Merge pull request #124 from openvax/modernize-py3

iskandr · web-flow · commit 3cdc033deb74 · 2026-04-05T14:19:08.000-04:00
Remove Python 2 compat: six, cached-property, __future__ imports
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -19,12 +19,11 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
diff --git a/isovar/__init__.py b/isovar/__init__.py
@@ -10,9 +10,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
-__version__ = "1.3.0"
+__version__ = "1.4.0"
 
 
 from .allele_read import AlleleRead
diff --git a/isovar/alignment_score.py b/isovar/alignment_score.py
@@ -15,9 +15,6 @@
 Sequence alignment helpers
 """
 
-from __future__ import print_function, division, absolute_import
-
-
 def alignment_score(a, b, min_subsequence_length=1):
     """
     Number of mismatches between all two input sequences, allows
diff --git a/isovar/allele_read.py b/isovar/allele_read.py
@@ -15,7 +15,6 @@
 allele (ref, alt, or otherwise), and suffix portions
 """
 
-from __future__ import print_function, division, absolute_import
 import logging
 
 from .string_helpers import convert_from_bytes_if_necessary, trim_N_nucleotides
diff --git a/isovar/assembly.py b/isovar/assembly.py
@@ -10,12 +10,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from collections import defaultdict
 
-from six.moves import range
-
 from .default_parameters import MIN_VARIANT_SEQUENCE_ASSEMBLY_OVERLAP_SIZE
 from .logging import get_logger
 
diff --git a/isovar/cli/__init__.py b/isovar/cli/__init__.py
@@ -13,8 +13,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 from .main_args import make_isovar_arg_parser, run_isovar_from_parsed_args
 from .protein_sequence_args import protein_sequence_creator_from_args
 from .rna_args import read_collector_from_args
diff --git a/isovar/cli/filter_args.py b/isovar/cli/filter_args.py
@@ -14,8 +14,6 @@
 Common command-line arguments for filtering Isovar results
 """
 
-from __future__ import print_function, division, absolute_import
-
 from collections import OrderedDict
 
 from ..default_parameters import (
diff --git a/isovar/cli/isovar_allele_counts.py b/isovar/cli/isovar_allele_counts.py
@@ -14,7 +14,6 @@
 Prints number of reads supporting ref, alt, and other alleles at variant loci.
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/isovar_allele_reads.py b/isovar/cli/isovar_allele_reads.py
@@ -14,7 +14,6 @@
 Prints names and sequences of reads overlapping a given set of variants.
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/isovar_main.py b/isovar/cli/isovar_main.py
@@ -15,8 +15,6 @@
 the RNA reads which overlap and protein sequences which can be constructed
 from reads that support the variant.
 """
-from __future__ import print_function, division, absolute_import
-
 import sys
 
 
diff --git a/isovar/cli/isovar_protein_sequences.py b/isovar/cli/isovar_protein_sequences.py
@@ -16,7 +16,6 @@
 a read count to each protein sequence.
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 
 
diff --git a/isovar/cli/isovar_reference_contexts.py b/isovar/cli/isovar_reference_contexts.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/isovar_translations.py b/isovar/cli/isovar_translations.py
@@ -15,7 +15,6 @@
 sequences using an RNAseq BAM from the same tissuie.
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/isovar_variant_reads.py b/isovar/cli/isovar_variant_reads.py
@@ -14,7 +14,6 @@
 Prints names and sequences of reads supporting a given set of variants.
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/isovar_variant_sequences.py b/isovar/cli/isovar_variant_sequences.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 import sys
 
 from ..logging import get_logger
diff --git a/isovar/cli/main_args.py b/isovar/cli/main_args.py
@@ -14,8 +14,6 @@
 Create parser and run Isovar from parsed args
 """
 
-from __future__ import print_function, division, absolute_import
-
 from varcode.cli import variant_collection_from_args
 
 from ..main import run_isovar
diff --git a/isovar/cli/output_args.py b/isovar/cli/output_args.py
@@ -15,9 +15,6 @@
 the CLI commands
 """
 
