CytoTable 0.0.14__tar.gz → 0.0.16__tar.gz

{cytotable-0.0.14 → cytotable-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: CytoTable
-Version: 0.0.14
+Version: 0.0.16
 Summary: Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
 License: BSD-3-Clause License
 Keywords: python,cellprofiler,single-cell-analysis,way-lab

cytotable-0.0.16/cytotable/__init__.py

@@ -0,0 +1,27 @@
+"""
+__init__.py for cytotable
+"""
+
+# note: version data is maintained by poetry-dynamic-versioning (do not edit)
+__version__ = "0.0.16"
+
+# filter warnings about pkg_resources deprecation
+# note: these stem from cloudpathlib google cloud
+# dependencies.
+import warnings
+
+warnings.filterwarnings(
+    "ignore",
+    message=(".*pkg_resources is deprecated as an API.*"),
+    category=UserWarning,
+    module="google_crc32c.__config__",
+)
+
+from .convert import convert
+from .exceptions import (
+    CytoTableException,
+    DatatypeException,
+    NoInputDataException,
+    SchemaException,
+)
+from .presets import config

{cytotable-0.0.14 → cytotable-0.0.16}/cytotable/convert.py

@@ -1653,4 +1653,7 @@ def convert(  # pylint: disable=too-many-arguments,too-many-locals
             **kwargs,
         )
 
+    # cleanup Parsl executor and related
+    parsl.dfk().cleanup()
+
     return output

{cytotable-0.0.14 → cytotable-0.0.16}/cytotable/utils.py

@@ -166,12 +166,6 @@ def _duckdb_reader() -> duckdb.DuckDBPyConnection:
         https://duckdb.org/docs/sql/configuration#configuration-reference
         */
         PRAGMA preserve_insertion_order=FALSE;
-
-        /*
-        Disable progress bar from displaying (defaults to TRUE)
-        See earlier documentation references above for more information.
-        */
-        SET enable_progress_bar=FALSE;
         """,
     )
 

{cytotable-0.0.14 → cytotable-0.0.16}/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 = "0.0.14"
+version = "0.0.16"
 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"
@@ -33,13 +33,21 @@ scipy = [
 [tool.poetry.group.dev.dependencies]
 pytest = ">=7.4,<9.0"
 pytest-cov = ">=4.1,<7.0"
-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.group.docs.dependencies]
+jupyterlab = "^4.4.3"
+jupyterlab-code-formatter = "^3.0.2"
+black = "^25.1.0"
+isort = "^6.0.1"
+jupytext = "^1.17.1"
+Sphinx = ">=6,<8"
+myst-parser = ">=2,<4"
+sphinxcontrib-mermaid = ">=0.9,<1.1"
+myst-nb = "^1.2.0"
 
 [tool.poetry.requires-plugins]
 poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] }
@@ -67,6 +75,9 @@ markers = [
   "large_data_tests: tests which involve the use of large data.",
 ]
 
+[tool.jupytext]
+formats = "ipynb,py:light"
+
 [tool.vulture]
 min_confidence = 80
 paths = [ "cytotable" ]

cytotable-0.0.14/cytotable/__init__.py

@@ -1,15 +0,0 @@
-"""
-__init__.py for cytotable
-"""
-
-# note: version data is maintained by poetry-dynamic-versioning (do not edit)
-__version__ = "0.0.14"
-
-from .convert import convert
-from .exceptions import (
-    CytoTableException,
-    DatatypeException,
-    NoInputDataException,
-    SchemaException,
-)
-from .presets import config