Use __all__ (#588)

* Start 0.8.0 Signed-off-by: zethson <lukas.heumos@posteo.net> * Use __all__ Signed-off-by: zethson <lukas.heumos@posteo.net> --------- Signed-off-by: zethson <lukas.heumos@posteo.net>
scverse · May 6, 2024 · d0c6a35 · d0c6a35
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diff --git 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
@@ -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
@@ -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
@@ -1 +1,3 @@
 from ._guide_rna import GuideAssignment
+
+__all__ = ["GuideAssignment"]
diff --git 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",
+]
Original file line number	Diff line number	Diff line change
		@@ -1 +1,3 @@
		from ._guide_rna import GuideAssignment

		__all__ = ["GuideAssignment"]