Bump requests from 2.28.2 to 2.31.0 (#129)

cytomining · Nov 13, 2023 · f5e45af · f5e45af
1 parent 35c348c
commit f5e45af
Show file tree

Hide file tree

Showing 3 changed files with 55 additions and 53 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/tests/test_convert.py b/tests/test_convert.py
@@ -32,7 +32,7 @@
 )
 from cytotable.exceptions import CytoTableException
 from cytotable.presets import config
-from cytotable.sources import _get_source_filepaths, _infer_source_datatype
+from cytotable.sources import _infer_source_datatype
 from cytotable.utils import (
     _column_sort,
     _duckdb_reader,
@@ -137,53 +137,6 @@ def test_extend_path(fx_tempdir: str):
     assert _expand_path(path=f"{subdir}/..") == pathlib.Path(fx_tempdir).resolve()
 
 
-def test_get_source_filepaths(
-    load_parsl_default: None, fx_tempdir: str, data_dir_cellprofiler: str
-):
-    """
-    Tests _get_source_filepaths
-    """
-
-    # test that no sources raises an exception
-    empty_dir = pathlib.Path(f"{fx_tempdir}/temp")
-    empty_dir.mkdir(parents=True, exist_ok=True)
-    with pytest.raises(Exception):
-        single_dir_result = _get_source_filepaths(
-            path=empty_dir,
-            targets=["image", "cells", "nuclei", "cytoplasm"],
-        ).result()
-
-    # check that single sqlite file is returned as desired
-    single_file_result = _get_source_filepaths(
-        path=pathlib.Path(
-            f"{data_dir_cellprofiler}/NF1_SchwannCell_data/all_cellprofiler.sqlite"
-        ),
-        targets=["cells"],
-    ).result()
-    assert len(set(single_file_result.keys())) == 1
-
-    # check that single csv file is returned as desired
-    single_file_result = _get_source_filepaths(
-        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman/Cells.csv"),
-        targets=["cells"],
-    ).result()
-    assert len(set(single_file_result.keys())) == 1
-
-    single_dir_result = _get_source_filepaths(
-        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman"),
-        targets=["cells"],
-    ).result()
-    # test that the single dir structure includes 1 unique key (for cells)
-    assert len(set(single_dir_result.keys())) == 1
-
-    single_dir_result = _get_source_filepaths(
-        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman"),
-        targets=["image", "cells", "nuclei", "cytoplasm"],
-    ).result()
-    # test that the single dir structure includes 4 unique keys
-    assert len(set(single_dir_result.keys())) == 4
-
-
 def test_prepend_column_name(load_parsl_default: None, fx_tempdir: str):
     """
     Tests _prepend_column_name

diff --git a/tests/test_convert_threaded.py b/tests/test_convert_threaded.py
@@ -10,11 +10,13 @@
 
 import parsl
 import pyarrow as pa
+import pytest
 from parsl.config import Config
 from parsl.executors import ThreadPoolExecutor
 from pyarrow import parquet
 
 from cytotable.convert import convert
+from cytotable.sources import _get_source_filepaths
 
 
 def test_convert_tpe_cellprofiler_csv(
@@ -198,3 +200,50 @@ def test_convert_s3_path_sqlite(
             [(name, "ascending") for name in s3_cytotable_table_nested.schema.names]
         )
     )
+
+
+def test_get_source_filepaths(
+    load_parsl_threaded: None, fx_tempdir: str, data_dir_cellprofiler: str
+):
+    """
+    Tests _get_source_filepaths
+    """
+
+    # test that no sources raises an exception
+    empty_dir = pathlib.Path(f"{fx_tempdir}/temp")
+    empty_dir.mkdir(parents=True, exist_ok=True)
+    with pytest.raises(Exception):
+        single_dir_result = _get_source_filepaths(
+            path=empty_dir,
+            targets=["image", "cells", "nuclei", "cytoplasm"],
+        ).result()
+
+    # check that single sqlite file is returned as desired
+    single_file_result = _get_source_filepaths(
+        path=pathlib.Path(
+            f"{data_dir_cellprofiler}/NF1_SchwannCell_data/all_cellprofiler.sqlite"
+        ),
+        targets=["cells"],
+    ).result()
+    assert len(set(single_file_result.keys())) == 1
+
+    # check that single csv file is returned as desired
+    single_file_result = _get_source_filepaths(
+        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman/Cells.csv"),
+        targets=["cells"],
+    ).result()
+    assert len(set(single_file_result.keys())) == 1
+
+    single_dir_result = _get_source_filepaths(
+        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman"),
+        targets=["cells"],
+    ).result()
+    # test that the single dir structure includes 1 unique key (for cells)
+    assert len(set(single_dir_result.keys())) == 1
+
+    single_dir_result = _get_source_filepaths(
+        path=pathlib.Path(f"{data_dir_cellprofiler}/ExampleHuman"),
+        targets=["image", "cells", "nuclei", "cytoplasm"],
+    ).result()
+    # test that the single dir structure includes 4 unique keys
+    assert len(set(single_dir_result.keys())) == 4