CytoTable 0.0.11__py3-none-any.whl → 0.0.13__py3-none-any.whl

cytotable/__init__.py

@@ -3,7 +3,7 @@ __init__.py for cytotable
 """
 
 # note: version data is maintained by poetry-dynamic-versioning (do not edit)
-__version__ = "0.0.11"
+__version__ = "0.0.13"
 
 from .convert import convert
 from .exceptions import (

cytotable/presets.py

@@ -41,6 +41,7 @@ config = {
         "CONFIG_JOINS": """
             SELECT
                 image.Metadata_ImageNumber,
+                COLUMNS('Image_FileName_.*'),
                 cytoplasm.* EXCLUDE (Metadata_ImageNumber),
                 cells.* EXCLUDE (Metadata_ImageNumber, Metadata_ObjectNumber),
                 nuclei.* EXCLUDE (Metadata_ImageNumber, Metadata_ObjectNumber)
@@ -92,6 +93,7 @@ config = {
                 per_image.Metadata_ImageNumber,
                 per_image.Image_Metadata_Well,
                 per_image.Image_Metadata_Plate,
+                COLUMNS('Image_FileName_.*'),
                 per_cytoplasm.* EXCLUDE (Metadata_ImageNumber),
                 per_cells.* EXCLUDE (Metadata_ImageNumber),
                 per_nuclei.* EXCLUDE (Metadata_ImageNumber)
@@ -148,6 +150,7 @@ config = {
                 image.Metadata_Well,
                 image.Image_Metadata_Site,
                 image.Image_Metadata_Row,
+                COLUMNS('Image_FileName_.*'),
                 cytoplasm.* EXCLUDE (Metadata_ImageNumber),
                 cells.* EXCLUDE (Metadata_ImageNumber),
                 nuclei.* EXCLUDE (Metadata_ImageNumber)
@@ -206,6 +209,7 @@ config = {
                 per_image.Metadata_ImageNumber,
                 per_image.Image_Metadata_Well,
                 per_image.Image_Metadata_Plate,
+                COLUMNS('Image_FileName_.*'),
                 per_cytoplasm.* EXCLUDE (Metadata_ImageNumber),
                 per_cells.* EXCLUDE (Metadata_ImageNumber),
                 per_nuclei.* EXCLUDE (Metadata_ImageNumber)
@@ -265,6 +269,7 @@ config = {
                 image.Metadata_ImageNumber,
                 image.Image_Metadata_Well,
                 image.Image_Metadata_Plate,
+                COLUMNS('Image_FileName_.*'),
                 cytoplasm.* EXCLUDE (Metadata_TableNumber, Metadata_ImageNumber),
                 cells.* EXCLUDE (Metadata_TableNumber, Metadata_ImageNumber),
                 nuclei.* EXCLUDE (Metadata_TableNumber, Metadata_ImageNumber)

cytotable/sources.py

@@ -163,14 +163,17 @@ def _get_source_filepaths(
         for unique_source in set(source["source_path"].name for source in sources):
             grouped_sources[unique_source.capitalize()] = [
                 # case for files besides sqlite
-                source if source["source_path"].suffix.lower() != ".sqlite"
-                # if we have sqlite entries, update the source_path to the parent
-                # (the parent table database file) as grouped key name will now
-                # encapsulate the table name details.
-                else {
-                    "source_path": source["source_path"].parent,
-                    "table_name": source["table_name"],
-                }
+                (
+                    source
+                    if source["source_path"].suffix.lower() != ".sqlite"
+                    # if we have sqlite entries, update the source_path to the parent
+                    # (the parent table database file) as grouped key name will now
+                    # encapsulate the table name details.
+                    else {
+                        "source_path": source["source_path"].parent,
+                        "table_name": source["table_name"],
+                    }
+                )
                 for source in sources
                 # focus only on entries which include the unique_source name
                 if source["source_path"].name == unique_source

cytotable/utils.py

@@ -415,7 +415,7 @@ def _arrow_type_cast_if_specified(
 
 
 def _expand_path(
-    path: Union[str, pathlib.Path, AnyPath]
+    path: Union[str, pathlib.Path, AnyPath],
 ) -> Union[pathlib.Path, AnyPath]:
     """
     Expands "~" user directory references with the user's home directory, and expands variable references with values from the environment. After user/variable expansion, the path is resolved and an absolute path is returned.
@@ -569,7 +569,7 @@ def _unwrap_source(
     source: Union[
         Dict[str, Union[parsl.dataflow.futures.AppFuture, Any]],
         Union[parsl.dataflow.futures.AppFuture, Any],
-    ]
+    ],
 ) -> Union[Dict[str, Any], Any]:
     """
     Helper function to unwrap futures from sources.
@@ -594,7 +594,7 @@ def _unwrap_source(
 
 
 def evaluate_futures(
-    sources: Union[Dict[str, List[Dict[str, Any]]], List[Any], str]
+    sources: Union[Dict[str, List[Dict[str, Any]]], List[Any], str],
 ) -> Any:
     """
     Evaluates any Parsl futures for use within other tasks.

