Merge pull request #46 from moshi4/develop

Bump to v1.2.0

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -24,19 +24,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+      - name: Install dependencies
+        run: pip install -e . pytest pytest-cov ruff
 
-      - name: Install Dependencies
-        run: poetry install -n
-
-      - name: Run black format check
-        run: poetry run black src tests --check --diff --verbose
+      - name: Run ruff format check
+        run: ruff format --check --diff
 
       - name: Run ruff lint check
-        run: poetry run ruff .
+        run: ruff check --diff
 
       - name: Run pytest
-        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term

README.md

@@ -14,6 +14,7 @@
 - [API Usage](#api-usage)
 - [Code Example](#code-example)
 - [Not Implemented Features](#not-implemented-features)
+- [Star History](#star-history)
 
 ## Overview
 
@@ -231,3 +232,7 @@ I may implement them when I feel like it.
 - Plot boxplot
 - Plot violin
 - Label position auto adjustment
+
+## Star History
+
+[![Star History Chart](https://api.star-history.com/svg?repos=moshi4/pyCirclize&type=Date)](https://star-history.com/#moshi4/pyCirclize&Date)

docs/circos_plot.ipynb

@@ -271,7 +271,7 @@
     "    trna_track = sector.add_track((67, 74), r_pad_ratio=0.1)\n",
     "    for feature in seqid2features[sector.name]:\n",
     "        if feature.type == \"CDS\":\n",
-    "            if feature.strand == 1:\n",
+    "            if feature.location.strand == 1:\n",
     "                f_cds_track.genomic_features([feature], fc=\"tomato\")\n",
     "            else:\n",
     "                r_cds_track.genomic_features([feature], fc=\"skyblue\")\n",

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyCirclize"
-version = "1.1.0"
+version = "1.2.0"
 description = "Circular visualization in Python"
 authors = ["moshi4"]
 license = "MIT"
@@ -26,25 +26,32 @@ minversion = "6.0"
 addopts = "--cov=src --tb=line --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
-# Lint Rules: https://beta.ruff.rs/docs/rules
 [tool.ruff]
-select = ["E", "F", "W", "I", "D", "B"]
-ignore = [
-    "D100",
-    "D101",
-    "D104",
-    "D105",
-    "D205",
-    "D400",
-    "D401",
-    "D403",
-    "D415",
-    "B905",
-]
 src = ["src", "tests"]
 line-length = 88
 
-[tool.ruff.pydocstyle]
+# Lint Rules: https://docs.astral.sh/ruff/rules/
+[tool.ruff.lint]
+select = [
+    "F", # pyflakes
+    "E", # pycodestyle (Error)
+    "W", # pycodestyle (Warning)
+    "I", # isort
+    "D", # pydocstyle
+]
+ignore = [
+    "D100", # Missing docstring in public module
+    "D101", # Missing docstring in public class
+    "D104", # Missing docstring in public package
+    "D105", # Missing docstring in magic method
+    "D205", # 1 blank line required between summary line and description
+    "D400", # First line should end with a period
+    "D401", # First line should be in imperative mood
+    "D403", # First word of the first line should be properly capitalized
+    "D415", # First line should end with a period, question mark, or exclamation point
+]
+
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
 [tool.poetry.dependencies]
@@ -55,15 +62,17 @@ numpy = ">=1.21.1"
 pandas = ">=1.3.5"
 
 [tool.poetry.group.dev.dependencies]
+ruff = ">=0.1.6"
 pytest = ">=7.1.2"
-black = ">=22.10.0"
-ruff = ">=0.0.264"
 pytest-cov = ">=4.0.0"
 ipykernel = ">=6.13.0"
+
+[tool.poetry.group.docs.dependencies]
 mkdocs = ">=1.2"
 mkdocstrings = { extras = ["python"], version = ">=0.19.0" }
 mkdocs-jupyter = ">=0.21.0"
 mkdocs-material = ">=8.2"
+black = ">=22.10.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.1.0"
+__version__ = "1.2.0"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -4,6 +4,7 @@
 import math
 import textwrap
 from collections import defaultdict
+from collections.abc import Mapping
 from copy import deepcopy
 from pathlib import Path
 from typing import Any, Callable
@@ -21,7 +22,13 @@
 
 from pycirclize import config, utils
 from pycirclize.parser import Bed, Matrix
-from pycirclize.patches import ArcLine, ArcRectangle, BezierCurve, Line
+from pycirclize.patches import (
+    ArcLine,
+    ArcRectangle,
+    BezierCurveLine,
+    BezierCurveLink,
+    Line,
+)
 from pycirclize.sector import Sector
 from pycirclize.track import Track
 from pycirclize.tree import TreeViz
@@ -32,20 +39,20 @@ class Circos:
 
