CytoTable 0.0.11__tar.gz → 0.0.12__tar.gz

{cytotable-0.0.11 → cytotable-0.0.12}/PKG-INFO

@@ -1,19 +1,19 @@
 Metadata-Version: 2.1
 Name: CytoTable
-Version: 0.0.11
+Version: 0.0.12
 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-0.0.11 → cytotable-0.0.12}/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__ = "0.0.12"
 
 from .convert import convert
 from .exceptions import (

{cytotable-0.0.11 → cytotable-0.0.12}/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-0.0.11 → cytotable-0.0.12}/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-0.0.11 → cytotable-0.0.12}/pyproject.toml

@@ -5,7 +5,7 @@ requires = [ "poetry-core>=1", "poetry-dynamic-versioning>=1,<2" ]
 [tool.poetry]
 name = "CytoTable"
 # note: version data is maintained by poetry-dynamic-versioning (do not edit)
-version = "0.0.11"
+version = "0.0.12"
 description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools."
 authors = [ "Cytomining Community" ]
 license = "BSD-3-Clause License"
@@ -16,7 +16,7 @@ documentation = "https://cytomining.github.io/CytoTable/"
 keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.13"
+python = ">=3.9,<3.14"
 pyarrow = ">=13.0.0"
 cloudpathlib = { extras = [ "all", "s3" ], version = "^0.18.0" }
 duckdb = ">=0.8.0,!=0.10.0,>=0.10.1"
@@ -31,15 +31,15 @@ scipy = [
 ]
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
-pytest-cov = "^4.1.0"
-Sphinx = "^6.0.0"
-myst-parser = "^2.0.0"
-sphinxcontrib-mermaid = "^0.9.0"
+pytest = ">=7.4,<9.0"
+pytest-cov = ">=4.1,<6.0"
+Sphinx = ">=6,<8"
+myst-parser = ">=2,<4"
+sphinxcontrib-mermaid = ">=0.9,<1.1"
 cytominer-database = "^0.3.4"
 pycytominer = "^1.1.0"
 dunamai = "^1.19.0"
-botocore = "^1.34.133"           # added to help avoid dependency reolution issues
+botocore = "^1.34.133"               # added to help avoid dependency reolution issues
 
 [tool.poetry-dynamic-versioning]
 enable = false