Merge pull request #81 from moshi4/develop

Bump to v1.8.0

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint check

requirements-dev.lock

@@ -29,9 +29,9 @@ certifi==2024.12.14
     # via requests
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.4.0
+charset-normalizer==3.4.1
     # via requests
-click==8.1.7
+click==8.1.8
     # via black
     # via mkdocs
     # via mkdocstrings
@@ -42,7 +42,7 @@ comm==0.2.2
     # via ipykernel
 contourpy==1.3.0
     # via matplotlib
-coverage==7.6.9
+coverage==7.6.10
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
@@ -67,9 +67,9 @@ fonttools==4.55.3
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-griffe==1.5.1
+griffe==1.5.4
     # via mkdocstrings-python
-identify==2.6.3
+identify==2.6.5
     # via pre-commit
 idna==3.10
     # via requests
@@ -80,7 +80,7 @@ importlib-metadata==8.5.0
     # via mkdocs-get-deps
     # via mkdocstrings
     # via nbconvert
-importlib-resources==6.4.5
+importlib-resources==6.5.2
     # via matplotlib
 iniconfig==2.0.0
     # via pytest
@@ -90,7 +90,7 @@ ipython==8.18.1
     # via ipykernel
 jedi==0.19.2
     # via ipython
-jinja2==3.1.4
+jinja2==3.1.5
     # via mkdocs
     # via mkdocs-material
     # via mkdocstrings
@@ -142,7 +142,7 @@ mdurl==0.1.2
 mergedeep==1.3.4
     # via mkdocs
     # via mkdocs-get-deps
-mistune==3.0.2
+mistune==3.1.0
     # via nbconvert
 mkdocs==1.6.1
     # via mkdocs-autorefs
@@ -161,13 +161,13 @@ mkdocs-material-extensions==1.3.1
     # via mkdocs-material
 mkdocstrings==0.27.0
     # via mkdocstrings-python
-mkdocstrings-python==1.12.2
+mkdocstrings-python==1.13.0
     # via mkdocstrings
 mypy-extensions==1.0.0
     # via black
 nbclient==0.10.2
     # via nbconvert
-nbconvert==7.16.4
+nbconvert==7.16.5
     # via mkdocs-jupyter
 nbformat==5.10.4
     # via jupytext
@@ -205,7 +205,7 @@ pathspec==0.12.1
     # via mkdocs
 pexpect==4.9.0
     # via ipython
-pillow==11.0.0
+pillow==11.1.0
     # via matplotlib
 platformdirs==4.3.6
     # via black
@@ -225,15 +225,15 @@ ptyprocess==0.7.0
 pure-eval==0.2.3
     # via stack-data
 pygenomeviz==1.5.0
-pygments==2.18.0
+pygments==2.19.1
     # via ipython
     # via mkdocs-jupyter
     # via mkdocs-material
     # via nbconvert
-pymdown-extensions==10.12
+pymdown-extensions==10.14
     # via mkdocs-material
     # via mkdocstrings
-pyparsing==3.2.0
+pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
     # via pytest-cov
@@ -267,15 +267,15 @@ requests==2.32.3
 rpds-py==0.22.3
     # via jsonschema
     # via referencing
-ruff==0.8.4
+ruff==0.9.1
 six==1.17.0
     # via python-dateutil
 soupsieve==2.6
     # via beautifulsoup4
 stack-data==0.6.3
     # via ipython
 tinycss2==1.4.0
-    # via nbconvert
+    # via bleach
 tomli==2.2.1
     # via black
     # via coverage
@@ -297,12 +297,13 @@ traitlets==5.14.3
 typing-extensions==4.12.2
     # via black
     # via ipython
+    # via mistune
     # via mkdocstrings
 tzdata==2024.2
     # via pandas
-urllib3==2.2.3
+urllib3==2.3.0
     # via requests
-virtualenv==20.28.0
+virtualenv==20.28.1
     # via pre-commit
 watchdog==6.0.0
     # via mkdocs

requirements.lock

@@ -18,7 +18,7 @@ cycler==0.12.1
     # via matplotlib
 fonttools==4.55.3
     # via matplotlib
-importlib-resources==6.4.5
+importlib-resources==6.5.2
     # via matplotlib
 kiwisolver==1.4.7
     # via matplotlib
@@ -34,9 +34,9 @@ packaging==24.2
     # via matplotlib
 pandas==2.2.3
     # via pycirclize
-pillow==11.0.0
+pillow==11.1.0
     # via matplotlib
-pyparsing==3.2.0
+pyparsing==3.2.1
     # via matplotlib
 python-dateutil==2.9.0.post0
     # via matplotlib

