Merge Primer*Weights into Primer3Parameters, remove Primer3Input (#112)

1. merges the `Primer*Weights` classes into their corresponding amplicon
and probe parameter classes (reduces 4 classes to two). The attributes
have the `_wt` suffix in their name. The
`primer3.primer3.primer3_weights` module is gone.
2. moves the `Primer3Input` functionality into `Primer3` directly.
`primer3.primer3.primer3_input` is now gone.
3. Adds in `WeightRange` for the weights when a value is out of range
(either less than, or greater than). Could use a better name?
4. `Primer3.design` now explicitly takes in the design task and target,
in addition to the params. It checks to make sure that the task (e.g.
design left primers) matches the params (e.g. amplicons).
5. Simplify `Primer3Task` (remove methods no longer used)

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",
 ]