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

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Files changed (53) hide show
  1. pertpy/__init__.py +3 -2
  2. pertpy/data/__init__.py +5 -1
  3. pertpy/data/_dataloader.py +2 -4
  4. pertpy/data/_datasets.py +203 -92
  5. pertpy/metadata/__init__.py +4 -0
  6. pertpy/metadata/_cell_line.py +826 -0
  7. pertpy/metadata/_compound.py +129 -0
  8. pertpy/metadata/_drug.py +242 -0
  9. pertpy/metadata/_look_up.py +582 -0
  10. pertpy/metadata/_metadata.py +73 -0
  11. pertpy/metadata/_moa.py +129 -0
  12. pertpy/plot/__init__.py +1 -9
  13. pertpy/plot/_augur.py +53 -116
  14. pertpy/plot/_coda.py +277 -677
  15. pertpy/plot/_guide_rna.py +17 -35
  16. pertpy/plot/_milopy.py +59 -134
  17. pertpy/plot/_mixscape.py +152 -391
  18. pertpy/preprocessing/_guide_rna.py +88 -4
  19. pertpy/tools/__init__.py +8 -13
  20. pertpy/tools/_augur.py +315 -17
  21. pertpy/tools/_cinemaot.py +143 -4
  22. pertpy/tools/_coda/_base_coda.py +1210 -65
  23. pertpy/tools/_coda/_sccoda.py +50 -21
  24. pertpy/tools/_coda/_tasccoda.py +27 -19
  25. pertpy/tools/_dialogue.py +164 -56
  26. pertpy/tools/_differential_gene_expression.py +240 -14
  27. pertpy/tools/_distances/_distance_tests.py +8 -8
  28. pertpy/tools/_distances/_distances.py +184 -34
  29. pertpy/tools/_enrichment.py +465 -0
  30. pertpy/tools/_milo.py +345 -11
  31. pertpy/tools/_mixscape.py +668 -50
  32. pertpy/tools/_perturbation_space/_clustering.py +5 -1
  33. pertpy/tools/_perturbation_space/_discriminator_classifiers.py +526 -0
  34. pertpy/tools/_perturbation_space/_perturbation_space.py +135 -43
  35. pertpy/tools/_perturbation_space/_simple.py +51 -10
  36. pertpy/tools/_scgen/__init__.py +1 -1
  37. pertpy/tools/_scgen/_scgen.py +701 -0
  38. pertpy/tools/_scgen/_utils.py +1 -3
  39. pertpy/tools/decoupler_LICENSE +674 -0
  40. {pertpy-0.6.0.dist-info → pertpy-0.7.0.dist-info}/METADATA +31 -12
  41. pertpy-0.7.0.dist-info/RECORD +53 -0
  42. {pertpy-0.6.0.dist-info → pertpy-0.7.0.dist-info}/WHEEL +1 -1
  43. pertpy/plot/_cinemaot.py +0 -81
  44. pertpy/plot/_dialogue.py +0 -91
  45. pertpy/plot/_scgen.py +0 -337
  46. pertpy/tools/_metadata/__init__.py +0 -0
  47. pertpy/tools/_metadata/_cell_line.py +0 -613
  48. pertpy/tools/_metadata/_look_up.py +0 -342
  49. pertpy/tools/_perturbation_space/_discriminator_classifier.py +0 -381
  50. pertpy/tools/_scgen/_jax_scgen.py +0 -370
  51. pertpy-0.6.0.dist-info/RECORD +0 -50
  52. /pertpy/tools/_scgen/{_jax_scgenvae.py → _scgenvae.py} +0 -0
  53. {pertpy-0.6.0.dist-info → pertpy-0.7.0.dist-info}/licenses/LICENSE +0 -0
pertpy/__init__.py CHANGED
@@ -2,7 +2,7 @@
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  __author__ = "Lukas Heumos"
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  __email__ = "lukas.heumos@posteo.net"
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- __version__ = "0.6.0"
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+ __version__ = "0.7.0"
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  import warnings
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@@ -11,9 +11,10 @@ from numba import NumbaDeprecationWarning
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  warnings.filterwarnings("ignore", category=NumbaDeprecationWarning)
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  warnings.filterwarnings("ignore", category=MatplotlibDeprecationWarning)
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- warnings.filterwarnings("ignore", category=UserWarning)
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+ warnings.filterwarnings("ignore", category=UserWarning, module="scvi._settings")
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  from . import data as dt
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+ from . import metadata as md
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  from . import plot as pl
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  from . import preprocessing as pp
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  from . import tools as tl
pertpy/data/__init__.py CHANGED
@@ -7,12 +7,14 @@ from pertpy.data._datasets import (
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  burczynski_crohn,
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  chang_2021,
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  cinemaot_example,
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+ combosciplex,
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  datlinger_2017,
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  datlinger_2021,
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  dialogue_example,
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  distance_example,
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  dixit_2016,
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  dixit_2016_raw,
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+ dong_2023,
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  frangieh_2021,
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  frangieh_2021_protein,
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  frangieh_2021_raw,
@@ -36,12 +38,14 @@ from pertpy.data._datasets import (
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  schraivogel_2020_tap_screen_chr8,
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  schraivogel_2020_tap_screen_chr11,
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  sciplex3_raw,
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+ sciplex_gxe1,
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  shifrut_2018,
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- smillie,
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+ smillie_2019,
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  srivatsan_2020_sciplex2,
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  srivatsan_2020_sciplex3,
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  srivatsan_2020_sciplex4,
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  stephenson_2021_subsampled,
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+ tasccoda_example,
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  tian_2019_day7neuron,
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  tian_2019_ipsc,
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  tian_2021_crispra,
pertpy/data/_dataloader.py CHANGED
@@ -2,7 +2,6 @@ import tempfile
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  from pathlib import Path
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  from random import choice
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  from string import ascii_lowercase
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- from typing import Union
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  from zipfile import ZipFile
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  import requests
@@ -13,7 +12,7 @@ from rich.progress import Progress
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  def _download( # pragma: no cover
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  url: str,
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  output_file_name: str = None,
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- output_path: Union[str, Path] = None,
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+ output_path: str | Path = None,
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  block_size: int = 1024,
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  overwrite: bool = False,
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  is_zip: bool = False,
@@ -64,5 +63,4 @@ def _download( # pragma: no cover
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  output_path = output_path or tempfile.gettempdir()
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  with ZipFile(download_to_path, "r") as zip_obj:
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  zip_obj.extractall(path=output_path)
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- extracted = zip_obj.namelist()
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- print(extracted)
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+ zip_obj.namelist()