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.7.2"
+__version__ = "1.8.0"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -1049,13 +1049,15 @@ def plotfig(
         # Plot all patches
         patches = []
         for patch in self._get_all_patches():
+            # Set clip_on=False to enable Patch to be displayed outside of Axes
+            patch.set_clip_on(False)
             # Collection cannot handle `zorder`, `hatch`
             # Separate default or user-defined `zorder`, `hatch` property patch
             if patch.get_zorder() == 1 and patch.get_hatch() is None:
                 patches.append(patch)
             else:
                 ax.add_patch(patch)
-        ax.add_collection(PatchCollection(patches, match_original=True))  # type: ignore
+        ax.add_collection(PatchCollection(patches, match_original=True, clip_on=False))  # type: ignore
 
         # Execute all plot functions
         for plot_func in self._get_all_plot_funcs():

src/pycirclize/config.py

@@ -16,6 +16,7 @@
 R_LIM = (MIN_R, MAX_R)
 AXIS_FACE_PARAM = dict(zorder=0.99, ec="none", edgecolor="none")
 AXIS_EDGE_PARAM = dict(zorder=1.01, fc="none", facecolor="none")
+REL_TOL = 1e-10  # Relative Tolerance
 
 # Circos Color Scheme
 # http://circos.ca/tutorials/lessons/configuration/colors/

src/pycirclize/sector.py

@@ -6,8 +6,6 @@
 from copy import deepcopy
 from pathlib import Path
 from typing import Any, Callable
-from urllib.parse import urlparse
-from urllib.request import urlopen
 
 import numpy as np
 from matplotlib.patches import Patch
@@ -213,8 +211,8 @@ def x_to_rad(self, x: float, ignore_range_error: bool = False) -> float:
         if not ignore_range_error:
             # Apply relative torelance value to sector range to avoid
             # unexpected invalid range error due to rounding errors (Issue #27, #67)
-            rel_tol = 1e-14
-            min_range, max_range = self.start - rel_tol, self.end + rel_tol
+            min_range = self.start - config.REL_TOL
+            max_range = self.end + config.REL_TOL
             if not min_range <= x <= max_range:
                 err_msg = f"{x=} is invalid range of '{self.name}' sector.\n{self}"
                 raise ValueError(err_msg)
@@ -390,7 +388,7 @@ def raster(
         Parameters
         ----------
         img : str | Path | Image
-            Image for plotting (`File Path`|`URL`|`PIL Image`)
+            Image data (`File Path`|`URL`|`PIL Image`)
         size : float, optional
             Image size (ratio to overall figure size)
         x : float | None, optional
@@ -421,13 +419,7 @@ def raster(
         text_kws = {} if text_kws is None else deepcopy(text_kws)
 
         # Load image data
-        if isinstance(img, str) and urlparse(img).scheme in ("http", "https"):
-            im = Image.open(urlopen(img))
-        elif isinstance(img, (str, Path)):
-            im = Image.open(str(img))
-        else:
-            im = img
-        im = im.convert("RGBA")
+        im = utils.load_image(img)
 
         # Draw border on image
         if border_width > 0:

src/pycirclize/track.py

@@ -14,6 +14,7 @@
 from matplotlib.colors import Colormap, Normalize
 from matplotlib.patches import Patch
 from matplotlib.projections.polar import PolarAxes
+from PIL import Image
 
