Merge pull request #91 from moshi4/develop

Bump to v1.9.1

Author: moshi4

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4

docs/circos_plot.ipynb

@@ -12,20 +12,22 @@
 -e file:.
 asttokens==3.0.0
     # via stack-data
-attrs==24.3.0
+attrs==25.3.0
     # via jsonschema
     # via referencing
-babel==2.16.0
+babel==2.17.0
     # via mkdocs-material
-beautifulsoup4==4.12.3
+backrefs==5.8
+    # via mkdocs-material
+beautifulsoup4==4.13.4
     # via nbconvert
-biopython==1.84
+biopython==1.85
     # via pycirclize
     # via pygenomeviz
-black==24.10.0
+black==25.1.0
 bleach==6.2.0
     # via nbconvert
-certifi==2024.12.14
+certifi==2025.1.31
     # via requests
 cfgv==3.4.0
     # via pre-commit
@@ -34,21 +36,20 @@ charset-normalizer==3.4.1
 click==8.1.8
     # via black
     # via mkdocs
-    # via mkdocstrings
 colorama==0.4.6
     # via griffe
     # via mkdocs-material
 comm==0.2.2
     # via ipykernel
 contourpy==1.3.0
     # via matplotlib
-coverage==7.6.10
+coverage==7.8.0
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
-debugpy==1.8.11
+debugpy==1.8.14
     # via ipykernel
-decorator==5.1.1
+decorator==5.2.1
     # via ipython
 defusedxml==0.7.1
     # via nbconvert
@@ -57,23 +58,23 @@ distlib==0.3.9
 exceptiongroup==1.2.2
     # via ipython
     # via pytest
-executing==2.1.0
+executing==2.2.0
     # via stack-data
 fastjsonschema==2.21.1
     # via nbformat
-filelock==3.16.1
+filelock==3.18.0
     # via virtualenv
-fonttools==4.55.3
+fonttools==4.57.0
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-griffe==1.5.4
+griffe==1.7.2
     # via mkdocstrings-python
-identify==2.6.5
+identify==2.6.9
     # via pre-commit
 idna==3.10
     # via requests
-importlib-metadata==8.5.0
+importlib-metadata==8.6.1
     # via jupyter-client
     # via markdown
     # via mkdocs
@@ -82,15 +83,15 @@ importlib-metadata==8.5.0
     # via nbconvert
 importlib-resources==6.5.2
     # via matplotlib
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
 ipykernel==6.29.5
     # via mkdocs-jupyter
 ipython==8.18.1
     # via ipykernel
 jedi==0.19.2
     # via ipython
-jinja2==3.1.5
+jinja2==3.1.6
     # via mkdocs
     # via mkdocs-material
     # via mkdocstrings
@@ -110,11 +111,11 @@ jupyter-core==5.7.2
     # via nbformat
 jupyterlab-pygments==0.3.0
     # via nbconvert
-jupytext==1.16.6
+jupytext==1.17.0
     # via mkdocs-jupyter
 kiwisolver==1.4.7
     # via matplotlib
-markdown==3.7
+markdown==3.8
     # via mkdocs
     # via mkdocs-autorefs
     # via mkdocs-material
@@ -142,32 +143,32 @@ mdurl==0.1.2
 mergedeep==1.3.4
     # via mkdocs
     # via mkdocs-get-deps
-mistune==3.1.0
+mistune==3.1.3
     # via nbconvert
 mkdocs==1.6.1
     # via mkdocs-autorefs
     # via mkdocs-jupyter
     # via mkdocs-material
