Use Names instead of StringList, bump biocutils (#10)

also does a better job at specifying dependencies with minor and major versions.

setup.cfg

@@ -49,9 +49,8 @@ python_requires = >=3.8
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    biocutils>=0.0.7
-    biocgenerics
-    biocframe>=0.4.0
+    biocutils>=0.1.2,<0.2.0
+    biocframe>=0.5.2,<0.6.0
     numpy
 
 

src/iranges/IRanges.py

@@ -5,7 +5,7 @@
 
 import biocutils as ut
 from biocframe import BiocFrame
-from biocgenerics import combine_rows, combine_seqs, show_as_cell
+from biocutils import Names, combine_rows, combine_sequences, show_as_cell
 from numpy import array, clip, int32, ndarray, printoptions, where, zeros
 
 from .interval import calc_gap_and_overlap, create_np_interval_vector
@@ -136,7 +136,7 @@ def _sanitize_names(self, names):
         if names is None:
             return None
         elif not isinstance(names, list):
-            names = list(names)
+            names = Names(names)
 
         return names
 
@@ -308,7 +308,7 @@ def end(self) -> ndarray:
         """
         return self.get_end()
 
-    def get_names(self) -> Union[None, List[str]]:
+    def get_names(self) -> Optional[Names]:
         """Get all names.
 
         Returns:
@@ -339,7 +339,7 @@ def set_names(
         return output
 
     @property
-    def names(self) -> Union[None, List[str]]:
+    def names(self) -> Optional[Names]:
         """Get all names.
 
         Returns:
@@ -1417,8 +1417,8 @@ def union(self, other: "IRanges") -> "IRanges":
         if not isinstance(other, IRanges):
             raise TypeError("'other' is not an IRanges object.")
 
-        all_starts = combine_seqs(self.start, other.start)
-        all_widths = combine_seqs(self.width, other.width)
+        all_starts = combine_sequences(self.start, other.start)
+        all_widths = combine_sequences(self.width, other.width)
 
         output = IRanges(all_starts, all_widths)
         output = output.reduce(min_gap_width=0, drop_empty_ranges=True)
@@ -1440,8 +1440,8 @@ def setdiff(self, other: "IRanges") -> "IRanges":
         if not isinstance(other, IRanges):
             raise TypeError("'other' is not an IRanges object.")
 
-        all_starts = combine_seqs(self.start, other.start)
-        all_ends = combine_seqs(self.end, other.end)
+        all_starts = combine_sequences(self.start, other.start)
+        all_ends = combine_sequences(self.end, other.end)
         start = min(all_starts)
         end = max(all_ends)
 
@@ -1467,8 +1467,8 @@ def intersect(self, other: "IRanges") -> "IRanges":
         if not isinstance(other, IRanges):
             raise TypeError("'other' is not an IRanges object.")
 
-        all_starts = combine_seqs(self.start, other.start)
-        all_ends = combine_seqs(self.end, other.end)
+        all_starts = combine_sequences(self.start, other.start)
+        all_ends = combine_sequences(self.end, other.end)
         start = min(all_starts)
         end = max(all_ends)
 
@@ -1814,7 +1814,7 @@ def follow(
         self._delete_ncls_index()
         return hits
 
-    def distance(self, query: "IRanges") -> List[int]:
+    def distance(self, query: "IRanges") -> List[Optional[int]]:
         """Calculate the pair-wise distance with intervals in query.
 
