Sematic version

.github/workflows/release.yaml

@@ -0,0 +1,55 @@
+name: Publish to PyPI
+
+
+on:
+  workflow_dispatch:
+    branches:
+      - main
+    inputs:
+      version:
+        description: 'Version to release'
+        required: true
+        default: 'patch'
+        type: choice
+        options:
+          - 'major'
+          - 'minor'
+          - 'patch'
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install Poetry
+        uses: Gr1N/setup-poetry@v8
+        with:
+          poetry-version: '1.8.3'
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Bump version
+        run: |
+          python handle_versioning.py ${{ github.event.inputs.version }}
+          git add pyproject.toml
+          git commit -m "Bump version to ${{ github.event.inputs.version }}"
+          git push
+
+      - name: Create tag
+        run: |
+          current_version=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
+          git tag $current_version
+          git push origin $current_version
+
+      - name: Publish to PyPI
+        env:
+          POETRY_PYPI_TOKEN: ${{ secrets.POETRY_PYPI_TOKEN }}
+        run: poetry publish --build

handle_versioning.py

@@ -0,0 +1,45 @@
+import semantic_version
+import toml
+
+
+def read_version():
+    with open("pyproject.toml", "r") as file:
+        pyproject = toml.load(file)
+    return semantic_version.Version(pyproject["tool"]["poetry"]["version"])
+
+
+def write_version(version):
+    with open("pyproject.toml", "r") as file:
+        pyproject = toml.load(file)
+    pyproject["tool"]["poetry"]["version"] = str(version)
+    with open("pyproject.toml", "w") as file:
+        toml.dump(pyproject, file)
+
+
+def bump_version(part):
+    version = read_version()
+    if part == "major":
+        new_version = version.next_major()
+    elif part == "minor":
+        new_version = version.next_minor()
+    elif part == "patch":
+        new_version = version.next_patch()
+    else:
+        raise ValueError("Invalid part: choose 'major', 'minor', or 'patch'")
+    write_version(new_version)
+    print(f"Updated version to {new_version}")
+
+
+if __name__ == "__main__":
+    import sys
+
+    if len(sys.argv) < 2 or sys.argv[1] not in ["read", "major", "minor", "patch"]:
+        raise ValueError("Missing command: choose 'read', 'major', 'minor', or 'patch")
+
+    command = sys.argv[1]
+    if command == "read":
+        current_version = read_version()
+        print(f"Current version is {current_version}")
+
+    else:
+        bump_version(command)

pyproject.toml

@@ -1,119 +1,68 @@
-# https://python-poetry.org/docs/pyproject
-# minimal required information
-
 [project]
 name = "osipi"
 version = "0.1.2"
-dependencies = [
-  "numpy",
-  "scipy"
-]
-
-# optional information
-
+dependencies = [ "numpy", "scipy",]
 description = "The authorative python package for perfusion MRI"
 readme = "README.md"
-authors = [
-  { name = "Luis Torres", email = "[email protected]" },
-  { name = "Steven Sourbron", email = "[email protected]" },
-  ]
-license = { file = "LICENSE" }
-classifiers = [
-  # How mature is this project? Common values are
-  #   3 - Alpha
-  #   4 - Beta
-  #   5 - Production/Stable
-  'Development Status :: 3 - Alpha',
-
-  # Indicate who your project is intended for
-  'Intended Audience :: Developers',
-  'Intended Audience :: Science/Research',
-  'Topic :: Scientific/Engineering',
-  'Operating System :: OS Independent',
-
-  'License :: OSI Approved :: Apache Software License',
-  "Programming Language :: Python",
-  "Programming Language :: Python :: 3"
-]
-keywords = ['python', "medical imaging", "perfusion", "MRI"]
-
+classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering", "Operating System :: OS Independent", "License :: OSI Approved :: Apache Software License", "Programming Language :: Python", "Programming Language :: Python :: 3",]
+keywords = [ "python", "medical imaging", "perfusion", "MRI",]
 requires-python = ">=3.6"
+[[project.authors]]
+name = "Luis Torres"
+email = "[email protected]"
 
-[project.urls]
-"Homepage" = "https://osipi.github.io/pypi"
+[[project.authors]]
+name = "Steven Sourbron"
+email = "[email protected]"
 
-[tool.setuptools.packages.find]
-where = ["src"]
+[project.license]
+file = "LICENSE"
+
+[project.urls]
+Homepage = "https://osipi.github.io/pypi"
 
