diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 00f119b8..901337fd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: - id: check-added-large-files - id: check-toml - repo: https://github.com/python-poetry/poetry - rev: 2.2.0 + rev: 2.2.1 hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt @@ -42,7 +42,7 @@ repos: - id: yamllint exclude: ".pre-commit-config.yaml" - repo: https://github.com/psf/black - rev: 25.1.0 + rev: 25.9.0 hooks: - id: black - repo: https://github.com/asottile/blacken-docs @@ -64,7 +64,7 @@ repos: hooks: - id: vulture - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.18.1 + rev: v1.18.2 hooks: - id: mypy exclude: > diff --git a/cytotable/convert.py b/cytotable/convert.py index a98e9b91..03fed58e 100644 --- a/cytotable/convert.py +++ b/cytotable/convert.py @@ -101,7 +101,7 @@ def _get_table_columns_and_types( ddb_reader.execute( select_query.replace("&select_source", select_source) ) - .arrow() + .fetch_arrow_table() .to_pylist() ) @@ -122,7 +122,7 @@ def _get_table_columns_and_types( ddb_reader.execute( select_query.replace("&select_source", "arrow_data_tbl") ) - .arrow() + .fetch_arrow_table() .to_pylist() ) else: @@ -509,7 +509,7 @@ def _source_pageset_to_parquet( /* optional ordering per pageset */ {"ORDER BY " + source['page_key'] if sort_output else ""}; """ - ).arrow(), + ).fetch_arrow_table(), where=result_filepath, ) # Include exception handling to read mixed-type data @@ -925,7 +925,7 @@ def _join_source_pageset( /* optional sorting per pagset */ {"ORDER BY " + page_key if sort_output else ""}; """ - ).arrow() + ).fetch_arrow_table() # drop nulls if specified if drop_null: diff --git a/cytotable/sources.py b/cytotable/sources.py index f2000492..c86358c5 100644 --- a/cytotable/sources.py +++ b/cytotable/sources.py @@ -134,7 +134,7 @@ def _get_source_filepaths( """, parameters=[str(element["source_path"])], ) - .arrow()["table_name"] + .fetch_arrow_table()["table_name"] .to_pylist() # make sure the table names match with compartment + metadata names if targets is not None diff --git a/tests/conftest.py b/tests/conftest.py index 14b28a69..315e3d49 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -500,7 +500,7 @@ def col_renames(name: str, table: pa.Table): AND nuclei.Metadata_ObjectNumber = cytoplasm.Metadata_Cytoplasm_Parent_Nuclei """ ) - .arrow() + .fetch_arrow_table() ) # reversed order column check as col removals will change index order @@ -566,7 +566,7 @@ def fixture_cellprofiler_merged_nf1data( AND nuclei.Nuclei_Number_Object_Number = cytoplasm.Cytoplasm_Parent_Nuclei """ ) - .arrow() + .fetch_arrow_table() .drop_null() ) diff --git a/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py b/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py index f78d0d06..71425ae1 100644 --- a/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py +++ b/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py @@ -29,7 +29,7 @@ FROM read_csv_auto('{data_file}') """ ) - .arrow() + .fetch_arrow_table() .schema, } ) @@ -65,7 +65,7 @@ /* select rows C and D to limit the dataset */ AND data_file."ROW" in ('C', 'D') """ - ).arrow(), + ).fetch_arrow_table(), # output the filtered data as a CSV to a new location output_file=( f"{TARGET_DATA_DIR}/{OUTPUT_FILENAME}" diff --git a/tests/test_convert.py b/tests/test_convert.py index 474f8543..2345330c 100644 --- a/tests/test_convert.py +++ b/tests/test_convert.py @@ -691,7 +691,7 @@ def test_run_export_workflow( ignore_errors=TRUE) """ ) - .arrow() + .fetch_arrow_table() ) parquet_result = parquet.ParquetDataset( path_or_paths=flattened_result["table"], @@ -756,7 +756,7 @@ def test_run_export_workflow_unsorted( ignore_errors=TRUE) """ ) - .arrow() + .fetch_arrow_table() ) parquet_result = parquet.ParquetDataset( path_or_paths=flattened_result["table"], @@ -1354,7 +1354,7 @@ def test_in_carta_to_parquet( SELECT * FROM read_csv_auto('{data_dir}/*.csv') """ - ).arrow() + ).fetch_arrow_table() # process the data with cytotable using in-carta preset cytotable_result = convert(