Merge pull request #74 from moshi4/develop

Bump to v1.7.0

Author: moshi4

.github/workflows/ci.yml

@@ -14,24 +14,26 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Install Rye
+        run: |
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
-      - name: Install dependencies
-        run: pip install -e . pytest pytest-cov ruff
+      - name: Install Python ${{ matrix.python-version }} & dependencies
+        run: |
+          rye pin ${{ matrix.python-version }}
+          rye sync --update-all --all-features
 
       - name: Run ruff lint check
-        run: ruff check --diff
+        run: rye run ruff check --diff
 
       - name: Run ruff format check
-        run: ruff format --check --diff
+        run: rye run ruff format --check --diff
 
       - name: Run pytest
-        run: pytest
+        run: rye run pytest

.github/workflows/publish_mkdocs.yml

@@ -12,15 +12,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install MkDocs & Plugins
+      - name: Install Rye
         run: |
-          pip install .
-          pip install mkdocs mkdocs-material mkdocs-jupyter mkdocstrings[python] black
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+
+      - name: Install Python & MkDocs & Plugins
+        run: rye sync
 
       - name: Publish document
-        run: mkdocs gh-deploy --force
+        run: rye run mkdocs gh-deploy --force

.github/workflows/publish_to_pypi.yml

@@ -15,18 +15,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install Poetry
+      - name: Install Rye
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
       - name: Build
-        run: poetry build
+        run: rye build
 
       - name: Publish
-        run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD
+        run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y

.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: v0.4.4
+    rev: v0.6.4
     hooks:
       - id: ruff
         name: ruff lint check

README.md

@@ -29,7 +29,7 @@ More detailed documentation is available [here](https://moshi4.github.io/pyCircl
 
 ## Installation
 
-`Python 3.8 or later` is required for installation.
+`Python 3.9 or later` is required for installation.
 
 **Install PyPI package:**
 

docs/index.md

@@ -20,7 +20,7 @@ pyCirclize was inspired by [circlize](https://github.com/jokergoo/circlize) and
 
 ## Installation
 
-`Python 3.8 or later` is required for installation.
+`Python 3.9 or later` is required for installation.
 
 **Install PyPI package:**
 

poetry.lock

@@ -1,11 +1,9 @@
-[tool.poetry]
+[project]
 name = "pyCirclize"
-version = "1.6.0"
+dynamic = ["version"]
 description = "Circular visualization in Python"
-authors = ["moshi4"]
+authors = [{ name = "moshi4", email = "" }]
 license = "MIT"
-homepage = "https://moshi4.github.io/pyCirclize/"
-repository = "https://github.com/moshi4/pyCirclize/"
 readme = "README.md"
 keywords = [
     "matplotlib",
@@ -19,14 +17,44 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Framework :: Matplotlib",
 ]
+requires-python = ">=3.9"
+dependencies = [
+    "matplotlib>=3.6.3",
+    "biopython>=1.80",
+    "numpy>=1.21",
+    "pandas>=1.3.5",
+]
+
+[project.urls]
+homepage = "https://moshi4.github.io/pyCirclize/"
+repository = "https://github.com/moshi4/pyCirclize/"
+
+[tool.hatch.version]
+path = "src/pycirclize/__init__.py"
+
+[tool.rye]
+managed = true
+dev-dependencies = [
+    "ruff>=0.4.0",
+    "pre-commit>=3.5.0",
+    "pytest>=8.0.0",
+    "pytest-cov>=4.0.0",
+    "ipykernel>=6.13.0",
+    # docs
+    "mkdocs>=1.2",
+    "mkdocstrings[python]>=0.19.0",
+    "mkdocs-jupyter>=0.21.0",
+    "mkdocs-material>=8.2",
+    "black>=22.3.0",
+]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "--cov=src --tb=long -vv --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
 [tool.ruff]
-src = ["src", "tests"]
+include = ["src/**.py", "tests/**.py"]
 line-length = 88
 
 # Lint Rules: https://docs.astral.sh/ruff/rules/
@@ -53,27 +81,6 @@ ignore = [
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.poetry.dependencies]
-python = "^3.8"
-matplotlib = ">=3.5.2"
-biopython = ">=1.80"
-numpy = ">=1.21.1"
-pandas = ">=1.3.5"
-
-[tool.poetry.group.dev.dependencies]
-ruff = ">=0.1.6"
-pre-commit = ">=3.5.0"
-pytest = ">=7.1.2"
-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"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"