fix #6, switch to nox

.codespellignore

@@ -0,0 +1,4 @@
+in
+out
+inout
+matchs

.github/workflows/main.yml

@@ -4,26 +4,23 @@ on: [push, pull_request, release]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox "poetry>=1.4" coveralls
-      - name: TOX
-        run: tox
+        run: pip install --no-cache-dir nox
+      - name: NOX
+        run: nox
       - name: Upload coverage data to coveralls.io
-        run: coveralls --service=github
+        run: nox -s dev -- coveralls --service=github
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
@@ -33,22 +30,28 @@ jobs:
     name: Indicate completion to coveralls.io
     needs: build
     runs-on: ubuntu-latest
-    container: python:3-slim
     steps:
-    - name: Finished
-      run: |
-        pip3 install --upgrade coveralls
-        coveralls --service=github --finish
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install --no-cache-dir nox
+      - name: Upload coverage data to coveralls.io
+        run: nox -s dev -- coveralls --service=github --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   publish:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     needs: coveralls
+    name: upload release to PyPI
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/checkout@v3
-      - name: Build and publish to pypi
-        uses: JRubics/poetry-publish@v1.17
-        with:
-          pypi_token: ${{ secrets.PYPI_TOKEN }}
+      - uses: actions/checkout@v4
+      - uses: pdm-project/setup-pdm@v4
+      - name: Publish package distributions to PyPI
+        run: pdm publish

.gitignore

@@ -1,15 +1,12 @@
-*.egg-info/
-*.xml
-.coverage
-.tox
+*.pyc
+/.*_cache/
+/.coverage
+/.nox/
+/.venv*
+/.pdm-python
+/dist/
+/docs.zip
+/report.xml
+/site/
+/.hypothesis
 .test2ref
-.venv
-.mypy_cache
-/.vscode
-/docs/api
-__pycache__
-build
-dist/
-_readthedocs/
-poetry.lock
-setup.py

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.3.7
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.2.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-toml
+  - id: check-xml
+  - id: debug-statements
+  - id: check-added-large-files
+  - id: check-merge-conflict
+  - id: mixed-line-ending
+    args:
+    - "--fix=lf"
+
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.5
+  hooks:
+  - id: remove-tabs
+    args: [--whitespaces-count, '2']  # defaults to: 4
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    args:
+    - "--write-changes"
+    - "--ignore-words=.codespellignore"
+    additional_dependencies:
+      - tomli
+    exclude: '^pdm\.lock$'

.readthedocs.yaml

@@ -8,11 +8,11 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
   commands:
     - pip install --upgrade --no-cache-dir pip
-    - pip install --no-cache-dir "poetry>=1.4"
-    - poetry install --with=doc --without=test
-    - poetry run make html -C docs
-    - cp -r docs/build _readthedocs
+    - pip install --no-cache-dir nox
+    - nox -s doc
+    - mkdir _readthedocs
+    - cp -r site _readthedocs/html

CONTRIBUTING.md

@@ -0,0 +1,54 @@
+* DOCME: refer github contribution guide
+* DOCME: our requirements
+
+## Testing
+
+### Create Environment
+
+Run these commands just the first time:
+
+```bash
+# Ensure python3 is installed
+python3 -m venv .venv
+source .venv/bin/activate
+pip install nox
+```
+
+### Enter Environment
+
+Run this command once you open a new shell:
+
+```bash
+source .venv/bin/activate
+```
+
+### Test Your Changes
+
+```bash
+# test
+nox -R
+```
+
+## Project Structure
+
+The project contains these files and directories:
+
+| File/Directory | Description |
+|---|---|
+| `src/` | Python Package Sources - the files this is all about. |
+| `pyproject.toml` | Python Package Meta File. Also contains all tool settings. |
+| `.gitignore` | Lists of files and directories ignored by version control system. |
+| `.github/` | Github Settings. |
+| `.readthedocs.yaml` | Documentation Server Configuration. |
+| `.pre-commit-config.yaml` | Pre-Commit Check Configuration. |
+
+Next to that, there are some temporary files ignored by version control system.
+
+| File/Directory | Description |
+|---|---|
+| `pdm.lock` | File with resolved python package dependencies |
+| `htmlcov/` | Test Execution Code Coverage Report in HTML format. |
+| `report.xml` | Test Execution Report. |
+| `.*_cache/` | Cache Directory. |
+| `.nox/` | [NOX][nox] directory. |
+| `.venv*` | Virtual Environments |

README.md

@@ -1,14 +1,12 @@
 [![PyPI Version](https://badge.fury.io/py/test2ref.svg)](https://badge.fury.io/py/test2ref)
 [![Python Build](https://github.com/nbiotcloud/test2ref/actions/workflows/main.yml/badge.svg)](https://github.com/nbiotcloud/test2ref/actions/workflows/main.yml)
-[![Documentation](https://readthedocs.org/projects/test2ref/badge/?version=latest)](https://test2ref.readthedocs.io/en/stable)
+[![Documentation](https://readthedocs.org/projects/test2ref/badge/?version=stable)](https://test2ref.readthedocs.io/en/stable/?badge=stable)
 [![Coverage Status](https://coveralls.io/repos/github/nbiotcloud/test2ref/badge.svg?branch=main)](https://coveralls.io/github/nbiotcloud/test2ref?branch=main)
 [![python-versions](https://img.shields.io/pypi/pyversions/test2ref.svg)](https://pypi.python.org/pypi/test2ref)
-[![pylint](https://img.shields.io/badge/linter-pylint-%231674b1?style=flat)](https://www.pylint.org/)
-[![black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # Testing Against Learned Reference Data
 
-* [Documentation](https://test2ref.readthedocs.io/en/latest/)
+* [Documentation](https://test2ref.readthedocs.io/en/stable/)
 * [PyPI](https://pypi.org/project/test2ref/)
 * [Sources](https://github.com/nbiotcloud/test2ref)
 * [Issues](https://github.com/nbiotcloud/test2ref/issues)

docs/contributing.md

@@ -0,0 +1,3 @@
+{%
+  include-markdown "../CONTRIBUTING.md"
+%}

docs/index.md

@@ -0,0 +1,15 @@
+[![PyPI Version](https://badge.fury.io/py/test2ref.svg)](https://badge.fury.io/py/test2ref)
+[![Python Build](https://github.com/nbiotcloud/test2ref/actions/workflows/main.yml/badge.svg)](https://github.com/nbiotcloud/test2ref/actions/workflows/main.yml)
+[![Documentation](https://readthedocs.org/projects/test2ref/badge/?version=stable)](https://test2ref.readthedocs.io/en/stable/)
+[![Coverage Status](https://coveralls.io/repos/github/nbiotcloud/test2ref/badge.svg?branch=main)](https://coveralls.io/github/nbiotcloud/test2ref?branch=main)
+[![versions](https://img.shields.io/pypi/pyversions/test2ref.svg)](https://github.com/nbiotcloud/test2ref)
+
+# Testing Against Learned Reference Data
+
+* [Documentation](https://test2ref.readthedocs.io/en/stable/)
+* [PyPI](https://pypi.org/project/test2ref/)
+* [Sources](https://github.com/nbiotcloud/test2ref)
+* [Issues](https://github.com/nbiotcloud/test2ref/issues)
+
+
+::: test2ref