Merge pull request #101 from moshi4/develop

Bump to v1.10.1

Author: moshi4

.github/workflows/ci.yml

@@ -11,29 +11,35 @@ on:
 jobs:
   CI:
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install Rye
-        run: |
-          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
-          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
 
       - name: Install Python ${{ matrix.python-version }} & dependencies
-        run: |
-          rye pin ${{ matrix.python-version }}
-          rye sync --update-all --all-features
+        run: uv sync --all-extras --all-groups --upgrade --python ${{ matrix.python-version }}
 
       - name: Run ruff lint check
-        run: rye run ruff check --diff
+        run: uv run ruff check --diff
 
       - name: Run ruff format check
-        run: rye run ruff format --check --diff
+        run: uv run ruff format --check --diff
 
       - name: Run pytest
-        run: rye run pytest
+        run: uv run pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src | tee pytest-coverage.txt
+
+      - name: Pytest Coverage Comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+        if: ${{ matrix.os=='ubuntu-latest' && matrix.python-version=='3.12' && !env.ACT }}

.github/workflows/publish_mkdocs.yml

@@ -12,13 +12,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install Rye
-        run: |
-          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
-          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
 
       - name: Install Python & MkDocs & Plugins
-        run: rye sync
+        run: uv sync
 
       - name: Publish document
-        run: rye run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.github/workflows/publish_to_pypi.yml

@@ -15,13 +15,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install Rye
-        run: |
-          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
-          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
 
       - name: Build
-        run: rye build
+        run: uv build
 
       - name: Publish
-        run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y
+        run: uv publish -u $PYPI_USERNAME --token $PYPI_PASSWORD

.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: v0.9.1
+    rev: v0.12.7
     hooks:
       - id: ruff
         name: ruff lint check

README.md

@@ -13,7 +13,7 @@
 - [Installation](#installation)
 - [API Usage](#api-usage)
 - [Code Example](#code-example)
-- [Not Implemented Features](#not-implemented-features)
+- [Tooltip Option](#tooltip-option)
 - [Star History](#star-history)
 
 ## Overview
@@ -29,7 +29,7 @@ More detailed documentation is available [here](https://moshi4.github.io/pyCircl
 
 ## Installation
 
-`Python 3.9 or later` is required for installation.
+`Python 3.10 or later` is required for installation.
 
 **Install PyPI package:**
 
@@ -139,7 +139,7 @@ for sector in circos.sectors:
         if gene_name is not None:
             labels.append(gene_name)
             label_pos_list.append(label_pos)
-    f_cds_track.xticks(label_pos_list, labels, label_size=6, label_orientation="vertical")
+            f_cds_track.annotate(label_pos, gene_name, label_size=6)
 
     # Plot xticks (interval = 10 Kb)
     r_cds_track.xticks_by_interval(
@@ -263,16 +263,23 @@ fig.savefig("example05.png")
 
 ![example05.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/example05.png)  
 
-## Not Implemented Features
+## Tooltip Option
 
-List of features implemented in other Circos plotting tools but not yet implemented in pyCirclize.
-I may implement them when I feel like it.
+pyCirclize supports tooltip display in jupyter using [ipympl](https://github.com/matplotlib/ipympl).
+To enable tooltip, install pycirclize with ipympl and call `circos.plotfig(tooltip=True)` method.
+Tooltip option is tested on jupyter notebooks in VScode and JupyterLab.
 
-- Plot histogram
-- Plot boxplot
-- Plot violin
-- Plot curved text
-- Adjust overlap label position
+```shell
+pip install pycirclize[tooltip]
+# or
+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.
+
+![pyCirclize_tooltip.gif](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/pyCirclize_tooltip.gif)  
 
 ## Star History