Refresh infra-structure and support cython 3.x (#16)

* Refresh infra-structure and support cython 3.x

* review actions

* add workflow_dispatch to ci-tests

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# Reference:
+#   - https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "daily"
+    labels:
+      - "new: pull request"
+      - "bot"

.github/workflows/ci-manifest.yml

@@ -0,0 +1,28 @@
+# Reference:
+#   - https://github.com/actions/checkout
+
+name: ci-manifest
+
+on:
+  pull_request:
+
+  push:
+    branches:
+      - "main"
+      - "v*x"
+      - "!conda-lock-auto-update"
+      - "!pre-commit-ci-update-config"
+      - "!dependabot/*"
+    tags:
+      - "v*"
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  manifest:
+    name: "check-manifest"
+    uses: scitools/workflows/.github/workflows/[email protected]

.github/workflows/ci-tests.yml

@@ -0,0 +1,59 @@
+name: ci-tests
+
+on:
+  pull_request:
+
+  push:
+    branches:
+      - "main"
+      - "v*x"
+      - "!conda-lock-auto-update"
+      - "!pre-commit-ci-update-config"
+      - "!dependabot/*"
+    tags:
+      - "v*"
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    name: "tests py${{ matrix.python-version }}"
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: "conda install"
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        python-version: ${{ matrix.python-version }}
+        activate-environment: mo-pack-dev
+        environment-file: requirements/mo_pack.yml
+        auto-update-conda: false
+        auto-activate-base: false
+
+    - name: "conda configuration"
+      run: |
+        conda info
+        conda list --explicit
+
+    - name: "test with py${{ matrix.python-version }}"
+      run: |
+        python setup.py build_ext --inplace
+        pytest

.gitignore

@@ -1,9 +1,166 @@
-*.pyc
+# Reference https://github.com/github/gitignore/blob/main/Python.gitignore
 
+# setuptools-scm
+_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.c
+*.so
+
+# Distribution / packaging
+.Python
 build/
+develop-eggs/
 dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
 
-lib/mo_pack.egg-info/
+# Cython debug symbols
+cython_debug/
 
-lib/mo_pack/_packing.c
-lib/mo_pack/_packing*.so
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+# See https://pre-commit.ci/#configuration
+
+ci:
+  autofix_prs: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      # Prevent giant files from being committed.
+    - id: check-added-large-files
+      # Check whether files parse as valid Python.
+    - id: check-ast
+      # Check for file name conflicts on case-insensitive file-systems.
+    - id: check-case-conflict
+      # Check for files that contain merge conflict strings.
+    - id: check-merge-conflict
+      # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
+    - id: debug-statements
+      # Check TOML file syntax.
+    - id: check-toml
+      # Check YAML file syntax.
+    - id: check-yaml
+      # Makes sure files end in a newline and only a newline
+    - id: end-of-file-fixer
+      exclude: nae.20100104-06_0001_0001.pp
+      # Replaces or checks mixed line ending
+    - id: mixed-line-ending
+      exclude: nae.20100104-06_0001_0001.pp
+      # Don't commit to main branch.
+      #- id: no-commit-to-branch
+      # Trims trailing whitespace
+    - id: trailing-whitespace
+      exclude: nae.20100104-06_0001_0001.pp
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+    - id: codespell
+      types_or: [python, markdown]
+      additional_dependencies: [tomli]
+
+  - repo: https://github.com/aio-libs/sort-all
+    rev: "v1.2.0"
+    hooks:
+      - id: sort-all
+        types: [file, python]
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.15"
+    hooks:
+      - id: validate-pyproject