 [project.optional-dependencies]
-tests = [
-  "pytest",
-  "matplotlib",
-]
-docs = [
-    "sphinx",
-    "pydata-sphinx-theme",
-    "myst-parser",
-    "sphinx-copybutton",
-    "sphinx-design",
-    "sphinx-remove-toctrees",
-    "autodocsumm",
-    "docutils",
-    "sphinxcontrib-applehelp",
-    "sphinxcontrib-devhelp",
-    "sphinxcontrib-htmlhelp",
-    "sphinxcontrib-jsmath",
-    "sphinxcontrib-qthelp",
-    "sphinxcontrib-serializinghtml",
-    "sphinx-gallery",
-]
+tests = [ "pytest", "matplotlib",]
+docs = [ "sphinx", "pydata-sphinx-theme", "myst-parser", "sphinx-copybutton", "sphinx-design", "sphinx-remove-toctrees", "autodocsumm", "docutils", "sphinxcontrib-applehelp", "sphinxcontrib-devhelp", "sphinxcontrib-htmlhelp", "sphinxcontrib-jsmath", "sphinxcontrib-qthelp", "sphinxcontrib-serializinghtml", "sphinx-gallery",]
 
 [tool.ruff]
-# Exclude a variety of commonly ignored directories.
-exclude = [
-    ".direnv", ".eggs", ".git", ".git-rewrite","__init__.py",
-    ".mypy_cache", ".nox", ".pants.d", ".pyenv", ".pytest_cache", ".pytype",
-    ".ruff_cache", ".svn", ".venv", ".vscode", "__pypackages__", "_build",
-    "buck-out", "build", "dist", "site-packages", "venv",
-]
-
+exclude = [ ".direnv", ".eggs", ".git", ".git-rewrite", "__init__.py", ".mypy_cache", ".nox", ".pants.d", ".pyenv", ".pytest_cache", ".pytype", ".ruff_cache", ".svn", ".venv", ".vscode", "__pypackages__", "_build", "buck-out", "build", "dist", "site-packages", "venv",]
 line-length = 100
 
+[tool.poetry]
+name = "osipi"
+version = "0.1.2"
+description = "The authorative python package for perfusion MRI"
+authors = [ "Luis Torres <[email protected]>", "Steven Sourbron <[email protected]>",]
+readme = "README.md"
 
 [tool.ruff.lint]
-# Enable Pyflakes (`F`), a subset of the pycodestyle (`E`) codes, and isort (`I`).
-select = ["E4", "E7", "E9", "F", "I"]
+select = [ "E4", "E7", "E9", "F", "I",]
 ignore = []
-fixable = ["ALL"]
+fixable = [ "ALL",]
 unfixable = []
 
 [tool.ruff.format]
-# Like Black, use double quotes for strings.
 quote-style = "double"
-
 indent-style = "space"
-
 skip-magic-trailing-comma = false
-
 line-ending = "auto"
 
 docstring-code-format = true
 
 docstring-code-line-length = 100
 
-[tool.poetry]
-name = "osipi"
-version = "0.1.2"
-description = "The authorative python package for perfusion MRI"
-authors = ["Luis Torres <[email protected]>", "Steven Sourbron <[email protected]>"]
-readme = "README.md"
-
 [tool.poetry.dependencies]
 python = "^3.9"
 numpy = "^1.21.2"
 scipy = "^1.7.3"
 matplotlib = "3.9.0"
 requests = "^2.32.3"
+semantic-version = "^2.10.0"
+toml = "^0.10.2"
+
+[tool.setuptools.packages.find]
+where = [ "src",]
 
 [tool.poetry.group.dev.dependencies]
 flake8 = "^7.0.0"
@@ -125,8 +74,17 @@ pytest-cov = "^5.0.0"
 autodocsumm = "^0.2.12"
 docutils = "^0.21.2"
 myst-parser = "^3.0.1"
-rstcheck = {extras = ["sphinx"], version = "^6.2.1"}
 mkdocs = "^1.6.0"
-mkdocs-material = {extras = ["imaging"], version = "^9.5.27"}
 mkdocs-gallery = "^0.10.1"
-mkdocstrings = {extras = ["crystal", "python"], version = "^0.25.1"}
+
+[tool.poetry.group.docs.dependencies.rstcheck]
+extras = [ "sphinx",]
+version = "^6.2.1"
+
+[tool.poetry.group.docs.dependencies.mkdocs-material]
+extras = [ "imaging",]
+version = "^9.5.27"
+
+[tool.poetry.group.docs.dependencies.mkdocstrings]
+extras = [ "crystal", "python",]
+version = "^0.25.1"