pertpy 0.6.0__py3-none-any.whl → 0.7.0__py3-none-any.whl

pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.6.0"
+__version__ = "0.7.0"
 
 import warnings
 
@@ -11,9 +11,10 @@ from numba import NumbaDeprecationWarning
 
 warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
 warnings.filterwarnings("ignore", category=MatplotlibDeprecationWarning)
-warnings.filterwarnings("ignore", category=UserWarning)
+warnings.filterwarnings("ignore", category=UserWarning, module="scvi._settings")
 
 from . import data as dt
+from . import metadata as md
 from . import plot as pl
 from . import preprocessing as pp
 from . import tools as tl

pertpy/data/__init__.py

@@ -7,12 +7,14 @@ from pertpy.data._datasets import (
     burczynski_crohn,
     chang_2021,
     cinemaot_example,
+    combosciplex,
     datlinger_2017,
     datlinger_2021,
     dialogue_example,
     distance_example,
     dixit_2016,
     dixit_2016_raw,
+    dong_2023,
     frangieh_2021,
     frangieh_2021_protein,
     frangieh_2021_raw,
@@ -36,12 +38,14 @@ from pertpy.data._datasets import (
     schraivogel_2020_tap_screen_chr8,
     schraivogel_2020_tap_screen_chr11,
     sciplex3_raw,
+    sciplex_gxe1,
     shifrut_2018,
-    smillie,
+    smillie_2019,
     srivatsan_2020_sciplex2,
     srivatsan_2020_sciplex3,
     srivatsan_2020_sciplex4,
     stephenson_2021_subsampled,
+    tasccoda_example,
     tian_2019_day7neuron,
     tian_2019_ipsc,
     tian_2021_crispra,

pertpy/data/_dataloader.py

@@ -2,7 +2,6 @@ import tempfile
 from pathlib import Path
 from random import choice
 from string import ascii_lowercase
-from typing import Union
 from zipfile import ZipFile
 
 import requests
@@ -13,7 +12,7 @@ from rich.progress import Progress
 def _download(  # pragma: no cover
     url: str,
     output_file_name: str = None,
-    output_path: Union[str, Path] = None,
+    output_path: str | Path = None,
     block_size: int = 1024,
     overwrite: bool = False,
     is_zip: bool = False,
@@ -64,5 +63,4 @@ def _download(  # pragma: no cover
         output_path = output_path or tempfile.gettempdir()
         with ZipFile(download_to_path, "r") as zip_obj:
             zip_obj.extractall(path=output_path)
-            extracted = zip_obj.namelist()
-            print(extracted)
+            zip_obj.namelist()