From d5df89fe3dc3b56d1485aa8cd3fd9ff30b7ccfa7 Mon Sep 17 00:00:00 2001 From: tfenne Date: Wed, 15 Jan 2025 05:34:14 -0700 Subject: [PATCH] Update imports in tests to use prymer over prymer.model --- tests/api/test_picking.py | 8 ++++---- tests/api/test_variant_lookup.py | 4 ++-- tests/conftest.py | 4 ++-- tests/model/test_minoptmax.py | 2 +- tests/model/test_oligo.py | 6 +++--- tests/model/test_primer_pair.py | 8 ++++---- tests/model/test_span.py | 4 ++-- tests/offtarget/test_offtarget.py | 8 ++++---- tests/primer3/test_primer3.py | 10 +++++----- tests/primer3/test_primer3_input.py | 6 +++--- tests/primer3/test_primer3_parameters.py | 2 +- tests/primer3/test_primer3_task.py | 4 ++-- 12 files changed, 33 insertions(+), 33 deletions(-) diff --git a/tests/api/test_picking.py b/tests/api/test_picking.py index 48f9f2a..69747ec 100644 --- a/tests/api/test_picking.py +++ b/tests/api/test_picking.py @@ -7,12 +7,12 @@ from fgpyo.fasta.builder import FastaBuilder from fgpyo.sequence import reverse_complement +from prymer import MinOptMax +from prymer import Oligo +from prymer import PrimerPair +from prymer import Span from prymer.api import picking from prymer.api.melting import calculate_long_seq_tm -from prymer.model import MinOptMax -from prymer.model import Oligo -from prymer.model import PrimerPair -from prymer.model import Span from prymer.primer3 import PrimerAndAmpliconWeights diff --git a/tests/api/test_variant_lookup.py b/tests/api/test_variant_lookup.py index d07ada0..f6d1367 100644 --- a/tests/api/test_variant_lookup.py +++ b/tests/api/test_variant_lookup.py @@ -12,6 +12,8 @@ from fgpyo.vcf.builder import VcfFieldType from pysam import VariantRecord +from prymer import Span +from prymer import Strand from prymer.api.variant_lookup import FileBasedVariantLookup from prymer.api.variant_lookup import SimpleVariant from prymer.api.variant_lookup import VariantOverlapDetector @@ -19,8 +21,6 @@ from prymer.api.variant_lookup import cached from prymer.api.variant_lookup import calc_maf_from_filter from prymer.api.variant_lookup import disk_based -from prymer.model import Span -from prymer.model import Strand @pytest.mark.parametrize( diff --git a/tests/conftest.py b/tests/conftest.py index 1e53365..d2a582a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -8,8 +8,8 @@ from fgpyo.fasta.sequence_dictionary import SequenceDictionary from fgpyo.fasta.sequence_dictionary import SequenceMetadata -from prymer.model import Span -from prymer.model import Strand +from prymer import Span +from prymer import Strand @pytest.fixture diff --git a/tests/model/test_minoptmax.py b/tests/model/test_minoptmax.py index 5492cb4..e5d526a 100644 --- a/tests/model/test_minoptmax.py +++ b/tests/model/test_minoptmax.py @@ -2,7 +2,7 @@ import pytest -from prymer.model import MinOptMax +from prymer import MinOptMax Numeric = TypeVar("Numeric", int, float) diff --git a/tests/model/test_oligo.py b/tests/model/test_oligo.py index f2223c5..5de090d 100644 --- a/tests/model/test_oligo.py +++ b/tests/model/test_oligo.py @@ -6,9 +6,9 @@ import pytest from fgpyo.fasta.sequence_dictionary import SequenceDictionary -from prymer.model import Oligo -from prymer.model import Span -from prymer.model import Strand +from prymer import Oligo +from prymer import Span +from prymer import Strand @pytest.mark.parametrize( diff --git a/tests/model/test_primer_pair.py b/tests/model/test_primer_pair.py index 980606e..c3d46a7 100644 --- a/tests/model/test_primer_pair.py +++ b/tests/model/test_primer_pair.py @@ -6,10 +6,10 @@ from fgpyo.fasta.sequence_dictionary import SequenceDictionary