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+++ b/pyproject.toml @@ -23,11 +23,19 @@ build-backend = "poetry_dynamic_versioning.backend" [tool.setuptools_scm] [tool.poetry.dependencies] -python = ">=3.8,<3.12" +python = ">=3.8,<3.13" pyarrow = ">=13.0.0" -cloudpathlib = {extras = ["all"], version = "^0.15.0"} -duckdb = ">=0.8.0,<0.10.0" +cloudpathlib = {extras = ["all"], version = "^0.18.0"} +duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" parsl = ">=2023.9.25" +numpy = [ + {version = "<=1.24.4", python = "<3.12"}, + {version = ">=1.26.0", python = ">=3.12"} +] +scipy = [ + {version = "<1.12.0", python = "<3.9"}, + {version = "^1.12.0", python = ">=3.9"} +] [tool.poetry.group.dev.dependencies] pytest = "^7.4.0" diff --git a/tests/test_convert_threaded.py b/tests/test_convert_threaded.py index 99b0959a..b62d1370 100644 --- a/tests/test_convert_threaded.py +++ b/tests/test_convert_threaded.py @@ -16,6 +16,7 @@ from pyarrow import parquet from cytotable.convert import convert +from cytotable.presets import config from cytotable.sources import _get_source_filepaths @@ -124,6 +125,11 @@ def test_convert_s3_path_sqlite( race conditions with nested pytest fixture post-yield deletions. """ + # create a modified join sql for deterministic comparisons + modified_joins = ( + str(config["cellprofiler_sqlite_pycytominer"]["CONFIG_JOINS"]) + " ORDER BY ALL" + ) + # local sqlite read local_cytotable_table = parquet.read_table( source=convert( @@ -135,16 +141,7 @@ def test_convert_s3_path_sqlite( dest_datatype="parquet", chunk_size=100, preset="cellprofiler_sqlite_pycytominer", - # note: we use the threadpoolexecutor to avoid issues with multiprocessing - # in moto / mocked S3 environments. - # See here for more: https://docs.getmoto.org/en/latest/docs/faq.html#is-moto-concurrency-safe - parsl_config=Config( - executors=[ - ThreadPoolExecutor( - label="tpe_for_cytotable_testing_moto_s3", - ) - ] - ), + joins=modified_joins, ) ) @@ -164,6 +161,7 @@ def test_convert_s3_path_sqlite( # sequential s3 SQLite files. See below for more information # https://cloudpathlib.drivendata.org/stable/caching/#automatically local_cache_dir=f"{fx_tempdir}/sqlite_s3_cache/1", + joins=modified_joins, ) ) @@ -183,6 +181,7 @@ def test_convert_s3_path_sqlite( # sequential s3 SQLite files. See below for more information # https://cloudpathlib.drivendata.org/stable/caching/#automatically local_cache_dir=f"{fx_tempdir}/sqlite_s3_cache/2", + joins=modified_joins, ) )