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Install iohub from PyPI #342

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merged 2 commits into from
Apr 15, 2023
Merged

Install iohub from PyPI #342

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c9790f8
pin iohub version to 0.1.0.dev3 from PyPI
ziw-liu Apr 15, 2023
ae05123
remove unused fixtures
ziw-liu Apr 15, 2023
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92 changes: 0 additions & 92 deletions recOrder/tests/conftest.py
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Original file line number Diff line number Diff line change
@@ -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}")
2 changes: 1 addition & 1 deletion setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -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 =
Expand Down