diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6e31fe7..bff3cb0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.10] + python-version: ["3.10"] os: [ubuntu-latest] runs-on: ${{ matrix.os }} steps: @@ -36,7 +36,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.10] + python-version: ["3.10"] os: [ubuntu-latest] runs-on: ${{ matrix.os }} steps: @@ -58,7 +58,7 @@ jobs: # strategy: # fail-fast: false # matrix: - # python-version: [3.10] + # python-version: ["3.10"] # os: [macos-latest] # runs-on: ${{ matrix.os }} # steps: @@ -76,7 +76,7 @@ jobs: # strategy: # fail-fast: false # matrix: - # python-version: [3.10] + # python-version: ["3.10"] # os: [windows-latest] # runs-on: ${{ matrix.os }} # steps: diff --git a/scdataloader/data.py b/scdataloader/data.py index 7cff6a6..b1d0b2b 100644 --- a/scdataloader/data.py +++ b/scdataloader/data.py @@ -1,7 +1,4 @@ -import json from dataclasses import dataclass, field -from pathlib import Path -from typing import List, Optional, Union import pandas as pd from torch.utils.data import Dataset as torchDataset @@ -200,7 +197,7 @@ def use_prior_network( ) self.add_prior_network(net) - def add_prior_network(self, prior_network: pd.DataFrame): + def add_prior_network(self, prior_network: pd.DataFrame, init_len): # validate the network dataframe required_columns: list[str] = ["target", "regulators"] optional_columns: list[str] = ["type", "weight"] diff --git a/scdataloader/mapped.py b/scdataloader/mapped.py index 39e8394..195ab22 100644 --- a/scdataloader/mapped.py +++ b/scdataloader/mapped.py @@ -1,7 +1,7 @@ from collections import Counter from functools import reduce from os import PathLike -from typing import List, Literal, Optional, Union, Iterable +from typing import List, Literal, Optional, Union import numpy as np import pandas as pd @@ -15,13 +15,6 @@ registry, ) from lamin_utils import logger -from lnschema_core.models import ( - Data, - Run, - __repr__, -) -from lamindb.dev._settings import settings -from lamindb.dev._run_context import run_context from lamindb.dev._data import _track_run_input diff --git a/scdataloader/preprocess.py b/scdataloader/preprocess.py index ffecc4b..a1024aa 100644 --- a/scdataloader/preprocess.py +++ b/scdataloader/preprocess.py @@ -1,4 +1,4 @@ -from typing import Dict, Optional, Union, Callable +from typing import Optional, Union, Callable from django.db import IntegrityError import numpy as np