rename files, bump version

Author: jkanche

CHANGELOG.md

@@ -1,12 +1,12 @@
 # Changelog
 
-## Version 0.8.0 - 0.8.1
+## Version 0.8.0 - 0.8.2
 
-- Rename module files to follow PEP guidelines
-- Rename `GenomicRangesList` to `CompressedGenomicRangesList` and now extends compressed-lists
+- Rename `GenomicRangesList` to `CompressedGenomicRangesList` and now extends compressed-lists.
 - Classes extend `BiocObject` from biocutils, provides a default metadata attribute and helper functions.
 - Rename `validate` to `_validate` for consistency with the rest of the packages and classes.
 - Fix for empty compressed genomic ranges list.
+- Aliases `GRanges` and `CompressedGRangesList`.
 
 ## Version 0.7.0 - 0.7.3
 

setup.cfg

@@ -50,10 +50,10 @@ python_requires = >=3.9
 install_requires =
     importlib-metadata; python_version<"3.8"
     biocframe>=0.7.1
-    iranges>=0.7.0
-    biocutils>=0.3.1
+    iranges>=0.7.1
+    biocutils>=0.3.3
+    compressed_lists>=0.4.3
     numpy
-    compressed_lists>=0.4.1
 
 [options.packages.find]
 where = src

src/genomicranges/granges.py src/genomicranges/GenomicRanges.pysrc/genomicranges/granges.py renamed to src/genomicranges/GenomicRanges.py

@@ -3340,3 +3340,7 @@ def _combine_GenomicRanges(*x: GenomicRanges) -> GenomicRanges:
 @ut.extract_row_names.register(GenomicRanges)
 def _rownames_gr(x: GenomicRanges):
     return x.get_names()
+
+
+class GRanges(GenomicRanges):
+    pass

src/genomicranges/__init__.py

@@ -15,8 +15,8 @@
 finally:
     del version, PackageNotFoundError
 
-from .granges import GenomicRanges
-from .grangeslist import CompressedGenomicRangesList
+from .GenomicRanges import GenomicRanges, GRanges
+from .grangeslist import CompressedGenomicRangesList, CompressedGRangesList
 from .io.gtf import read_gtf
 from .io.ucsc import read_ucsc
 from .sequence_info import SeqInfo

src/genomicranges/grangeslist.py

@@ -8,7 +8,7 @@
 from compressed_lists.split_generic import _generic_register_helper, splitAsCompressedList
 from iranges import CompressedIRangesList, IRanges
 
-from .granges import GenomicRanges, _combine_GenomicRanges
+from .GenomicRanges import GenomicRanges, _combine_GenomicRanges
 from .sequence_info import SeqInfo
 
 __author__ = "jkanche"
@@ -373,3 +373,7 @@ def _(
     return CompressedGenomicRangesList(
         unlist_data=partitioned_data, partitioning=groups_or_partitions, metadata=metadata
     )
+
+
+class CompressedGRangesList(CompressedGenomicRangesList):
+    pass

src/genomicranges/io/gtf.py

@@ -128,6 +128,6 @@ def read_gtf(
     """
     compressed = True if file.endswith("gz") else False
     data = parse_gtf(file, compressed=compressed, skiprows=skiprows, comment=comment)
-    from ..granges import GenomicRanges
+    from ..GenomicRanges import GenomicRanges
 
     return GenomicRanges.from_pandas(data)

src/genomicranges/io/ucsc.py

@@ -58,6 +58,6 @@ def read_ucsc(
     compressed = True
     data = parse_gtf(path, compressed=compressed)
 
-    from ..granges import GenomicRanges
+    from ..GenomicRanges import GenomicRanges
 
     return GenomicRanges.from_pandas(data)

tests/test_gr_comparisons.py

@@ -4,7 +4,7 @@
 from biocframe import BiocFrame
 from iranges import IRanges
 
-from genomicranges.granges import GenomicRanges
+from genomicranges.GenomicRanges import GenomicRanges
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"

tests/test_gr_coverage.py

@@ -1,4 +1,4 @@
-from genomicranges.granges import GenomicRanges
+from genomicranges.GenomicRanges import GenomicRanges
 from iranges import IRanges
 from biocframe import BiocFrame
 from random import random

tests/test_gr_flank.py

@@ -4,7 +4,7 @@
 from biocframe import BiocFrame
 from iranges import IRanges
 
-from genomicranges.granges import GenomicRanges
+from genomicranges.GenomicRanges import GenomicRanges
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"