refactor: revert thermo-related attributes, params, weights; revert d…

…oc-tests and unit-tests

docs/overview.md

@@ -3,7 +3,7 @@
 The `prymer` Python library is intended to be used for three main purposes:
 
 1. [Clustering targets](#clustering-targets) into larger amplicons prior to designing primers.
-2. [Designing oligos](#designing-primers) using Primer3 for each target from (1).
+2. [Designing](#designing-primers) primers (single and paired) and internal hybridization probes using Primer3 for each target from (1).
 3. [Build and Picking a set of primer pairs](#build-and-picking-primer-pairs) from the design candidates produced in (2).
 
 ## Clustering Targets
@@ -18,7 +18,7 @@ amplicons prior to primer design.
 Designing primers (left or right) or primer pairs using Primer3 is primarily performed using the 
 [`Primer3`][prymer.primer3.primer3.Primer3] class, which wraps the
 [`primer3` command line tool](https://github.com/primer3-org/primer3).  The 
-[`design_oligos()`][prymer.primer3.primer3.Primer3.design_oligos] facilitates the design of primers (single and paired) and internal hybridization probes 
+[`design()`][prymer.primer3.primer3.Primer3.design] method facilitates the design of primers (single and paired) and internal hybridization probes 
 for a single target. The `Primer3` instance is intended to be re-used to design primers across multiple targets, or 
 re-design (after changing parameters) for the same target, or both!
 

prymer/api/oligo.py

@@ -1,7 +1,7 @@
 """
 # Oligo Class and Methods
 
-This module contains a class and class methods to represent an oligo designed by Primer3.
+This module contains a class and class methods to represent an oligo (e.g., designed by Primer3).
 
 Oligos can represent single primer and/or internal probe designs.
 
@@ -88,20 +88,10 @@ class Oligo(OligoLike, Metric["Oligo"]):
     The penalty for a primer is set by the combination of `PrimerAndAmpliconParameters` and
     `PrimerWeights`, whereas a probe penalty is set by `ProbeParameters` and `ProbeWeights`.
 
-    The values for `self_any`, `self_any_th`, `self_end`, `self_end_th`, and `hairpin_th`
-    are emitted by Primer3 as part of oligo design. These attributes are optional to maintain
-    flexibility for reading in and writing `Oligo` objects, espeically when design settings are
-    inconsistent.
-
     Attributes:
         tm: the calculated melting temperature of the oligo
         penalty: the penalty or score for the oligo
         span: the mapping of the primer to the genome
-        self_any: probe self-complementarity, expressed as local alignment score
-        self_any_th: probe self-complementarity, expressed as melting temperature
-        self_end: 3' end complementarity, expressed as local alignment score
-        self_end_th: 3' end complementarity, expressed as melting temperature
-        hairpin_th: hairpin formation thermodynamics of the oligo as calculated by Primer3
         bases: the base sequence of the oligo (excluding any tail)
         tail: an optional tail sequence to put on the 5' end of the primer
         name: an optional name to use for the primer
@@ -111,11 +101,6 @@ class Oligo(OligoLike, Metric["Oligo"]):
     tm: float
     penalty: float
     span: Span
-    self_any: Optional[float] = None
-    self_any_th: Optional[float] = None
-    self_end: Optional[float] = None
-    self_end_th: Optional[float] = None
-    hairpin_th: Optional[float] = None
     bases: Optional[str] = None
     tail: Optional[str] = None
 

prymer/api/oligo_like.py

@@ -25,7 +25,6 @@
 from abc import abstractmethod
 from dataclasses import dataclass
 from typing import Optional
-from typing import TypeVar
 from typing import assert_never
 
 from fgpyo.sequence import gc_content
@@ -124,7 +123,3 @@ def _strand_to_location_string(self) -> str:
             case _:  # pragma: no cover
                 # Not calculating coverage on this line as it should be impossible to reach
                 assert_never(f"Encountered unhandled Strand value: {self.span.strand}")
-
-
-OligoLikeType = TypeVar("OligoLikeType", bound=OligoLike)
-"""Type variable for classes generic over `OligoLike` types."""

