Re-organizing key dataclasses into a single model.py and then exposing those for import from prymer.

prymer/__init__.py

@@ -0,0 +1,7 @@
+from prymer.model import MinOptMax
+from prymer.model import Oligo
+from prymer.model import PrimerPair
+from prymer.model import Span
+from prymer.model import Strand
+
+__all__ = ["Strand", "Span", "Oligo", "PrimerPair", "MinOptMax"]

prymer/api/__init__.py

@@ -1,10 +1,4 @@
-from prymer.api.minoptmax import MinOptMax
-from prymer.api.oligo import Oligo
 from prymer.api.picking import build_primer_pairs
-from prymer.api.primer_pair import PrimerPair
-from prymer.api.span import BedLikeCoords
-from prymer.api.span import Span
-from prymer.api.span import Strand
 from prymer.api.variant_lookup import FileBasedVariantLookup
 from prymer.api.variant_lookup import SimpleVariant
 from prymer.api.variant_lookup import VariantLookup
@@ -14,13 +8,7 @@
 from prymer.api.variant_lookup import disk_based
 
 __all__ = [
-    "MinOptMax",
     "build_primer_pairs",
-    "Oligo",
-    "PrimerPair",
-    "Span",
-    "Strand",
-    "BedLikeCoords",
     "VariantType",
     "SimpleVariant",
     "VariantLookup",

prymer/api/coordmath.py

@@ -1,51 +1,7 @@
 """
-# Methods for coordinate-based math and interval manipulation.
-
-Contains the following public methods:
-
-- [`require_same_refname()`][prymer.api.coordmath.require_same_refname] -- ensures that all
-    provided intervals have the same reference name.
-- [`get_locus_string()`][prymer.api.coordmath.get_locus_string] -- returns a formatted
-    string for an interval (`<refname>:<start>-<end>`).
-- [`get_closed_end()`][prymer.api.coordmath.get_closed_end] -- gets the closed end of an
-    interval given its start and length.
-
+# Methods for coordinate-based math.
 """
 
-from pybedlite.overlap_detector import Interval
-
-
-def require_same_refname(*intervals: Interval) -> None:
-    """
-    Require that the input intervals all have the same refname.
-
-    Args:
-        intervals: one or more intervals
-
-    Raises:
-        ValueError: if the intervals do not all have the same refname.
-    """
-
-    refnames = set(i.refname for i in intervals)
-    if len(refnames) != 1:
-        raise ValueError(f"`intervals` must have exactly one refname\n Found {sorted(refnames)}")
-
-
-def get_locus_string(record: Interval) -> str:
-    """
-    Get the locus-string for an interval.
-
-    The output string will have the format `<refname>:<start>-<end>`
-    No conversion on coordinates is performed, so the output is 0-based, open-ended.
-
-    Args:
-        record: The interval to get the locus-string for.
-
-    Returns:
-        A locus-string for the interval.
-    """
-    return f"{record.refname}:{record.start}-{record.end}"
-
 
 def get_closed_end(start: int, length: int) -> int:
     """