{cytotable-0.0.11.dist-info → cytotable-0.0.13.dist-info}/METADATA

@@ -1,19 +1,18 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: CytoTable
-Version: 0.0.11
+Version: 0.0.13
 Summary: Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
-Home-page: https://github.com/cytomining/CytoTable
 License: BSD-3-Clause License
 Keywords: python,cellprofiler,single-cell-analysis,way-lab
 Author: Cytomining Community
-Requires-Python: >=3.8,<3.13
+Requires-Python: >=3.9,<3.14
 Classifier: License :: Other/Proprietary License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: cloudpathlib[all,s3] (>=0.18.0,<0.19.0)
 Requires-Dist: duckdb (>=0.10.1)
 Requires-Dist: numpy (<=1.24.4) ; python_version < "3.12"

cytotable-0.0.13.dist-info/RECORD

@@ -0,0 +1,11 @@
+cytotable/__init__.py,sha256=oohhN_5xl7FYudOQeaflYlKCwL0fBBM_ANxuuPKSFYM,316
+cytotable/constants.py,sha256=w_AUm_fKKXeZjnZxbHf-dxq7NN7BkvCWbkGK24sfzLw,1872
+cytotable/convert.py,sha256=5VHnw0eGdfXTbSfeEoPAPVa-dtobM6VHkIJwscLe68M,60651
+cytotable/exceptions.py,sha256=NhkMswjCB0HeVHqlLXzBlyHunQIp_4eBFmyAPu0Nf30,482
+cytotable/presets.py,sha256=rmDOJ-r2yXj0Kr9GlnINKQR8QA3BVLM5z0UAiV0kK0k,15036
+cytotable/sources.py,sha256=LBkLxOhKo-g3_RYAEQnipV6dxbn7IQETDKfd81jjWSo,12371
+cytotable/utils.py,sha256=9zOEFWtGauzoZEJD-2PWFhzHeLlbzKHYfYCcZB4mag8,22581
+cytotable-0.0.13.dist-info/LICENSE,sha256=lPK3PtUMP-f1EOFMUr8h3FvuMh89x249Hvm4lchTsv0,1528
+cytotable-0.0.13.dist-info/METADATA,sha256=N7p0JoPHS_mhT1EfytBddcxB2fL3qECsJM7an9IaAaw,3374
+cytotable-0.0.13.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+cytotable-0.0.13.dist-info/RECORD,,

{cytotable-0.0.11.dist-info → cytotable-0.0.13.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.1.1
 Root-Is-Purelib: true
 Tag: py3-none-any

cytotable-0.0.11.dist-info/RECORD

@@ -1,11 +0,0 @@
-cytotable/__init__.py,sha256=KSVr7xOOrpmQ_ybzcsZkblTAzPIYEq7_bm-Cjc874FM,316
-cytotable/constants.py,sha256=w_AUm_fKKXeZjnZxbHf-dxq7NN7BkvCWbkGK24sfzLw,1872
-cytotable/convert.py,sha256=5VHnw0eGdfXTbSfeEoPAPVa-dtobM6VHkIJwscLe68M,60651
-cytotable/exceptions.py,sha256=NhkMswjCB0HeVHqlLXzBlyHunQIp_4eBFmyAPu0Nf30,482
-cytotable/presets.py,sha256=CpUrVSCfsV9CDvNfkNj-rAOguA68lb2-w7g-XMcHezU,14806
-cytotable/sources.py,sha256=TY4dkbwh1PDCNapmMHE09Ey7QPYPhmp5DeErh3Wp4rw,12283
-cytotable/utils.py,sha256=tywZg1Gr78ebLlOp8R7trkiV7jsQ4iiZt4B6qG6SrxY,22578
-cytotable-0.0.11.dist-info/LICENSE,sha256=lPK3PtUMP-f1EOFMUr8h3FvuMh89x249Hvm4lchTsv0,1528
-cytotable-0.0.11.dist-info/METADATA,sha256=sOvdWxld2Ryyjd5bluZt8Z78uElg1CyWG0UIRJn0F8E,3424
-cytotable-0.0.11.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-cytotable-0.0.11.dist-info/RECORD,,