     def __init__(
         self,
-        sectors: dict[str, int] | dict[str, float],
+        sectors: Mapping[str, int | float],
         start: float = 0,
         end: float = 360,
         *,
         space: float | list[float] = 0,
         endspace: bool = True,
-        sector2start_pos: dict[str, int] | dict[str, float] | None = None,
+        sector2start_pos: Mapping[str, int | float] | None = None,
         sector2clockwise: dict[str, bool] | None = None,
         show_axis_for_debug: bool = False,
     ):
         """
         Parameters
         ----------
-        sectors : dict[str, int] | dict[str, float]
+        sectors : Mapping[str, int | float]
             Sector name & size dict
         start : float, optional
             Plot start degree (`-360 <= start < end <= 360`)
@@ -55,7 +62,7 @@ def __init__(
             Space degree(s) between sector
         endspace : bool, optional
             If True, insert space after the end sector
-        sector2start_pos : dict[str, int] | dict[str, float] | None, optional
+        sector2start_pos : Mapping[str, int | float] | None, optional
             Sector name & start position dict. By default, `start_pos=0`.
         sector2clockwise : dict[str, bool] | None, optional
             Sector name & clockwise bool dict. By default, `clockwise=True`.
@@ -693,7 +700,7 @@ def link(
                 rad_start2, rad_end2 = rad_end2, rad_start2
 
         # Create bezier curve path patch
-        bezier_curve = BezierCurve(
+        bezier_curve_link = BezierCurveLink(
             rad_start1,
             rad_end1,
             r1,
@@ -705,7 +712,75 @@ def link(
             arrow_length_ratio,
             **kwargs,
         )
-        self._patches.append(bezier_curve)
+        self._patches.append(bezier_curve_link)
+
+    def link_line(
+        self,
+        sector_pos1: tuple[str, float],
+        sector_pos2: tuple[str, float],
+        r1: float | None = None,
+        r2: float | None = None,
+        *,
+        color: str = "black",
+        height_ratio: float = 0.5,
+        direction: int = 0,
+        arrow_height: float = 3.0,
+        arrow_width: float = 2.0,
+        **kwargs,
+    ) -> None:
+        """Plot link line to specified position within or between sectors
+
+        Parameters
+        ----------
+        sector_pos1 : tuple[str, float]
+            Link line sector position1 (name, position)
+        sector_pos2 : tuple[str, float]
+            Link line sector position2 (name, position)
+        r1 : float | None, optional
+            Link line radius end position for sector_pos1.
+            If None, lowest radius position of track in target sector is set.
+        r2 : float | None, optional
+            Link line radius end position for sector_pos2.
+            If None, lowest radius position of track in target sector is set.
+        color : str, optional
+            Link line color
+        height_ratio : float, optional
+            Bezier curve height ratio
+        direction : int, optional
+            `0`: No direction edge shape (Default)
+            `1`: Forward direction arrow edge shape (pos1 -> pos2)
+            `-1`: Reverse direction arrow edge shape (pos1 <- pos2)
+            `2`: Bidirectional arrow edge shape (pos1 <-> pos2)
+        arrow_height : float, optional
+            Arrow height size (Radius unit)
+        arrow_width : float, optional
+            Arrow width size (Degree unit)
+        **kwargs : dict, optional
+            Patch properties (e.g. `lw=1.0, ls="dashed", ...`)
+            <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
+        """
+        # Set data for plot link
+        name1, pos1 = sector_pos1
+        name2, pos2 = sector_pos2
+        sector1, sector2 = self.get_sector(name1), self.get_sector(name2)
+        r1 = sector1.get_lowest_r() if r1 is None else r1
+        r2 = sector2.get_lowest_r() if r2 is None else r2
+        rad_pos1, rad_pos2 = sector1.x_to_rad(pos1), sector2.x_to_rad(pos2)
+
+        kwargs.update(color=color)
+
+        bezier_curve_line = BezierCurveLine(
+            rad_pos1,
+            r1,
+            rad_pos2,
+            r2,
+            height_ratio,
+            direction,
+            arrow_height,
+            arrow_width,
+            **kwargs,
+        )
+        self._patches.append(bezier_curve_line)
 
     def colorbar(
         self,
@@ -809,7 +884,7 @@ def plotfig(
         for plot_func in self._get_all_plot_funcs():
             plot_func(ax)
 
-        return fig  # type: ignore
+        return fig
 
     def savefig(
         self,
@@ -887,7 +962,7 @@ def _initialize_figure(
         """
         fig = plt.figure(figsize=figsize, dpi=dpi, tight_layout=True)
         ax = fig.add_subplot(projection="polar")
-        return fig, ax  # type: ignore
+        return fig, ax
 
     def _initialize_polar_axes(self, ax: PolarAxes) -> None:
         """Initialize polar axes params