         Args:
@@ -1847,7 +1847,7 @@ def distance(self, query: "IRanges") -> List[int]:
         return all_distances
 
 
-@combine_seqs.register
+@combine_sequences.register
 def _combine_IRanges(*x: IRanges) -> IRanges:
     has_names = False
     for y in x:
@@ -1865,8 +1865,8 @@ def _combine_IRanges(*x: IRanges) -> IRanges:
                 all_names += [""] * len(y)
 
     return IRanges(
-        start=combine_seqs(*[y._start for y in x]),
-        width=combine_seqs(*[y._width for y in x]),
+        start=combine_sequences(*[y._start for y in x]),
+        width=combine_sequences(*[y._width for y in x]),
         names=all_names,
         mcols=combine_rows(*[y._mcols for y in x]),
         metadata=x[0]._metadata,

tests/test_IRanges.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pytest
 from biocframe import BiocFrame
-from biocgenerics import combine_seqs
+from biocutils import combine_sequences
 from iranges import IRanges
 
 __author__ = "Aaron Lun"
@@ -171,22 +171,22 @@ def test_IRanges_combine():
 
     x = IRanges(starts, widths)
     y = IRanges(starts2, widths2)
-    comb = combine_seqs(x, y)
+    comb = combine_sequences(x, y)
     assert (comb.get_start() == np.array([1, 2, 3, 4, 10, 20, 30, 40])).all()
     assert (comb.get_width() == np.array([4, 5, 6, 7, 50, 60, 70, 80])).all()
     assert comb.get_names() is None
 
     x = IRanges(starts, widths, mcols=BiocFrame({"foo": ["a", "b", "c", "d"]}))
     y = IRanges(starts2, widths2, mcols=BiocFrame({"foo": ["A", "B", "C", "D"]}))
-    comb = combine_seqs(x, y)
+    comb = combine_sequences(x, y)
     assert comb.get_mcols().column("foo") == ["a", "b", "c", "d", "A", "B", "C", "D"]
 
     x = IRanges(starts, widths, names=["a", "b", "c", "d"])
     y = IRanges(starts2, widths2, names=["A", "B", "C", "D"])
-    comb = combine_seqs(x, y)
+    comb = combine_sequences(x, y)
     assert comb.get_names() == ["a", "b", "c", "d", "A", "B", "C", "D"]
 
     x = IRanges(starts, widths)
     y = IRanges(starts2, widths2, names=["A", "B", "C", "D"])
-    comb = combine_seqs(x, y)
+    comb = combine_sequences(x, y)
     assert comb.get_names() == ["", "", "", "", "A", "B", "C", "D"]

tests/test_interrange.py

@@ -27,7 +27,7 @@ def test_reduce():
 
     assert all(np.equal(reduced.start, [-6, -2, 6, 9]))
     assert all(np.equal(reduced.width, [3, 7, 0, 6]))
-    assert reduced.mcols.colnames == ["revmap"]
+    assert reduced.mcols.colnames.as_list() == ["revmap"]
 
 
 def test_reduce_drop_ranges():
@@ -38,7 +38,7 @@ def test_reduce_drop_ranges():
     reduced = x.reduce(drop_empty_ranges=True)
     assert all(np.equal(reduced.start, [-6, -2, 9]))
     assert all(np.equal(reduced.width, [3, 7, 6]))
-    assert reduced.mcols.colnames == []
+    assert reduced.mcols.colnames.as_list() == []
 
 
 def test_reduce_drop_ranges_and_revmap():
@@ -49,7 +49,7 @@ def test_reduce_drop_ranges_and_revmap():
     reduced = x.reduce(drop_empty_ranges=True, with_reverse_map=True)
     assert all(np.equal(reduced.start, [-6, -2, 9]))
     assert all(np.equal(reduced.width, [3, 7, 6]))
-    assert reduced.mcols.colnames == ["revmap"]
+    assert reduced.mcols.colnames.as_list() == ["revmap"]
 
 
 def test_gap():
@@ -82,4 +82,4 @@ def test_disjoin_with_revmap():
     dj = x.disjoin(with_reverse_map=True)
     assert all(np.equal(dj.start, [-6, -4, -2, 0, 1, 3, 9, 10, 13]))
     assert all(np.equal(dj.width, [2, 1, 2, 1, 2, 2, 1, 3, 2]))
-    assert dj.mcols.colnames == ["revmap"]
+    assert dj.mcols.colnames.as_list() == ["revmap"]