     # via mkdocstrings
-mkdocs-autorefs==1.2.0
+mkdocs-autorefs==1.4.1
     # via mkdocstrings
     # via mkdocstrings-python
 mkdocs-get-deps==0.2.0
     # via mkdocs
 mkdocs-jupyter==0.25.1
-mkdocs-material==9.5.49
+mkdocs-material==9.6.12
     # via mkdocs-jupyter
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
-mkdocstrings==0.27.0
+mkdocstrings==0.29.1
     # via mkdocstrings-python
-mkdocstrings-python==1.13.0
+mkdocstrings-python==1.16.10
     # via mkdocstrings
 mypy-extensions==1.0.0
     # via black
 nbclient==0.10.2
     # via nbconvert
-nbconvert==7.16.5
+nbconvert==7.16.6
     # via mkdocs-jupyter
 nbformat==5.10.4
     # via jupytext
@@ -205,20 +206,19 @@ pathspec==0.12.1
     # via mkdocs
 pexpect==4.9.0
     # via ipython
-pillow==11.1.0
+pillow==11.2.1
     # via matplotlib
-platformdirs==4.3.6
+platformdirs==4.3.7
     # via black
     # via jupyter-core
     # via mkdocs-get-deps
-    # via mkdocstrings
     # via virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==4.0.1
-prompt-toolkit==3.0.48
+pre-commit==4.2.0
+prompt-toolkit==3.0.51
     # via ipython
-psutil==6.1.1
+psutil==7.0.0
     # via ipykernel
 ptyprocess==0.7.0
     # via pexpect
@@ -230,20 +230,20 @@ pygments==2.19.1
     # via mkdocs-jupyter
     # via mkdocs-material
     # via nbconvert
-pymdown-extensions==10.14
+pymdown-extensions==10.14.3
     # via mkdocs-material
     # via mkdocstrings
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via pytest-cov
-pytest-cov==6.0.0
+pytest-cov==6.1.1
 python-dateutil==2.9.0.post0
     # via ghp-import
     # via jupyter-client
     # via matplotlib
     # via pandas
-pytz==2024.2
+pytz==2025.2
     # via pandas
 pyyaml==6.0.2
     # via jupytext
@@ -254,20 +254,18 @@ pyyaml==6.0.2
     # via pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-pyzmq==26.2.0
+pyzmq==26.4.0
     # via ipykernel
     # via jupyter-client
-referencing==0.35.1
+referencing==0.36.2
     # via jsonschema
     # via jsonschema-specifications
-regex==2024.11.6
-    # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-rpds-py==0.22.3
+rpds-py==0.24.0
     # via jsonschema
     # via referencing
-ruff==0.9.1
+ruff==0.11.6
 six==1.17.0
     # via python-dateutil
 soupsieve==2.6
@@ -294,16 +292,18 @@ traitlets==5.14.3
     # via nbclient
     # via nbconvert
     # via nbformat
-typing-extensions==4.12.2
+typing-extensions==4.13.2
+    # via beautifulsoup4
     # via black
     # via ipython
     # via mistune
-    # via mkdocstrings
-tzdata==2024.2
+    # via mkdocstrings-python
+    # via referencing
+tzdata==2025.2
     # via pandas
-urllib3==2.3.0
+urllib3==2.4.0
     # via requests
-virtualenv==20.28.1
+virtualenv==20.30.0
     # via pre-commit
 watchdog==6.0.0
     # via mkdocs

