Extract the body of the main for loop in build_primer_pairs() into an alternative constructor on PrimerPair

[msto]

This would reduce the complexity of that function, make it easier for the user to write custom pairing functions, and make things easier to test.

prymer/prymer/api/picking.py

Lines 139 to 177 in 8cbc1a2

	with NtThermoAlign() as ntthal:
	# generate all the primer pairs that don't violate hard size and Tm constraints
	for lp in left_primers:
	for rp in right_primers:
	if rp.span.end - lp.span.start + 1 > amplicon_sizes.max:
	continue
	amp_mapping = Span(refname=target.refname, start=lp.span.start, end=rp.span.end)
	amp_bases = bases[
	amp_mapping.start - region_start : amp_mapping.end - region_start + 1
	]
	amp_tm = calculate_long_seq_tm(amp_bases)
	if amp_tm < amplicon_tms.min or amp_tm > amplicon_tms.max:
	continue
	if max_heterodimer_tm is not None:
	if ntthal.duplex_tm(lp.bases, rp.bases) > max_heterodimer_tm:
	continue
	penalty = score(
	left_primer=lp,
	right_primer=rp,
	amplicon=amp_mapping,
	amplicon_tm=amp_tm,
	amplicon_sizes=amplicon_sizes,
	amplicon_tms=amplicon_tms,
	weights=weights,
	)
	pp = PrimerPair(
	left_primer=lp,
	right_primer=rp,
	amplicon_sequence=amp_bases,
	amplicon_tm=amp_tm,
	penalty=penalty,
	)
	yield pp

e.g.

@classmethod
def from_primers(cls, left_primer: Oligo, right_primer: Oligo, ...) -> "PrimerPair"
    ...

and so the body becomes:

for left_primer, right_primer in itertools.product(left_primers, right_primers):
    pair = PrimerPair.from_primers(
        left_primer=left_primer, 
        right_primer=right_primer,
        ...
        )
        
    # Implement filtering in terms of PrimerPair attributes
    ...
    
    yield pair

The constructor could accept an optional Path or FastaFile from which to extract the amplicon sequence. The constructor could accept the various amplicon parameters and weights to compute the score internally, or simply have the score be provided as an argument.