prymer/api/primer.py

@@ -1,64 +1,4 @@
-"""
-# Primer Class and Methods
-
-This module contains a class and class methods to represent a primer (e.g. designed by Primer3)
-
-Class attributes include the primer sequence, melting temperature, and the score of the primer. The
-mapping of the primer to the genome is also stored.
-
-Optional attributes include naming information and a tail sequence  to attach to the 5' end of the
-primer (if applicable).
-
-## Examples of interacting with the `Primer` class
-
-```python
->>> from prymer.api.span import Span, Strand
->>> primer_span = Span(refname="chr1", start=1, end=20)
->>> primer = Oligo(tm=70.0, penalty=-123.0, span=primer_span)
->>> primer.longest_hp_length()
-0
->>> primer.length
-20
->>> primer.name is None
-True
->>> primer = Oligo(tm=70.0, penalty=-123.0, span=primer_span)
->>> primer.longest_hp_length()
-0
->>> primer.untailed_length()
-20
->>> primer.tailed_length()
-20
->>> primer = primer.with_tail(tail="GATTACA")
->>> primer.untailed_length()
-20
->>> primer.tailed_length()
-27
->>> primer = primer.with_name(name="foobar")
->>> primer.name
-'foobar'
-
-```
-
-Primers may also be written to a file and subsequently read back in, as the `Primer` class is an
-`fgpyo` `Metric` class:
-
-```python
->>> from pathlib import Path
->>> left_span = Span(refname="chr1", start=1, end=20)
->>> left = Oligo(tm=70.0, penalty=-123.0, span=left_span)
->>> right_span = Span(refname="chr1", start=101, end=120)
->>> right = Oligo(tm=70.0, penalty=-123.0, span=right_span)
->>> path = Path("/tmp/path/to/primers.txt")
->>> Oligo.write(path, left, right)  # doctest: +SKIP
->>> primers = Oligo.read(path)  # doctest: +SKIP
->>> list(primers)  # doctest: +SKIP
-[
-    Primer(tm=70.0, penalty=-123.0, span=amplicon_span, bases="G"*20),
-    Primer(tm=70.0, penalty=-123.0, span=amplicon_span, bases="T"*20)
-]
-
-```
-"""
+"""This module is deprecated - see prymer/api/oligo.py"""
 
 import warnings
 from dataclasses import dataclass
@@ -68,8 +8,12 @@
 
 @dataclass(frozen=True, init=True, slots=True)
 class Primer(Oligo):
-    """A deprecated alias for `Oligo` intended to maintain backwards
-    compatibility with earlier releases of `prymer`."""
+    """
+    A deprecated alias for `Oligo`.
+
+    This class exists to maintain backwards compatibility with earlier releases of `prymer`
+    and may be removed in a future version.
+    """
 
     warnings.warn(
         "The Primer class was deprecated, use Oligo instead",

prymer/api/primer_pair.py

@@ -37,7 +37,7 @@ class methods to represent a primer pair.  The primer pair is comprised of a lef
 Span(refname='chr1', start=21, end=100, strand=<Strand.POSITIVE: '+'>)
 
 >>> list(primer_pair)
-[Oligo(name=None, tm=70.0, penalty=-123.0, span=Span(refname='chr1', start=1, end=20, strand=<Strand.POSITIVE: '+'>), self_any=None, self_any_th=None, self_end=None, self_end_th=None, hairpin_th=None, bases='GGGGGGGGGGGGGGGGGGGG', tail=None), Oligo(name=None, tm=70.0, penalty=-123.0, span=Span(refname='chr1', start=101, end=120, strand=<Strand.NEGATIVE: '-'>), self_any=None, self_any_th=None, self_end=None, self_end_th=None, hairpin_th=None, bases='TTTTTTTTTTTTTTTTTTTT', tail=None)]
+[Oligo(name=None, tm=70.0, penalty=-123.0, span=Span(refname='chr1', start=1, end=20, strand=<Strand.POSITIVE: '+'>), bases='GGGGGGGGGGGGGGGGGGGG', tail=None), Oligo(name=None, tm=70.0, penalty=-123.0, span=Span(refname='chr1', start=101, end=120, strand=<Strand.NEGATIVE: '-'>), bases='TTTTTTTTTTTTTTTTTTTT', tail=None)]
 
 ```
 """  # noqa: E501

prymer/primer3/primer3.py

@@ -43,7 +43,7 @@
 
 ```
 
-The `design_oligos()` method on `Primer3` is used to design the primers given a
+The `design()` method on `Primer3` is used to design the primers given a
 [`Primer3Input`][prymer.primer3.primer3_input.Primer3Input].  The latter includes all the
 parameters and target region.
 
