diff --git a/dev_requirments.txt b/dev_requirments.txt index c755e4a..5f0165a 100644 --- a/dev_requirments.txt +++ b/dev_requirments.txt @@ -1,6 +1,6 @@ numpy pymongo -scikit-image +scikit-image@ https://github.com/brianreicher/scikit-image daisy pytest mwatershed@ git+https://github.com/pattonw/mwatershed diff --git a/setup.cfg b/setup.cfg index cb25e95..e192c13 100644 --- a/setup.cfg +++ b/setup.cfg @@ -22,7 +22,7 @@ include_package_data = True install_requires = numpy pymongo - scikit-image + scikit-image @ https://github.com/brianreicher/scikit-image daisy mwatershed @ git+https://github.com/pattonw/mwatershed funlib.geometry @ git+https://github.com/funkelab/funlib.geometry diff --git a/tests/mongo_tests.py b/tests/mongo_tests.py deleted file mode 100644 index 4c6c64f..0000000 --- a/tests/mongo_tests.py +++ /dev/null @@ -1,51 +0,0 @@ -import unittest -import pymongo -from funlib.persistence import open_ds, Array, graphs, prepare_ds -import logging - - -logger: logging.Logger = logging.getLogger(__name__) - - -class MongoGraphTests(unittest.TestCase): - def test_connection(self): - db_host: str = "mongodb://localhost:27017" - db_name: str = "seg" - - mongo_drop = pymongo.MongoClient(db_host)[db_name] - collection_names: list = mongo_drop.list_collection_names() - - sample_name: str = "htem4413041148969302336" - for collection_name in collection_names: - if sample_name in collection_name: - logger.info(f"Dropping {collection_name}") - mongo_drop[collection_name].drop() - - logger.info("Opening MongoDBGraphProvider...") - rag_provider = graphs.MongoDbGraphProvider( - db_name=db_name, - host=db_host, - mode="r+", - directed=False, - position_attribute=["center_z", "center_y", "center_x"], - edges_collection=f"{sample_name}_edges", - nodes_collection=f"{sample_name}_nodes", - meta_collection=f"{sample_name}_meta", - ) - - connect_succes: bool = True - - if rag_provider.client is not None: - connect_succes = True - - self.assertEqual(connect_succes, True) - - def test_write(self): - pass - - def test_read(self): - pass - - -if __name__ == "__main__": - unittest.main()