Merge pull request #104 from moshi4/develop

Bump to v1.10.1

Author: moshi4

.github/workflows/ci.yml

@@ -29,10 +29,10 @@ jobs:
         run: uv sync --all-extras --all-groups --upgrade --python ${{ matrix.python-version }}
 
       - name: Run ruff lint check
-        run: uv run ruff check --diff
+        run: uv run ruff check src tests
 
       - name: Run ruff format check
-        run: uv run ruff format --check --diff
+        run: uv run ruff format src tests
 
       - name: Run pytest
         run: uv run pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src | tee pytest-coverage.txt
@@ -42,4 +42,4 @@ jobs:
         with:
           pytest-coverage-path: pytest-coverage.txt
           junitxml-path: pytest.xml
-        if: ${{ matrix.os=='ubuntu-latest' && matrix.python-version=='3.12' && !env.ACT }}
+        if: ${{ matrix.os=='ubuntu-latest' && matrix.python-version=='3.12' }}

README.md

@@ -277,7 +277,7 @@ conda install -c conda-forge pycirclize ipympl
 
 > [!WARNING]
 > Interactive tooltip plots require live python kernel.
-> Be aware that tooltips are not always enabled in the notebook after plotting.
+> Be aware that tooltips are not permanently enabled in the notebook after plotting.
 
 ![pyCirclize_tooltip.gif](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/pyCirclize_tooltip.gif)  
 

docs/chord_diagram.ipynb

@@ -416,7 +416,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": ".venv",
+   "display_name": "pycirclize (3.10.16)",
    "language": "python",
    "name": "python3"
   },
@@ -430,7 +430,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.10.18"
   }
  },
  "nbformat": 4,

docs/circos_plot.ipynb

@@ -62,28 +62,43 @@ addopts = "--cov=src --tb=long -vv --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
 [tool.ruff]
-include = ["src/**.py", "tests/**.py"]
 line-length = 88
 
 # Lint Rules: https://docs.astral.sh/ruff/rules/
 [tool.ruff.lint]
 select = [
-    "F", # pyflakes
-    "E", # pycodestyle (Error)
-    "W", # pycodestyle (Warning)
-    "I", # isort
-    "D", # pydocstyle
+    "I",   # isort
+    "F",   # pyflakes
+    "E",   # pycodestyle (Error)
+    "W",   # pycodestyle (Warning)
+    "D",   # pydocstyle
+    "UP",  # pyupgrade
+    "PL",  # Pylint
+    "ANN", # flake8-annotations
+    "TC",  # flake8-type-checking
+    "B",   # flake8-bugbear
+    "SIM", # flake8-simplify
+    "ARG", # flake8-unused-arguments
+    "PTH", # flake8-use-pathlib
+    "RUF", # Ruff-specific rules
 ]
 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
+    "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
+    "ANN002",  # Missing type annotation for *{name}
+    "ANN003",  # Missing type annotation for **{name}
+    "PTH123",  # open() should be replaced by Path.open()
+    "PLR0913", # Too many arguments in function definition ({c_args} > {max_args})
+    "PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
+    "PLW2901", # Outer {outer_kind} variable {name} overwritten by inner {inner_kind} target
+    "UP038",   # Deprecated: Use X | Y in {} call instead of (X, Y)
 ]
 
 [tool.ruff.lint.pydocstyle]

docs/comparative_genomics.ipynb

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.10.0"
+__version__ = "1.10.1"
 
 __all__ = [
     "Circos",