From 90f202d577113dc4f2ddf11a56c4a8463d445260 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marek=20Wiewi=C3=B3rka?= <marek.wiewiorka@gmail.com>
Date: Wed, 18 Dec 2024 20:22:53 +0100
Subject: [PATCH] Fixing native deps (#36)
---
Cargo.toml | 2 +-
polars_bio/__init__.py | 1 -
polars_bio/range_op.py | 2 +-
polars_bio/range_op_helpers.py | 3 ++-
polars_bio/range_op_io.py | 2 +-
pyproject.toml | 2 +-
tests/test_bioframe.py | 2 +-
tests/test_native.py | 5 +++--
tests/test_pandas.py | 5 +++--
tests/test_polars.py | 5 +++--
10 files changed, 16 insertions(+), 13 deletions(-)
diff --git a/Cargo.toml b/Cargo.toml
index 4a68f5f..37951f6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
[package]
name = "polars_bio"
-version = "0.2.10"
+version = "0.2.11"
edition = "2021"
[lib]
diff --git a/polars_bio/__init__.py b/polars_bio/__init__.py
index 9ce0127..4dd35a7 100644
--- a/polars_bio/__init__.py
+++ b/polars_bio/__init__.py
@@ -1,6 +1,5 @@
import logging
-from .polars_bio import FilterOp
from .range_op import ctx, nearest, overlap
logging.basicConfig()
diff --git a/polars_bio/range_op.py b/polars_bio/range_op.py
index 2edaf21..1676957 100644
--- a/polars_bio/range_op.py
+++ b/polars_bio/range_op.py
@@ -4,11 +4,11 @@
import polars as pl
from typing_extensions import TYPE_CHECKING, Union
-from .polars_bio import FilterOp, RangeOp, RangeOptions
from .range_op_helpers import Context, _validate_overlap_input, range_operation
if TYPE_CHECKING:
pass
+from polars_bio.polars_bio import FilterOp, RangeOp, RangeOptions
DEFAULT_INTERVAL_COLUMNS = ["contig", "pos_start", "pos_end"]
diff --git a/polars_bio/range_op_helpers.py b/polars_bio/range_op_helpers.py
index 0ee970b..519206e 100644
--- a/polars_bio/range_op_helpers.py
+++ b/polars_bio/range_op_helpers.py
@@ -4,12 +4,13 @@
import pandas as pd
import polars as pl
-from .polars_bio import (
+from polars_bio.polars_bio import (
BioSessionContext,
RangeOptions,
range_operation_frame,
range_operation_scan,
)
+
from .range_op_io import _df_to_arrow, _get_schema, _rename_columns, range_lazy_scan
diff --git a/polars_bio/range_op_io.py b/polars_bio/range_op_io.py
index b8dbaf5..5b5c035 100644
--- a/polars_bio/range_op_io.py
+++ b/polars_bio/range_op_io.py
@@ -8,7 +8,7 @@
import pyarrow.compute as pc
from polars.io.plugins import register_io_source
-from .polars_bio import (
+from polars_bio.polars_bio import (
BioSessionContext,
RangeOptions,
range_operation_frame,
diff --git a/pyproject.toml b/pyproject.toml
index 9d8da98..8378f16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "maturin"
[project]
name = "polars-bio"
-version = "0.2.10"
+version = "0.2.11"
description = "Blazing fast genomic operations on large Python dataframes"
authors = []
requires-python = ">=3.9"
diff --git a/tests/test_bioframe.py b/tests/test_bioframe.py
index f450cb4..752f97d 100644
--- a/tests/test_bioframe.py
+++ b/tests/test_bioframe.py
@@ -3,7 +3,7 @@
from _expected import BIO_PD_DF1, BIO_PD_DF2
import polars_bio as pb
-from polars_bio import FilterOp
+from polars_bio.polars_bio import FilterOp
class TestOverlapBioframe:
diff --git a/tests/test_native.py b/tests/test_native.py
index 8ee02d2..82d20f5 100644
--- a/tests/test_native.py
+++ b/tests/test_native.py
@@ -9,6 +9,7 @@
)
import polars_bio as pb
+from polars_bio.polars_bio import FilterOp
class TestOverlapNative:
@@ -16,7 +17,7 @@ class TestOverlapNative:
DF_OVER_PATH1,
DF_OVER_PATH2,
output_type="pandas.DataFrame",
- overlap_filter=pb.FilterOp.Weak,
+ overlap_filter=FilterOp.Weak,
)
def test_overlap_count(self):
@@ -35,7 +36,7 @@ class TestNearestNative:
DF_NEAREST_PATH1,
DF_NEAREST_PATH2,
output_type="pandas.DataFrame",
- overlap_filter=pb.FilterOp.Weak,
+ overlap_filter=FilterOp.Weak,
)
def test_nearest_count(self):
diff --git a/tests/test_pandas.py b/tests/test_pandas.py
index 91655ae..71695a9 100644
--- a/tests/test_pandas.py
+++ b/tests/test_pandas.py
@@ -9,6 +9,7 @@
)
import polars_bio as pb
+from polars_bio.polars_bio import FilterOp
class TestOverlapPandas:
@@ -16,7 +17,7 @@ class TestOverlapPandas:
PD_OVERLAP_DF1,
PD_OVERLAP_DF2,
output_type="pandas.DataFrame",
- overlap_filter=pb.FilterOp.Weak,
+ overlap_filter=FilterOp.Weak,
)
def test_overlap_count(self):
@@ -35,7 +36,7 @@ class TestNearestPandas:
PD_NEAREST_DF1,
PD_NEAREST_DF2,
output_type="pandas.DataFrame",
- overlap_filter=pb.FilterOp.Weak,
+ overlap_filter=FilterOp.Weak,
)
def test_nearest_count(self):
diff --git a/tests/test_polars.py b/tests/test_polars.py
index 68edbe0..a559c4c 100644
--- a/tests/test_polars.py
+++ b/tests/test_polars.py
@@ -8,14 +8,15 @@
)
import polars_bio as pb
+from polars_bio.polars_bio import FilterOp
class TestOverlapPolars:
result_frame = pb.overlap(
- PL_DF1, PL_DF2, output_type="polars.DataFrame", overlap_filter=pb.FilterOp.Weak
+ PL_DF1, PL_DF2, output_type="polars.DataFrame", overlap_filter=FilterOp.Weak
)
result_lazy = pb.overlap(
- PL_DF1, PL_DF2, output_type="polars.LazyFrame", overlap_filter=pb.FilterOp.Weak
+ PL_DF1, PL_DF2, output_type="polars.LazyFrame", overlap_filter=FilterOp.Weak
).collect()
expected = PL_DF_OVERLAP