From d0c6a35d2fc16752dde1da1e8c4f02e359737879 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Mon, 6 May 2024 01:13:07 -0700 Subject: [PATCH] Use __all__ (#588) * Start 0.8.0 Signed-off-by: zethson * Use __all__ Signed-off-by: zethson --------- Signed-off-by: zethson --- pertpy/data/__init__.py | 57 ++++++++++++++++++++++++++++++++ pertpy/metadata/__init__.py | 2 ++ pertpy/plot/__init__.py | 2 ++ pertpy/preprocessing/__init__.py | 2 ++ pertpy/tools/__init__.py | 23 +++++++++++++ 5 files changed, 86 insertions(+) diff --git a/pertpy/data/__init__.py b/pertpy/data/__init__.py index 89da7868..82095736 100644 --- a/pertpy/data/__init__.py +++ b/pertpy/data/__init__.py @@ -54,3 +54,60 @@ xie_2017, zhao_2021, ) + +__all__ = [ + "adamson_2016_pilot", + "adamson_2016_upr_epistasis", + "adamson_2016_upr_perturb_seq", + "aissa_2021", + "bhattacherjee", + "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", + "frangieh_2021_rna", + "gasperini_2019_atscale", + "gasperini_2019_highmoi", + "gasperini_2019_lowmoi", + "gehring_2019", + "haber_2017_regions", + "kang_2018", + "mcfarland_2020", + "norman_2019", + "norman_2019_raw", + "papalexi_2021", + "replogle_2022_k562_essential", + "replogle_2022_k562_gwps", + "replogle_2022_rpe1", + "sc_sim_augur", + "schiebinger_2019_16day", + "schiebinger_2019_18day", + "schraivogel_2020_tap_screen_chr8", + "schraivogel_2020_tap_screen_chr11", + "sciplex3_raw", + "sciplex_gxe1", + "shifrut_2018", + "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", + "tian_2021_crispri", + "weinreb_2020", + "xie_2017", + "zhao_2021", +] diff --git a/pertpy/metadata/__init__.py b/pertpy/metadata/__init__.py index ff928f31..22162bbf 100644 --- a/pertpy/metadata/__init__.py +++ b/pertpy/metadata/__init__.py @@ -2,3 +2,5 @@ from pertpy.metadata._compound import Compound from pertpy.metadata._drug import Drug from pertpy.metadata._moa import Moa + +__all__ = ["CellLine", "Compound", "Drug", "Moa"] diff --git a/pertpy/plot/__init__.py b/pertpy/plot/__init__.py index 36be5496..b1abe18d 100644 --- a/pertpy/plot/__init__.py +++ b/pertpy/plot/__init__.py @@ -3,3 +3,5 @@ from pertpy.plot._guide_rna import GuideRnaPlot as guide from pertpy.plot._milopy import MilopyPlot as milo from pertpy.plot._mixscape import MixscapePlot as ms + +__all__ = ["AugurpyPlot", "CodaPlot", "GuideRnaPlot", "MilopyPlot", "MixscapePlot"] diff --git a/pertpy/preprocessing/__init__.py b/pertpy/preprocessing/__init__.py index 98afebc8..8075a6a0 100644 --- a/pertpy/preprocessing/__init__.py +++ b/pertpy/preprocessing/__init__.py @@ -1 +1,3 @@ from ._guide_rna import GuideAssignment + +__all__ = ["GuideAssignment"] diff --git a/pertpy/tools/__init__.py b/pertpy/tools/__init__.py index 2b30df43..11f8cd53 100644 --- a/pertpy/tools/__init__.py +++ b/pertpy/tools/__init__.py @@ -17,3 +17,26 @@ ) from pertpy.tools._perturbation_space._simple import CentroidSpace, DBSCANSpace, KMeansSpace, PseudobulkSpace from pertpy.tools._scgen import SCGEN + +__all__ = [ + "Augur", + "Cinemaot", + "Sccoda", + "Tasccoda", + "Dialogue", + "DifferentialGeneExpression", + "DistanceTest", + "Distance", + "Enrichment", + "Milo", + "Mixscape", + "ClusteringSpace", + "DiscriminatorClassifierSpace", + "LRClassifierSpace", + "MLPClassifierSpace", + "CentroidSpace", + "DBSCANSpace", + "KMeansSpace", + "PseudobulkSpace", + "SCGEN", +]