Merge Primer*Weights into Primer3Parameters, remove Primer3Input

prymer/api/picking.py

@@ -30,7 +30,7 @@
 from prymer.model import Oligo
 from prymer.model import PrimerPair
 from prymer.model import Span
-from prymer.primer3 import PrimerAndAmpliconWeights
+from prymer.primer3 import PrimerParameters
 
 
 def score(
@@ -40,7 +40,7 @@ def score(
     amplicon_tm: float,
     amplicon_sizes: MinOptMax[int],
     amplicon_tms: MinOptMax[float],
-    weights: PrimerAndAmpliconWeights,
+    params: PrimerParameters,
 ) -> float:
     """Score the amplicon in a manner similar to Primer3
 
@@ -59,7 +59,7 @@ def score(
         amplicon_tm: the melting temperature of the amplicon
         amplicon_sizes: minimum, optimal, and maximum amplicon sizes (lengths)
         amplicon_tms: minimum, optimal, and maximum amplicon Tms
-        weights: the set of penalty weights
+        params: the set of primer3 parameters
 
     Returns:
         the penalty for the whole amplicon.
@@ -73,9 +73,9 @@ def score(
     if amplicon_sizes.opt == 0:
         size_penalty = 0.0
     elif amplicon.length > amplicon_sizes.opt:
-        size_penalty = (amplicon.length - amplicon_sizes.opt) * weights.product_size_gt
+        size_penalty = (amplicon.length - amplicon_sizes.opt) * params.amplicon_size_wt.gt
     else:
-        size_penalty = (amplicon_sizes.opt - amplicon.length) * weights.product_size_lt
+        size_penalty = (amplicon_sizes.opt - amplicon.length) * params.amplicon_size_wt.lt
 
     # The penalty for the amplicon melting temperature.
     # The difference in melting temperature between the calculated and optimal is weighted by the
@@ -84,9 +84,9 @@ def score(
     if amplicon_tms.opt == 0.0:
         tm_penalty = 0.0
     elif amplicon_tm > amplicon_tms.opt:
-        tm_penalty = (amplicon_tm - amplicon_tms.opt) * weights.product_tm_gt
+        tm_penalty = (amplicon_tm - amplicon_tms.opt) * params.amplicon_tm_wt.gt
     else:
-        tm_penalty = (amplicon_tms.opt - amplicon_tm) * weights.product_tm_lt
+        tm_penalty = (amplicon_tms.opt - amplicon_tm) * params.amplicon_tm_wt.lt
 
     # Put it all together
     return left_primer.penalty + right_primer.penalty + size_penalty + tm_penalty
@@ -99,7 +99,7 @@ def build_primer_pairs(  # noqa: C901
     amplicon_sizes: MinOptMax[int],
     amplicon_tms: MinOptMax[float],
     max_heterodimer_tm: Optional[float],
-    weights: PrimerAndAmpliconWeights,
+    params: PrimerParameters,
     fasta_path: Path,
     thermo: Optional[Thermo] = None,
 ) -> Iterator[PrimerPair]:
@@ -116,11 +116,11 @@ def build_primer_pairs(  # noqa: C901
         amplicon_sizes: minimum, optimal, and maximum amplicon sizes (lengths)
         amplicon_tms: minimum, optimal, and maximum amplicon Tms
         max_heterodimer_tm: if supplied, heterodimer Tms will be calculated for primer pairs,
-          and those exceeding the maximum Tm will be discarded
-        weights: the set of penalty weights
+            and those exceeding the maximum Tm will be discarded
+        params: the set of penalty params
         fasta_path: the path to the FASTA file from which the amplicon sequence will be retrieved.
         thermo: a [`Thermo`][prymer.Thermo] instance for performing thermodynamic calculations
-          including amplicon tm; if not provided, a default Thermo instance will be created
+            including amplicon tm; if not provided, a default Thermo instance will be created
 
     Returns:
         An iterator over all the valid primer pairs, sorted by primer pair penalty.
@@ -197,7 +197,7 @@ def build_primer_pairs(  # noqa: C901
                 amplicon_tm=amp_tm,
                 amplicon_sizes=amplicon_sizes,
                 amplicon_tms=amplicon_tms,
-                weights=weights,
+                params=params,
             )
 
             pairings.append((i, j, penalty, amp_tm))

prymer/model.py

@@ -83,6 +83,48 @@ def __str__(self) -> str:
         return f"(min:{self.min}, opt:{self.opt}, max:{self.max})"
 
 
+@dataclass(slots=True, frozen=True, init=True)
+class Weights:
+    """Stores a pair of penalty weights.
+
+    Weights are used when comparing a primer or probe property (e.g. primer length) to the optimal
+    parameterized value.  If the value is less than, then the `lt` weight is used.  If the value is
+    greater than, then the `gt` weight is used.
+
+    The two values can be either int or float values but must be of the same type within one
+    Range object (for example, `lt` cannot be a float while `gt` is an int).
+
+    Examples of interacting with the `Range` class
+
+    ```python
+    >>> range = Weights(lt=1.0, gt=4.0)
+    >>> print(range)
+    (lt:1.0, gt:4.0)
+    >>> list(range)
+    [1.0, 4.0]
+
+    ```
+
+    Attributes:
+        lt: the minimum value (inclusive)
+        gt: the maximum value (inclusive)
+
+    Raises:
+        ValueError: if lt and gt are not the same type
+    """
+
+    lt: float
+    gt: float
+
+    def __iter__(self) -> Iterator[float]:
+        """Returns an iterator of min and max"""
+        return iter([self.lt, self.gt])
+
+    def __str__(self) -> str:
+        """Returns a string representation of min and max"""
+        return f"(lt:{self.lt}, gt:{self.gt})"
+
+
 @unique
 class Strand(StrEnum):
     """Represents the strand of a span to the genome."""

prymer/primer3/__init__.py

@@ -2,30 +2,26 @@
 from prymer.primer3.primer3 import Primer3Failure
 from prymer.primer3.primer3 import Primer3Result
 from prymer.primer3.primer3_failure_reason import Primer3FailureReason
-from prymer.primer3.primer3_input import Primer3Input
 from prymer.primer3.primer3_input_tag import Primer3InputTag
-from prymer.primer3.primer3_parameters import PrimerAndAmpliconParameters
+from prymer.primer3.primer3_parameters import Primer3Parameters
+from prymer.primer3.primer3_parameters import PrimerParameters
 from prymer.primer3.primer3_parameters import ProbeParameters
 from prymer.primer3.primer3_task import DesignLeftPrimersTask
 from prymer.primer3.primer3_task import DesignPrimerPairsTask
 from prymer.primer3.primer3_task import DesignRightPrimersTask
 from prymer.primer3.primer3_task import PickHybProbeOnly
-from prymer.primer3.primer3_weights import PrimerAndAmpliconWeights
-from prymer.primer3.primer3_weights import ProbeWeights
 
 __all__ = [
     "Primer3",
     "Primer3Result",
     "Primer3Failure",
     "Primer3FailureReason",
-    "Primer3Input",
     "Primer3InputTag",
     "DesignLeftPrimersTask",
     "DesignPrimerPairsTask",
     "DesignRightPrimersTask",
     "PickHybProbeOnly",
-    "PrimerAndAmpliconParameters",
+    "Primer3Parameters",
+    "PrimerParameters",
     "ProbeParameters",
-    "ProbeWeights",
-    "PrimerAndAmpliconWeights",
 ]