Support py3.12, move to rye (#45)

* move to rye and increase testing to support py3.12

* fix test workflow

* add coverage workflow

.github/workflows/package_testing.yml

@@ -9,39 +9,40 @@ on:
   pull_request:
     branches: [ main ]
 
+env:
+  MAIN_PYTHON_VERSION: "3.12"
+
 jobs:
   # Build and test
   build:
     if: github.repository_owner == 'galactic-forensics'
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Checkout repo
+      uses: actions/checkout@v4
+    - name: Install the latest version of rye
+      uses: eifinger/setup-rye@v2
+    - name: Sync Rye
+      run: |
+        rye pin ${{ matrix.python-version }}
+        rye sync --all-features
+    - name: Run Tests and doctests
+      run: |
+        rye test
+        rye run test_docs
+    - name: Run Lint on one python
+      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
+      run: rye lint
+    - name: Run Pytest with coverage
+      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
       run: |
-        python -m pip install --upgrade pip
-        pip install nox
-        pip install .[test]
-    - name: Run nox
-      run: nox --no-error-on-missing-interpreters
-    - name: Generate coverage report
-      run: pytest
-    - name: Upload coverage to Codecov
+        rye run test_cov
+    - name: Upload coverage reports to Codecov
+      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION && github.repository_owner == 'galactic-forensics' }}
       uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        directory: ./coverage/reports/
-        env_vars: OS,PYTHON
-        fail_ci_if_error: true
-        files: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-        path_to_write_report: ./coverage/codecov_report.txt
-        verbose: true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/python-publish.yml

@@ -7,26 +7,24 @@ on:
   release:
     types: [created]
 
+env:
+  PYTHON_VERSION: "3.12"
+
 jobs:
   deploy:
     if: github.repository_owner == 'galactic-forensics'
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build twine
-        pip install .
-    - name: Build and publish
-      env:
-        PYPI_USERNAME: '__token__'
-        PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-      run: |
-        python -m build
-        python -m twine upload dist/* -u $PYPI_USERNAME -p $PYPI_PASSWORD
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Install the latest version of rye
+        uses: eifinger/setup-rye@v2
+      - name: Sync Rye
+        run: |
+          rye pin ${{ env.PYTHON_VERSION }}
+          rye sync
+      - name: Build and release the controller
+        run: |
+          rye build
+          rye publish --token ${{ secrets.PYPI_TOKEN }} --yes

.gitignore

@@ -81,9 +81,6 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
@@ -130,6 +127,3 @@ dmypy.json
 
 # PyCharm
 .idea/
-
-# scm version
-ceresfit/_version.py

.pre-commit-config.yaml

@@ -2,15 +2,19 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
-    -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
--   repo: https://github.com/psf/black
-    rev: 24.3.0
-    hooks:
-    -   id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.2.2
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.15.1
     hooks:
       - id: pyupgrade
-        args: [ --py36-plus ]
+        args: [ --py38-plus ]

.python-version

@@ -0,0 +1 @@
+3.12

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Reto Trappitsch
+Copyright (c) 2023-2024 Reto Trappitsch
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -6,7 +6,7 @@
 [![codecov](https://codecov.io/gh/galactic-forensics/CEREsFit/branch/main/graph/badge.svg?token=C8KN5UE831)](https://codecov.io/gh/galactic-forensics/CEREsFit)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/galactic-forensics/CEREsFit/main.svg)](https://results.pre-commit.ci/latest/github/galactic-forensics/CEREsFit/main)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Rye](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/rye/main/artwork/badge.json)](https://rye-up.com)
 
 The goal of CEREsFit (Correlated Errors Regression Estimate Fit)
 is to provide a python package
@@ -63,24 +63,34 @@ can be found
 
 ## Development & Contributing
 
-If you would like to contribute,
-clone the GitHub repo and then install the package locally from within the folder via:
+This project is developed using [Rye](https://rye-up.com/).
+After cloning,
+you can simply run
+
+```rye sync```
+
+in the project folder and you should be good to go.
+
+Code auto formatting is implemented using
+[`pre-commit`](https://pre-commit.com/) hooks.
+
+For local formatting and linting,
+please use
 
 ```
-pip install -e .[dev]
+rye fmt
+rye lint
 ```
 
-If you also want to install the full test environment,
-run:
+For running tests, use:
 
 ```
-pip install -e .[dev,test]
+rye test
+rye run test_docs
 ```
 
-Code auto formatting is implemented using
-[`pre-commit`](https://pre-commit.com/) hooks.
-Full testing of the package can be done with
-[`nox`](https://nox.thea.codes/en/stable/index.html).
+The first of these commands runs `pytest`,
+the second checks the documentation tests using `xdoctest`.
 
 Please feel free to raise issues on GitHub
 and open pull requests if you have a feature to be added.

pyproject.toml

@@ -1,57 +1,55 @@
-[build-system]
-requires = ["flit_scm"]
-build-backend = "flit_scm:buildapi"
-
 [project]
-authors = [{name = "Reto Trappitsch", email = "[email protected]"}]
+name = "ceresfit"
+version = "0.3.0"
+description = "Linear Regression for data set with correlated or uncorrelated uncertainties in both axes."
+authors = [
+    { name = "Reto Trappitsch", email = "[email protected]" }
+]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Operating System :: OS Independent",
     "License :: OSI Approved :: MIT License",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Physics",
 ]
-dependencies = ["numpy", "scipy"]
-dynamic = ["version", "description"]
-license = {file = "LICENSE"}
-name = "ceresfit"
+dependencies = [
+    "numpy",
+    "scipy"
+]
 readme = "README.md"
-requires-python=">=3.8"
+requires-python = ">= 3.8"
+license = { text = "MIT" }
 
-[project.urls]
-Source = "https://github.com/galactic-forensics/CEREsFit"
-
-[project.optional-dependencies]
-dev = [
-    "nox"
-]
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
-test = [
-    "darglint>=1.5.1",
-    "flake8>=4,<5",
-    "flake8-bandit",
-    "flake8-black",
-    "flake8-bugbear",
-    "flake8-docstrings",
-    "flake8-import-order",
-    "bandit<=1.7.2",
-    "pytest>=6.0",
+[tool.rye]
+managed = true
+dev-dependencies = [
+    "pytest>=8.0",
     "pytest-cov",
+    "xdoctest>=1.1.3",
 ]
 
-[tool.flit.sdist]
-exclude = ["examples/", ".gitignore"]
+[tool.rye.scripts]
+test_cov = "pytest --cov --cov-report xml"
+test_docs = "xdoctest ceresfit --all"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ceresfit"]
 
 [tool.pytest.ini_options]
-minversion = "6.0"
+minversion = "8.0"
 addopts = "--cov=ceresfit --cov-report=xml"
 testpaths = "tests"
-
-[tool.setuptools_scm]
-write_to = "ceresfit/_version.py"