-from __future__ import print_function, division, absolute_import
-
-
 def add_output_args(
         parser,
         filename="output.csv",
diff --git a/isovar/cli/protein_sequence_args.py b/isovar/cli/protein_sequence_args.py
@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 from ..default_parameters import MAX_PROTEIN_SEQUENCES_PER_VARIANT
 from ..main import ProteinSequenceCreator
 from ..dataframe_helpers import protein_sequences_generator_to_dataframe
diff --git a/isovar/cli/reference_context_args.py b/isovar/cli/reference_context_args.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from varcode.cli.variant_args import (
     make_variants_parser,
     variant_collection_from_args
diff --git a/isovar/cli/rna_args.py b/isovar/cli/rna_args.py
@@ -14,8 +14,6 @@
 Common command-line arguments for all Isovar commands which use RNA
 """
 
-from __future__ import print_function, division, absolute_import
-
 from pysam import AlignmentFile
 
 from varcode.cli import make_variants_parser, variant_collection_from_args
diff --git a/isovar/cli/translation_args.py b/isovar/cli/translation_args.py
@@ -15,8 +15,6 @@
 cDNA into protein sequences.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from ..default_parameters import (
     MIN_TRANSCRIPT_PREFIX_LENGTH,
     MAX_REFERENCE_TRANSCRIPT_MISMATCHES,
diff --git a/isovar/cli/variant_sequences_args.py b/isovar/cli/variant_sequences_args.py
@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 from ..default_parameters import (
     MIN_VARIANT_SEQUENCE_COVERAGE,
     VARIANT_SEQUENCE_LENGTH,
diff --git a/isovar/common.py b/isovar/common.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from collections import defaultdict
 import numpy as np
 
diff --git a/isovar/dataframe_builder.py b/isovar/dataframe_builder.py
@@ -10,14 +10,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 from collections import OrderedDict
-from six import integer_types, text_type, binary_type
 
 from varcode import Variant
 import pandas as pd
 
-VALID_ELEMENT_TYPES = integer_types + (text_type, binary_type, float, bool)
+VALID_ELEMENT_TYPES = (int, str, bytes, float, bool)
 
 # values of these types are automatically converted to their size or length
 # unless some other conversion function is provided
diff --git a/isovar/dataframe_helpers.py b/isovar/dataframe_helpers.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 import pandas as pd
 
 from .allele_read import AlleleRead
diff --git a/isovar/default_parameters.py b/isovar/default_parameters.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 """
 Gathered all the default function parameters in a single module, so that these
 values can be easily shared between modules and also between commandline
diff --git a/isovar/dna.py b/isovar/dna.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 """
 This module implements basic DNA functionality in Python strings to
 to avoid having to depend on a bigger library such as BioPython.
diff --git a/isovar/effect_prediction.py b/isovar/effect_prediction.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from varcode.effects.effect_classes import ExonicSpliceSite, CodingMutation
 
 from .logging import get_logger
diff --git a/isovar/filtering.py b/isovar/filtering.py
@@ -14,8 +14,6 @@
 Functions used to annotate IsovarResult objects with filters.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from collections import OrderedDict
 import operator
 
diff --git a/isovar/genetic_code.py b/isovar/genetic_code.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 """
 GeneticCode objects contain the rules for translating cDNA into a protein
 sequence: the set of valid start and stop codons, as well as which
diff --git a/isovar/isovar_result.py b/isovar/isovar_result.py
@@ -18,11 +18,9 @@
 and any protein sequences which were successfully translated for it.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from collections import OrderedDict
 