@@ -63,13 +63,13 @@
     primer_and_amplicon_params=params, \
     task=DesignLeftPrimersTask(), \
 )
->>> left_result = designer.design_oligos(design_input=design_input)
+>>> left_result = designer.design(design_input=design_input)
 
 ```
 
 The `left_result` returns the [`Primer3Result`][prymer.primer3.primer3.Primer3Result]
 container class.   It contains two attributes:
-1. `filtered_designs`: filtered and ordered (by objective function score) list of primer pairs or
+1. `designs`: filtered and ordered (by objective function score) list of primer pairs or
     single primers that were returned by Primer3.
 2. `failures`: ordered list of [`Primer3Failures`][prymer.primer3.primer3.Primer3Failure]
     detailing design failure reasons and corresponding count.
@@ -84,7 +84,7 @@
 
 ```
 
-While`filtered_designs` attribute on `Primer3Result` may be used to access the list of primers or
+While the `designs` attribute on `Primer3Result` may be used to access the list of primers or
 primer pairs, it is more convenient to use the `primers()` and `primer_pairs()` methods
 to return the designed primers or primer pairs (use the method corresponding to the input task) so
 that the proper type is returned (i.e. [`Primer`][prymer.api.primer.Primer] or
@@ -343,7 +343,7 @@ def _screen_pair_results(
                 valid_primer_pair_designs.append(primer_pair)
         return valid_primer_pair_designs, dinuc_pair_failures
 
-    def design_oligos(self, design_input: Primer3Input) -> Primer3Result:  # noqa: C901
+    def design(self, design_input: Primer3Input) -> Primer3Result:  # noqa: C901
         """Designs primers, primer pairs, and/or internal probes given a target region.
 
         Args:
@@ -491,7 +491,7 @@ def _build_oligos(
 
         Args:
             design_input: the target region, design task, specifications, and scoring penalties
-            design_results: design results emitted by Primer3 and captured by design_oligos()
+            design_results: design results emitted by Primer3 and captured by design()
             design_region: the padded design region
             design_task: the design task
             unmasked_design_seq: the reference sequence corresponding to the target region
@@ -537,9 +537,6 @@ def _build_oligos(
                     tm=float(design_results[f"PRIMER_{design_task.task_type}_{idx}_TM"]),
                     penalty=float(design_results[f"PRIMER_{design_task.task_type}_{idx}_PENALTY"]),
                     span=span,
-                    self_any_th=float(design_results[f"{key}_SELF_ANY_TH"]),
-                    self_end_th=float(design_results[f"{key}_SELF_END_TH"]),
-                    hairpin_th=float(design_results[f"{key}_HAIRPIN_TH"]),
                 )
             )
         return primers
@@ -581,7 +578,7 @@ def _build_primer_pairs(
 
         Args:
             design_input: the target region, design task, specifications, and scoring penalties
-            design_results: design results emitted by Primer3 and captured by design_oligos()
+            design_results: design results emitted by Primer3 and captured by design()
             design_region: the padded design region
             unmasked_design_seq: the reference sequence corresponding to the target region
 

prymer/primer3/primer3_input.py

@@ -72,11 +72,6 @@
 PRIMER_MAX_NS_ACCEPTED -> 1
 PRIMER_LOWERCASE_MASKING -> 1
 PRIMER_NUM_RETURN -> 5
-PRIMER_MAX_SELF_ANY -> 8.0
-PRIMER_MAX_SELF_ANY_TH -> 53.0
-PRIMER_MAX_SELF_END -> 3.0
-PRIMER_MAX_SELF_END_TH -> 53.0
-PRIMER_MAX_HAIRPIN_TH -> 53.0
 PRIMER_PAIR_WT_PRODUCT_SIZE_LT -> 1
 PRIMER_PAIR_WT_PRODUCT_SIZE_GT -> 1
 PRIMER_PAIR_WT_PRODUCT_TM_LT -> 0.0
@@ -90,9 +85,6 @@
 PRIMER_WT_SIZE_GT -> 0.1
 PRIMER_WT_TM_LT -> 1.0
 PRIMER_WT_TM_GT -> 1.0
-PRIMER_WT_SELF_ANY_TH -> 0.0
-PRIMER_WT_SELF_END_TH -> 0.0
-PRIMER_WT_HAIRPIN_TH -> 0.0
 """
 
 from dataclasses import MISSING