Install iohub from PyPI (#342)

* pin iohub version to 0.1.0.dev3 from PyPI

* remove unused fixtures

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}")

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 =