Merge pull request #159 from zktuong/v0.2.4

slicing and check contigs
zktuong · Jul 6, 2022 · 04586e2 · 04586e2
2 parents 312cca5 + 85e8e30
commit 04586e2
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diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ Original preprint:
 
 Illustration of the `Dandelion` class slots
 
-![](docs/notebooks/img/dandelion_class.png)
+![](docs/notebooks/img/dandelion_class2.png)
 
 Please refer to the [documentation](https://sc-dandelion.readthedocs.io/) or the notebooks [here](https://nbviewer.jupyter.org/github/zktuong/dandelion/tree/latest/docs/notebooks/):
 

diff --git a/dandelion/__init__.py b/dandelion/__init__.py
@@ -2,47 +2,47 @@
 # @Author: kt16
 # @Date:   2020-05-12 18:11:20
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2022-06-18 14:33:17
+# @Last Modified time: 2022-07-06 08:09:19
 """init module."""
 from . import preprocessing as pp
 from . import utilities as utl
 from . import tools as tl
 from . import plotting as pl
 from .utilities import (
-    read_pkl,
-    read_h5,
+    concat,
+    Dandelion,
+    from_scirpy,
+    load_data,
     read_10x_airr,
     read_10x_vdj,
-    from_scirpy,
+    read_h5,
+    read_h5ddl,
+    read_pkl,
     to_scirpy,
-    Dandelion,
     update_metadata,
-    concat,
-    load_data,
 )
-from .logging import __version__, __author__, __email__, __classifiers__
+from .logging import __author__, __email__, __classifiers__, __version__
 from . import logging
 
-read_h5ddl = read_h5
 
 __all__ = [
-    "pp",
-    "utl",
-    "tl",
+    "__author__",
+    "__classifiers__",
+    "__email__",
+    "__version__",
+    "concat",
+    "Dandelion",
+    "from_scirpy",
+    "load_data",
+    "logging",
     "pl",
-    "read_pkl",
-    "read_h5",
+    "pp",
     "read_10x_airr",
     "read_10x_vdj",
-    "from_scirpy",
+    "read_h5",
+    "read_pkl",
+    "tl",
     "to_scirpy",
-    "Dandelion",
     "update_metadata",
-    "concat",
-    "load_data",
-    "__version__",
-    "__author__",
-    "__email__",
-    "__classifiers__",
-    "logging",
+    "utl",
 ]
diff --git a/dandelion/logging/__init__.py b/dandelion/logging/__init__.py
@@ -2,16 +2,16 @@
 # @Author: kt16
 # @Date:   2020-05-12 18:11:20
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2022-06-18 14:30:45
+# @Last Modified time: 2022-07-03 21:53:35
 """init module."""
-from ._logging import print_versions, print_header
-from ._metadata import __version__, __author__, __email__, __classifiers__
+from ._logging import print_header, print_versions
+from ._metadata import __author__, __email__, __classifiers__, __version__
 
 __all__ = [
-    "print_versions",
-    "print_header",
-    "__version__",
     "__author__",
-    "__email__",
     "__classifiers__",
+    "__email__",
+    "__version__",
+    "print_header",
+    "print_versions",
 ]
diff --git a/dandelion/logging/_logging.py b/dandelion/logging/_logging.py
@@ -2,7 +2,7 @@
 # @Author: Kelvin
 # @Date:   2021-02-06 13:18:58
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2022-06-18 14:31:46
+# @Last Modified time: 2022-07-03 21:54:08
 """logging module."""
 from typing import Sequence
 

diff --git a/dandelion/plotting/__init__.py b/dandelion/plotting/__init__.py
@@ -2,24 +2,22 @@
 # @Author: Kelvin
 # @Date:   2020-05-13 23:21:45
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2022-06-18 14:30:52
+# @Last Modified time: 2022-07-04 08:29:04
 """init module."""
 from ._plotting import (
-    random_palette,
-    clone_network,
     barplot,
-    stackedbarplot,
-    spectratype,
-    clone_rarefaction,
+    clone_network,
     clone_overlap,
+    clone_rarefaction,
+    spectratype,
+    stackedbarplot,
 )
 
 __all__ = [
-    "random_palette",
-    "clone_network",
     "barplot",
-    "stackedbarplot",
-    "spectratype",
-    "clone_rarefaction",
+    "clone_network",
     "clone_overlap",
+    "clone_rarefaction",
+    "spectratype",
+    "stackedbarplot",
 ]