-from cached_property import cached_property
+from functools import cached_property
 
 from .common import safediv
 from .alignment_score import alignment_score
diff --git a/isovar/locus_read.py b/isovar/locus_read.py
@@ -16,8 +16,6 @@
 for extracting variant nucleotides.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from .value_object import ValueObject
 
 
diff --git a/isovar/logging.py b/isovar/logging.py
@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 import logging
 import logging.config
 import pkg_resources
diff --git a/isovar/main.py b/isovar/main.py
@@ -11,9 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
-from six import string_types
 from varcode import load_vcf
 from pysam import AlignmentFile
 from collections import OrderedDict
@@ -133,10 +130,10 @@ def run_isovar(
     `protein_sequences` field of the IsovarVar result will be empty
     if no sequences could be determined.
     """
-    if isinstance(variants, string_types):
+    if isinstance(variants, str):
         variants = load_vcf(variants)
 
-    if isinstance(alignment_file, string_types):
+    if isinstance(alignment_file, str):
         alignment_file = AlignmentFile(
             alignment_file,
             threads=decompression_threads)
diff --git a/isovar/phasing.py b/isovar/phasing.py
@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from collections import defaultdict, Counter
 
 from .default_parameters import MIN_SHARED_FRAGMENTS_FOR_PHASING
diff --git a/isovar/protein_sequence.py b/isovar/protein_sequence.py
@@ -16,8 +16,6 @@
 associated with its supporting (and non-supporting but overlapping) RNA reads.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from .common import normalize_base0_range_indices
 from .translation_key import TranslationKey
 from .translation import Translation
diff --git a/isovar/protein_sequence_creator.py b/isovar/protein_sequence_creator.py
@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import print_function, division, absolute_import
-
 from .default_parameters import (
     MIN_TRANSCRIPT_PREFIX_LENGTH,
     MAX_REFERENCE_TRANSCRIPT_MISMATCHES,
diff --git a/isovar/protein_sequence_helpers.py b/isovar/protein_sequence_helpers.py
@@ -17,8 +17,6 @@
 ProteinSequence.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from .common import groupby
 from .logging import get_logger
 from .protein_sequence import ProteinSequence
diff --git a/isovar/read_collector.py b/isovar/read_collector.py
@@ -10,10 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
-from six import integer_types
-
 from .default_parameters import (
     USE_SECONDARY_ALIGNMENTS,
     USE_DUPLICATE_READS,
diff --git a/isovar/read_evidence.py b/isovar/read_evidence.py
@@ -16,8 +16,6 @@
 they support the reference, somatic allele, or some other allele.
 """
 
-from __future__ import print_function, division, absolute_import
-
 from .allele_read_helpers import split_reads_into_ref_alt_other
 from .variant_helpers import trim_variant
 from .value_object import ValueObject
diff --git a/isovar/reference_coding_sequence_key.py b/isovar/reference_coding_sequence_key.py
diff --git a/isovar/reference_context.py b/isovar/reference_context.py
diff --git a/isovar/reference_context_helpers.py b/isovar/reference_context_helpers.py
diff --git a/isovar/reference_sequence_key.py b/isovar/reference_sequence_key.py
diff --git a/isovar/string_helpers.py b/isovar/string_helpers.py
diff --git a/isovar/translation.py b/isovar/translation.py
diff --git a/isovar/translation_helpers.py b/isovar/translation_helpers.py
diff --git a/isovar/translation_key.py b/isovar/translation_key.py
diff --git a/isovar/value_object.py b/isovar/value_object.py
diff --git a/isovar/variant_helpers.py b/isovar/variant_helpers.py
diff --git a/isovar/variant_orf.py b/isovar/variant_orf.py
diff --git a/isovar/variant_orf_helpers.py b/isovar/variant_orf_helpers.py
diff --git a/isovar/variant_sequence.py b/isovar/variant_sequence.py
diff --git a/isovar/variant_sequence_creator.py b/isovar/variant_sequence_creator.py
diff --git a/isovar/variant_sequence_helpers.py b/isovar/variant_sequence_helpers.py
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
diff --git a/tests/test_dataframe_builder.py b/tests/test_dataframe_builder.py
diff --git a/tests/test_reference_sequence_key.py b/tests/test_reference_sequence_key.py
