Merge pull request #44 from moshi4/develop

Bump to v1.1.0

.github/workflows/publish_mkdocs.yml

@@ -12,10 +12,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Setup Python 3.9
+      - name: Setup Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.11"
 
       - name: Install MkDocs & Plugins
         run: |

.github/workflows/publish_to_pypi.yml

@@ -15,10 +15,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Setup Python 3.9
+      - name: Setup Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.11"
 
       - name: Install Poetry
         run: |

README.md

@@ -195,7 +195,7 @@ group_name2species_list = dict(
     Monotremata=["Tachyglossus_aculeatus", "Ornithorhynchus_anatinus"],
     Marsupialia=["Monodelphis_domestica", "Vombatus_ursinus"],
     Xenarthra=["Choloepus_didactylus", "Dasypus_novemcinctus"],
-    Afrotheria=["Trichechus_manatus_latirostris", "Chrysochloris_asiatica"],
+    Afrotheria=["Trichechus_manatus", "Chrysochloris_asiatica"],
     Euarchontes=["Galeopterus_variegatus", "Theropithecus_gelada"],
     Glires=["Oryctolagus_cuniculus", "Microtus_oregoni"],
     Laurasiatheria=["Talpa_occidentalis", "Mirounga_leonina"],

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyCirclize"
-version = "1.0.0"
+version = "1.1.0"
 description = "Circular visualization in Python"
 authors = ["moshi4"]
 license = "MIT"

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -311,6 +311,7 @@ def initialize_from_tree(
         reverse: bool = False,
         ladderize: bool = False,
         line_kws: dict[str, Any] | None = None,
+        label_formatter: Callable[[str], str] | None = None,
         align_line_kws: dict[str, Any] | None = None,
     ) -> tuple[Circos, TreeViz]:
         """Initialize Circos instance from phylogenetic tree
@@ -349,6 +350,10 @@ def initialize_from_tree(
         align_line_kws : dict[str, Any] | None, optional
             Patch properties (e.g. `dict(lw=1, ls="dotted", alpha=1.0, ...)`)
             <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
+        label_formatter : Callable[[str], str] | None, optional
+            User-defined label text format function to change plot label text content.
+            For example, if you want to change underscore of the label to space,
+            set `lambda t: t.replace("_", " ")`.
 
         Returns
         -------
@@ -374,6 +379,7 @@ def initialize_from_tree(
             reverse=reverse,
             ladderize=ladderize,
             line_kws=line_kws,
+            label_formatter=label_formatter,
             align_line_kws=align_line_kws,
         )
         return circos, tv

src/pycirclize/parser/genbank.py

@@ -171,6 +171,8 @@ def calc_gc_skew(
             window_size = int(len(seq) / 500)
         if step_size is None:
             step_size = int(len(seq) / 1000)
+        if window_size == 0 or step_size == 0:
+            window_size, step_size = len(seq), int(len(seq) / 2)
         pos_list = list(range(0, len(seq), step_size)) + [len(seq)]
         for pos in pos_list:
             window_start_pos = pos - int(window_size / 2)
@@ -218,6 +220,8 @@ def calc_gc_content(
             window_size = int(len(seq) / 500)
         if step_size is None:
             step_size = int(len(seq) / 1000)
+        if window_size == 0 or step_size == 0:
+            window_size, step_size = len(seq), int(len(seq) / 2)
         pos_list = list(range(0, len(seq), step_size)) + [len(seq)]
         for pos in pos_list:
             window_start_pos = pos - int(window_size / 2)

src/pycirclize/track.py

@@ -1149,6 +1149,7 @@ def tree(
         ladderize: bool = False,
         line_kws: dict[str, Any] | None = None,
         align_line_kws: dict[str, Any] | None = None,
+        label_formatter: Callable[[str], str] | None = None,
     ) -> TreeViz:
         """Plot tree
 
@@ -1181,6 +1182,10 @@ def tree(
         align_line_kws : dict[str, Any] | None, optional
             Patch properties (e.g. `dict(lw=1, ls="dotted", alpha=1.0, ...)`)
             <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
+        label_formatter : Callable[[str], str] | None, optional
+            User-defined label text format function to change plot label text content.
+            For example, if you want to change underscore of the label to space,
+            set `lambda t: t.replace("_", " ")`.
 
         Returns
         -------
@@ -1199,6 +1204,7 @@ def tree(
             ladderize=ladderize,
             line_kws=line_kws,
             align_line_kws=align_line_kws,
+            label_formatter=label_formatter,
             track=self,
         )
         self._trees.append(tv)
@@ -1207,7 +1213,7 @@ def tree(
 
     def genomic_features(
         self,
-        features: list[SeqFeature],
+        features: SeqFeature | list[SeqFeature],
         *,
         plotstyle: str = "box",
         r_lim: tuple[float, float] | None = None,
@@ -1218,8 +1224,8 @@ def genomic_features(
 
         Parameters
         ----------
-        features : list[SeqFeature]
-            Biopython's SeqFeature list
+        features : SeqFeature | list[SeqFeature]
+            Biopython's SeqFeature or SeqFeature list
         plotstyle : str, optional
             Plot style (`box` or `arrow`)
         r_lim : tuple[float, float] | None, optional
@@ -1230,6 +1236,9 @@ def genomic_features(
             Patch properties (e.g. `fc="red", ec="blue", lw=1.0, ...`)
             <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
         """
+        if isinstance(features, SeqFeature):
+            features = [features]
+
         if r_lim is None:
             r_lim = self.r_plot_lim
         else:

src/pycirclize/tree.py

@@ -6,7 +6,7 @@
 from copy import deepcopy
 from functools import cached_property
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Callable
 from urllib.parse import urlparse
 from urllib.request import urlopen
 
@@ -40,6 +40,7 @@ def __init__(
         ladderize: bool = False,
         line_kws: dict[str, Any] | None = None,
         align_line_kws: dict[str, Any] | None = None,
+        label_formatter: Callable[[str], str] | None = None,
         track: Track,
     ):
         """
@@ -69,6 +70,10 @@ def __init__(
         align_line_kws : dict[str, Any] | None, optional
             Patch properties (e.g. `dict(lw=1, ls="dotted", alpha=1.0, ...)`)
             <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
+        label_formatter : Callable[[str], str] | None, optional
+            User-defined label text format function to change plot label text content.
+            For example, if you want to change underscore of the label to space,
+            set `lambda t: t.replace("_", " ")`.
         track : Track
             Track for tree visualization
         """
@@ -106,6 +111,8 @@ def __init__(
         self._node2label_props: dict[str, dict[str, Any]] = defaultdict(lambda: {})
         self._node2line_props: dict[str, dict[str, Any]] = defaultdict(lambda: {})
 
+        self._label_formatter: Callable[[str], str] | None = label_formatter
+
     ############################################################
     # Properties
     ############################################################
@@ -617,6 +624,9 @@ def _plot_tree_label(self) -> None:
             _text_kws.update(params)
             _text_kws.update(self._node2label_props[label])
 
+            # Apply label text format function if defined
+            if self._label_formatter is not None:
+                label = self._label_formatter(label)
             # Plot label if text size > 0
             if float(_text_kws["size"]) > 0:
                 self.track.text(label, x, r, **_text_kws)  # type: ignore