 from pycirclize import config, utils
 from pycirclize.parser import StackedBarTable
@@ -289,7 +290,9 @@ def rect(
         rad = min(rad_rect_start, rad_rect_end)
         width = abs(rad_rect_end - rad_rect_start)
         if r_lim is not None:
-            if not min(self.r_lim) <= min(r_lim) < max(r_lim) <= max(self.r_lim):
+            min_range = min(self.r_lim) - config.REL_TOL
+            max_range = max(self.r_lim) + config.REL_TOL
+            if not min_range <= min(r_lim) < max(r_lim) <= max_range:
                 raise ValueError(f"{r_lim=} is invalid track range.\n{self}")
             radr, height = (rad, min(r_lim)), max(r_lim) - min(r_lim)
         elif ignore_pad:
@@ -332,7 +335,9 @@ def arrow(
         if r_lim is None:
             r, dr = min(self.r_plot_lim), self.r_plot_size
         else:
-            if not min(self.r_lim) <= min(r_lim) < max(r_lim) <= max(self.r_lim):
+            min_range = min(self.r_lim) - config.REL_TOL
+            max_range = max(self.r_lim) + config.REL_TOL
+            if not min_range <= min(r_lim) < max(r_lim) <= max_range:
                 raise ValueError(f"{r_lim=} is invalid track range.\n{self}")
             r, dr = min(r_lim), max(r_lim) - min(r_lim)
         arc_arrow = ArcArrow(
@@ -575,14 +580,12 @@ def yticks(
                 x_lim = (self.end, self.end + x_tick_length)
                 x_text = self.end + (x_tick_length + x_label_margin)
                 deg_text = math.degrees(self.x_to_rad(x_text, True))
-                is_lower_loc = -270 <= deg_text < -90 or 90 <= deg_text < 270
-                ha = "right" if is_lower_loc else "left"
+                ha = "right" if utils.plot.is_lower_loc(deg_text) else "left"
             elif side == "left":
                 x_lim = (self.start, self.start - x_tick_length)
                 x_text = self.start - (x_tick_length + x_label_margin)
                 deg_text = math.degrees(self.x_to_rad(x_text, True))
-                is_lower_loc = -270 <= deg_text < -90 or 90 <= deg_text < 270
-                ha = "left" if is_lower_loc else "right"
+                ha = "left" if utils.plot.is_lower_loc(deg_text) else "right"
             else:
                 raise ValueError(f"{side=} is invalid ('right' or 'left').")
             # Plot yticks
@@ -1142,6 +1145,69 @@ def heatmap(
                     text_r = sum(rect_r_lim) / 2
                     self.text(text_value, text_x, text_r, **text_kws)
 
+    def raster(
+        self,
+        img: str | Path | Image.Image,
+        *,
+        w: float = 1.0,
+        h: float = 1.0,
+        rotate: bool = True,
+        **kwargs,
+    ) -> None:
+        """Plot raster image
+
+        Parameters
+        ----------
+        img : str | Path | Image.Image
+            Image data (`File Path`|`URL`|`PIL Image`)
+        w : float, optional
+            Width ratio (`0.0 - 1.0`)
+        h : float, optional
+            Height ratio (`0.0 - 1.0`)
+        rotate : bool, optional
+            If True, rotate image 180 degrees if track is in lower location
+            (`-270 <= degree < -90`|`90 <= degree < 270`)
+        **kwargs : dict, optional
+            Axes.pcolormesh properties
+            <https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.pcolormesh.html>
+        """
+        # Check range of value
+        if not 0.0 < w <= 1.0:
+            raise ValueError(f"{w=} is invalid (0.0 < w <= 1.0).")
+        if not 0.0 < h <= 1.0:
+            raise ValueError(f"{h=} is invalid (0.0 < h <= 1.0).")
+
+        # Calculate radian (size, start, end)
+        rad_size = self.rad_size * w
+        rad_pad = self.rad_size * ((1.0 - w) / 2)
+        rad_start, rad_end = min(self.rad_lim) + rad_pad, max(self.rad_lim) - rad_pad
+        # Calculate radius (size, start, end)
+        r_size = self.r_size * h
+        r_pad = self.r_size * ((1.0 - h) / 2)
+        r_start, r_end = min(self.r_lim) + r_pad, max(self.r_lim) - r_pad
+
+        # Load image
+        img = utils.load_image(img)
+
+        # Rotate image 180 degrees if track is in lower location
+        track_center_deg = sum(self.deg_lim) / 2
+        if rotate and utils.plot.is_lower_loc(track_center_deg):
+            img = img.rotate(180)
+
+        # Resize image
+        pixel_w = int(rad_size / (np.pi / 1000))
+        pixel_h = int(r_size * 10)
+        resize_img = img.resize((pixel_w, pixel_h))
+
+        # Setup radian & radius positions for plotting image by pcolormesh
+        rad_list = np.linspace(rad_start, rad_end, resize_img.width)
+        r_list = np.linspace(r_end, r_start, resize_img.height)
+
+        def plot_raster(ax: PolarAxes):
+            ax.pcolormesh(rad_list, r_list, np.array(resize_img), **kwargs)
+
+        self._plot_funcs.append(plot_raster)
+
     def tree(
         self,
         tree_data: str | Path | Tree,

src/pycirclize/utils/__init__.py

@@ -6,7 +6,12 @@
     load_example_tree_file,
     load_prokaryote_example_file,
 )
-from pycirclize.utils.helper import ColorCycler, calc_group_spaces, is_pseudo_feature
+from pycirclize.utils.helper import (
+    ColorCycler,
+    calc_group_spaces,
+    is_pseudo_feature,
+    load_image,
+)
 
 __all__ = [
     "plot",
@@ -18,4 +23,5 @@
     "ColorCycler",
     "calc_group_spaces",
     "is_pseudo_feature",
+    "load_image",
 ]