from fgpyo.sequence import reverse_complement -from prymer.model import Oligo -from prymer.model import PrimerPair -from prymer.model import Span -from prymer.model import Strand +from prymer import Oligo +from prymer import PrimerPair +from prymer import Span +from prymer import Strand @dataclass(init=True, frozen=True) diff --git a/tests/model/test_span.py b/tests/model/test_span.py index 2605600..b744fe9 100644 --- a/tests/model/test_span.py +++ b/tests/model/test_span.py @@ -1,8 +1,8 @@ import pytest from fgpyo.fasta.sequence_dictionary import SequenceDictionary -from prymer.model import Span -from prymer.model import Strand +from prymer import Span +from prymer import Strand @pytest.mark.parametrize( diff --git a/tests/offtarget/test_offtarget.py b/tests/offtarget/test_offtarget.py index b28ab5f..99cc68a 100644 --- a/tests/offtarget/test_offtarget.py +++ b/tests/offtarget/test_offtarget.py @@ -5,10 +5,10 @@ import pytest from fgpyo.sam import Cigar -from prymer.model import Oligo -from prymer.model import PrimerPair -from prymer.model import Span -from prymer.model import Strand +from prymer import Oligo +from prymer import PrimerPair +from prymer import Span +from prymer import Strand from prymer.offtarget.bwa import BWA_EXECUTABLE_NAME from prymer.offtarget.bwa import BwaHit from prymer.offtarget.bwa import BwaResult diff --git a/tests/primer3/test_primer3.py b/tests/primer3/test_primer3.py index d7955af..8c0ce6f 100644 --- a/tests/primer3/test_primer3.py +++ b/tests/primer3/test_primer3.py @@ -6,12 +6,12 @@ import pytest from fgpyo.sequence import reverse_complement +from prymer import MinOptMax +from prymer import Oligo +from prymer import PrimerPair +from prymer import Span +from prymer import Strand from prymer.api.variant_lookup import cached -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 from prymer.primer3.primer3 import Primer3 from prymer.primer3.primer3 import Primer3Failure from prymer.primer3.primer3 import Primer3Result diff --git a/tests/primer3/test_primer3_input.py b/tests/primer3/test_primer3_input.py index 71b2c25..e855e29 100644 --- a/tests/primer3/test_primer3_input.py +++ b/tests/primer3/test_primer3_input.py @@ -1,8 +1,8 @@ import pytest -from prymer.model import MinOptMax -from prymer.model import Span -from prymer.model import Strand +from prymer import MinOptMax +from prymer import Span +from prymer import Strand from prymer.primer3 import DesignLeftPrimersTask from prymer.primer3 import DesignPrimerPairsTask from prymer.primer3 import DesignRightPrimersTask diff --git a/tests/primer3/test_primer3_parameters.py b/tests/primer3/test_primer3_parameters.py index 115e0cd..47f397f 100644 --- a/tests/primer3/test_primer3_parameters.py +++ b/tests/primer3/test_primer3_parameters.py @@ -2,7 +2,7 @@ import pytest -from prymer.model import MinOptMax +from prymer import MinOptMax from prymer.primer3.primer3_input_tag import Primer3InputTag from prymer.primer3.primer3_parameters import PrimerAndAmpliconParameters from prymer.primer3.primer3_parameters import ProbeParameters diff --git a/tests/primer3/test_primer3_task.py b/tests/primer3/test_primer3_task.py index b4cdf81..eaf80b7 100644 --- a/tests/primer3/test_primer3_task.py +++ b/tests/primer3/test_primer3_task.py @@ -1,7 +1,7 @@ import pytest -from prymer.model import Span -from prymer.model import Strand +from prymer import Span +from prymer import Strand from prymer.primer3.primer3_input_tag import Primer3InputTag from prymer.primer3.primer3_task import DesignLeftPrimersTask from prymer.primer3.primer3_task import DesignPrimerPairsTask