docs/radar_chart.ipynb

@@ -10,13 +10,13 @@
 #   universal: false
 
 -e file:.
-biopython==1.84
+biopython==1.85
     # via pycirclize
 contourpy==1.3.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.55.3
+fonttools==4.57.0
     # via matplotlib
 importlib-resources==6.5.2
     # via matplotlib
@@ -34,18 +34,18 @@ packaging==24.2
     # via matplotlib
 pandas==2.2.3
     # via pycirclize
-pillow==11.1.0
+pillow==11.2.1
     # via matplotlib
-pyparsing==3.2.1
+pyparsing==3.2.3
     # via matplotlib
 python-dateutil==2.9.0.post0
     # via matplotlib
     # via pandas
-pytz==2024.2
+pytz==2025.2
     # via pandas
 six==1.17.0
     # via python-dateutil
-tzdata==2024.2
+tzdata==2025.2
     # via pandas
 zipp==3.21.0
     # via importlib-resources

requirements-dev.lock

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.9.0"
+__version__ = "1.9.1"
 
 __all__ = [
     "Circos",

requirements.lock

@@ -81,9 +81,7 @@ def __init__(
         space_num = len(sectors) if endspace else len(sectors) - 1
         if isinstance(space, (list, tuple)):
             if len(space) != space_num:
-                err_msg = f"{space=} is invalid.\n"
-                err_msg += f"Length of space list must be {space_num}."
-                raise ValueError(err_msg)
+                raise ValueError(f"{space=} is invalid.\nLength of space list must be {space_num}.")  # fmt: skip  # noqa: E501
             space_list = list(space) + [0]
             space_deg_size = sum(space)
         else:
@@ -169,8 +167,7 @@ def ax(self) -> PolarAxes:
         Can't access `ax` property before calling `circos.plotfig()` method
         """
         if self._ax is None:
-            err_msg = "Can't access ax property before calling `circos.plotfig() method"
-            raise ValueError(err_msg)
+            raise ValueError("Can't access ax property before calling `circos.plotfig() method")  # fmt:skip  # noqa: E501
         return self._ax
 
     ############################################################
@@ -1034,8 +1031,7 @@ def plotfig(
             # Check PolarAxes or not
             if not isinstance(ax, PolarAxes):
                 ax_class_name = type(ax).__name__
-                err_msg = f"Input ax is not PolarAxes (={ax_class_name})."
-                raise ValueError(err_msg)
+                raise ValueError(f"Input ax is not PolarAxes (={ax_class_name}).")
             fig = ax.get_figure()
         self._initialize_polar_axes(ax)
 
@@ -1121,12 +1117,9 @@ def _check_degree_range(self, start: float, end: float) -> None:
         """
         min_deg, max_deg = -360, 360
         if not min_deg <= start < end <= max_deg:
-            err_msg = "start-end must be "
-            err_msg += f"'{min_deg} <= start < end <= {max_deg}' ({start=}, {end=})"
-            raise ValueError(err_msg)
+            raise ValueError(f"start-end must be '{min_deg} <= start < end <= {max_deg}' ({start=}, {end=})")  # fmt: skip  # noqa: E501
         if end - start > max_deg:
-            err_msg = f"'end - start' must be less than {max_deg} ({start=}, {end=})"
-            raise ValueError(err_msg)
+            raise ValueError(f"'end - start' must be less than {max_deg} ({start=}, {end=})")  # fmt: skip  # noqa: E501
 
     def _to_sector2range(
         self,
@@ -1138,8 +1131,7 @@ def _to_sector2range(
             if isinstance(value, (tuple, list)):
                 sector_start, sector_end = value
                 if not sector_start < sector_end:
-                    err_msg = f"{sector_end=} must be larger than {sector_start=}."
-                    raise ValueError(err_msg)
+                    raise ValueError(f"{sector_end=} must be larger than {sector_start=}.")  # fmt: skip  # noqa: E501
                 sector2range[name] = (sector_start, sector_end)
             else:
                 sector2range[name] = (0, value)
@@ -1234,8 +1226,7 @@ def _adjust_annotation(self) -> None:
         if len(ann_list) == 0 or config.ann_adjust.max_iter <= 0:
             return
         if len(ann_list) > config.ann_adjust.limit:
-            warn_msg = f"Too many annotations(={len(ann_list)}). Annotation position adjustment is not done."  # noqa: E501
-            warnings.warn(warn_msg)
+            warnings.warn(f"Too many annotations(={len(ann_list)}). Annotation position adjustment is not done.")  # fmt: skip  # noqa: E501
             return
 
         def get_ann_window_extent(ann: Annotation) -> Bbox:

src/pycirclize/__init__.py

@@ -18,7 +18,7 @@
 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
+EPSILON = 1e-10
 
 # Circos Color Scheme
 # http://circos.ca/tutorials/lessons/configuration/colors/