809 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -48,7 +48,7 @@ install_requires =
 	napari;'arm64' in platform_machine # without Qt and skimage
 	PyQt6;'arm64' in platform_machine
 	importlib-metadata
-	iohub @ git+https://github.com/czbiohub/iohub.git@v0.1.0dev1
+	iohub==0.1.0.dev3
 	
 [options.extras_require]
 dev =

From ae051239e6b21035ee658af39a825ee4d627e7e1 Mon Sep 17 00:00:00 2001
From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
Date: Fri, 14 Apr 2023 17:33:35 -0700
Subject: [PATCH 2/2] remove unused fixtures

---
 recOrder/tests/conftest.py | 92 --------------------------------------
 1 file changed, 92 deletions(-)

diff --git a/recOrder/tests/conftest.py b/recOrder/tests/conftest.py
index 612917cf..e69de29b 100644
--- a/recOrder/tests/conftest.py
+++ b/recOrder/tests/conftest.py
@@ -1,92 +0,0 @@
-import pytest
-import shutil
-import os
-from wget import download
-
-
-@pytest.fixture(scope="session")
-def setup_test_data():
-    # create /pytest_temp/ and /pytest_temp/rawdata/ folders,
-    temp_folder = os.path.join(os.getcwd(), "pytest_temp")
-    test_data = os.path.join(temp_folder, "test_data")
-    if not os.path.isdir(temp_folder):
-        os.mkdir(temp_folder)
-        print("\nsetting up temp folder")
-    if not os.path.isdir(test_data):
-        os.mkdir(test_data)
-
-    #  download data to /pytest_temp/ folder if it doesn't already exist
-    url = "https://zenodo.org/record/6983916/files/recOrder_test_data.zip?download=1"
-    output = os.path.join(test_data, "recOrder_test_Data.zip")
-    if not os.listdir(test_data):
-        print("Downloading test files...")
-        download(url, out=output)
-        shutil.unpack_archive(output, extract_dir=test_data)
-
-    yield test_data
-
-
-@pytest.fixture()
-def get_ometiff_data_dir(setup_test_data):
-    test_data = setup_test_data
-
-    ometiff_data = os.path.join(
-        test_data,
-        "2022_08_04_recOrder_pytest_20x_04NA",
-        "2T_3P_16Z_128Y_256X_Kazansky_1",
-    )
-
-    return test_data, ometiff_data
-
-
-@pytest.fixture()
-def get_zarr_data_dir(setup_test_data):
-    test_data = setup_test_data
-
-    zarr_data = os.path.join(
-        test_data,
-        "2022_08_04_recOrder_pytest_20x_04NA_zarr",
-        "2T_3P_16Z_128Y_256X_Kazansky.zarr",
-    )
-
-    return test_data, zarr_data
-
-
-@pytest.fixture()
-def get_bf_data_dir(setup_test_data):
-    test_data = setup_test_data
-
-    bf_data = os.path.join(
-        test_data,
-        "2022_08_04_recOrder_pytest_20x_04NA_BF",
-        "2T_3P_16Z_128Y_256X_Kazansky_BF_1",
-    )
-
-    return test_data, bf_data
-
-
-@pytest.fixture()
-def get_pycromanager_data_dir(setup_test_data):
-    test_data = setup_test_data
-
-    pm_data = os.path.join(test_data, "mm2.0-20210713_pm0.13.2_2p_3t_2c_7z_1")
-
-    return test_data, pm_data
-
-
-# create /pytest_temp/data_save folder for each test then delete when test is done
-@pytest.fixture(scope="function")
-def setup_data_save_folder():
-    temp_folder = os.path.join(os.getcwd(), "pytest_temp")
-    data_save_folder = os.path.join(temp_folder, "data_save")
-    if not os.path.isdir(data_save_folder):
-        os.mkdir(data_save_folder)
-        print("\nsetting up data_save folder")
-
-    yield data_save_folder
-
-    try:
-        # remove temp folder
-        shutil.rmtree(data_save_folder)
-    except OSError as e:
-        print(f"Error while deleting temp folder: {e.strerror}")