rename files, bump version

Author: jkanche

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## Version 0.6.0
+## Version 0.6.0 - 0.6.1
 
 - Classes now extend `BiocObject` from biocutils, which provides a metadata field.
 - `valdiate` is renamed to `_validate` for consistency with other classes and packages.

setup.cfg

@@ -49,9 +49,9 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    genomicranges>=0.8.1
-    biocframe>=0.7.0
-    biocutils>=0.3.2
+    genomicranges>=0.8.2
+    biocframe>=0.7.2
+    biocutils>=0.3.3
 
 [options.packages.find]
 where = src

src/summarizedexperiment/rse.py …experiment/RangedSummarizedExperiment.pysrc/summarizedexperiment/rse.py renamed to src/summarizedexperiment/RangedSummarizedExperiment.py src/summarizedexperiment/rse.py renamed to src/summarizedexperiment/RangedSummarizedExperiment.py

@@ -16,7 +16,7 @@
     relaxed_merge_assays,
 )
 from ._frameutils import is_pandas
-from .se import SummarizedExperiment
+from .SummarrizedExperiment import SummarizedExperiment
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -274,7 +274,7 @@ def __str__(self) -> str:
         )
         output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n"
 
-        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}"
 
         return output
 

src/summarizedexperiment/se.py …rizedexperiment/SummarrizedExperiment.pysrc/summarizedexperiment/se.py renamed to src/summarizedexperiment/SummarrizedExperiment.py src/summarizedexperiment/se.py renamed to src/summarizedexperiment/SummarrizedExperiment.py

@@ -131,7 +131,7 @@ def combine_columns(self, *other) -> SummarizedExperiment:
     def to_rangedsummarizedexperiment(self):
         """Coerce to :py:class:`summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`"""
 
-        from .rse import RangedSummarizedExperiment
+        from .RangedSummarizedExperiment import RangedSummarizedExperiment
 
         return RangedSummarizedExperiment(
             assays=self._assays,

src/summarizedexperiment/__init__.py

@@ -15,5 +15,5 @@
 finally:
     del version, PackageNotFoundError
 
-from .se import SummarizedExperiment
-from .rse import RangedSummarizedExperiment
+from .SummarrizedExperiment import SummarizedExperiment
+from .RangedSummarizedExperiment import RangedSummarizedExperiment

src/summarizedexperiment/base.py

@@ -353,7 +353,7 @@ def __str__(self) -> str:
         )
         output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n"
 
-        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}\n"
+        output += f"metadata({str(len(self.metadata))}): {ut.print_truncated_list(list(self.metadata.keys()), sep=' ', include_brackets=False, transform=lambda y: y)}"
 
         return output
 

tests/data/summarized_experiments.py

@@ -2,7 +2,7 @@
 import numpy as np
 import scipy.sparse as sp
 from biocframe import BiocFrame
-from summarizedexperiment.se import SummarizedExperiment
+from summarizedexperiment.SummarrizedExperiment import SummarizedExperiment
 
 
 ncols = 10

tests/test_RSE.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 import pytest
-from summarizedexperiment.rse import RangedSummarizedExperiment
+from summarizedexperiment.RangedSummarizedExperiment import RangedSummarizedExperiment
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"

tests/test_RSE_methods.py

@@ -4,8 +4,8 @@
 import numpy as np
 import pandas as pd
 import pytest
-from summarizedexperiment.rse import RangedSummarizedExperiment
-from summarizedexperiment.se import SummarizedExperiment
+from summarizedexperiment.RangedSummarizedExperiment import RangedSummarizedExperiment
+from summarizedexperiment.SummarrizedExperiment import SummarizedExperiment
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"

tests/test_SE.py

@@ -3,7 +3,7 @@
 from biocframe import BiocFrame
 import numpy as np
 import pandas as pd
-from summarizedexperiment.se import SummarizedExperiment
+from summarizedexperiment.SummarrizedExperiment import SummarizedExperiment
 import delayedarray
 from anndata import AnnData