finished merging template

.bumpversion.cfg

@@ -0,0 +1,7 @@
+[bumpversion]
+current_version = 0.0.1
+commit = True
+tag = True
+files = pyproject.toml lipyd/_metadata.py
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
+serialize = {major}.{minor}.{patch}

.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+    require_ci_to_pass: no
+
+coverage:
+    status:
+        project:
+            default:
+                # Require 1% coverage, i.e., always succeed
+                target: 1
+        patch: false
+        changes: false
+
+comment:
+    layout: diff, flags, files
+    behavior: once
+    require_base: no

.coveragerc

@@ -0,0 +1,22 @@
+[paths]
+source =
+    project_name
+    */site-packages/Lipyd
+
+[run]
+branch = true
+parallel = true
+source = Lipyd
+omit = */__init__.py
+
+[report]
+exclude_lines =
+    \#.*pragma:\s*no.?cover
+
+    if __name__ == .__main__.
+
+    ^\s*raise AssertionError\b
+    ^\s*raise NotImplementedError\b
+    ^\s*return NotImplemented\b
+show_missing = true
+precision = 2

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[Makefile]
+indent_style = tab

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Package build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    package:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v2
+        -   name: Set up Python 3.10
+            uses: actions/setup-python@v2
+            with:
+                python-version: '3.10'
+        -   name: Install build dependencies
+            run: python -m pip install --upgrade pip wheel twine build
+        -   name: Build package
+            run: python -m build
+        -   name: Check package
+            run: twine check --strict dist/*.whl

.github/workflows/sphinx_autodoc.yaml

@@ -0,0 +1,55 @@
+name: Sphinx build docs on push
+on:
+-   push
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Check out main
+            uses: actions/checkout@main
+        -   name: Setup Python
+            uses: actions/setup-python@v2
+            with:
+                python-version: 3.10.5
+        -   name: Load cached Poetry installation
+            uses: actions/cache@v2
+            with:
+                path: ~/.local
+                key: poetry-0
+        -   name: Install Poetry
+            uses: snok/install-poetry@v1
+            with:
+                virtualenvs-create: true
+                virtualenvs-in-project: true
+                installer-parallel: true
+        -   name: Poetry disable modern-installation
+            run: poetry config installer.modern-installation false
+        -   name: Load cached venv
+            id: cached-poetry-dependencies
+            uses: actions/cache@v2
+            with:
+                path: .venv
+                key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+        -   name: Install dependencies
+            if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+            run: poetry install --no-interaction --no-root
+        -   name: Install library
+            run: poetry install --no-interaction
+        -   name: Build documentation
+            run: poetry run make html --directory docs/
+        -   name: Commit files
+            run: |
+                git config --local user.email "[email protected]"
+                git config --local user.name "GitHub Action"
+                touch docs/_build/html/.nojekyll
+                git add -f docs/_build/
+                git commit -m "Update autodoc" -a
+    # using https://github.com/marketplace/actions/push-git-subdirectory-as-branch
+        -   name: Deploy
+            uses: s0/git-publish-subdir-action@develop
+            env:
+                REPO: self
+                BRANCH: gh-pages
+                FOLDER: docs/_build/html
+                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yaml

@@ -0,0 +1,57 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0}
+
+        strategy:
+            fail-fast: false
+            matrix:
+                python: [3.8, 3.9, 3.10]
+                os: [ubuntu-latest, macos-latest]
+
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+        -   uses: actions/checkout@v2
+        -   name: Set up Python ${{ matrix.python }}
+            uses: actions/setup-python@v4
+            with:
+                python-version: ${{ matrix.python }}
+                cache: pip
+                cache-dependency-path: '**/pyproject.toml'
+
+        -   name: Install test dependencies
+            run: |
+                python -m pip install --upgrade pip wheel
+                pip install codecov
+        -   name: Install dependencies
+            run: |
+                pip install ".[dev,test]"
+        -   name: Install pip dependencies
+            run: |
+                python -m pip install --upgrade pip
+        -   name: Test
+            env:
+                MPLBACKEND: agg
+                PLATFORM: ${{ matrix.os }}
+                DISPLAY: :42
+            run: |
+                pytest -v --cov --color=yes
+        -   name: Upload coverage
+            env:
+                CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+            run: |
+                codecov --no-color --required --flags unittests

.gitignore

@@ -1,4 +1,23 @@
-build/
-dist/
+*~
+__pycache__/
+/build/
+/docs/_build/
+/docs/generated/
+.DS_Store
+/.vscode/
+/*.egg-info/
+*.egg
+*.prof
+*.coverage
+*.pickle
+/out/
+*.log
+/dist/
+*.pye
 *.pyc
-*.egg-info/
+*.kate-swp
+/.tox/
+/.idea/
+/.pytest_cache/
+/.cache/
+/data/

.pre-commit-config.yaml

@@ -0,0 +1,110 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+-   commit
+-   push
+minimum_pre_commit_version: 2.7.1
+repos:
+-   repo: https://github.com/deeenes/unexport
+    rev: 0.4.0-patch0-3
+    hooks:
+    -   id: unexport
+        args: [--refactor, --single_quotes]
+        exclude: __init__.py$
+-   repo: https://github.com/google/yapf
+    rev: v0.40.2
+    hooks:
+    -   id: yapf
+        additional_dependencies: [toml]
+        stages: [manual]
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    -   id: black
+        additional_dependencies: [toml]
+        stages: [manual]
+-   repo: https://github.com/Instagram/Fixit
+    rev: 9d59f968e84bd2773f34b0069eeeaad3ce783254
+    hooks:
+    -   id: fixit-run-rules
+        stages: [manual]
+-   repo: https://github.com/timothycrosley/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        additional_dependencies: [toml]
+-   repo: https://github.com/snok/pep585-upgrade
+    rev: v1.0
+    hooks:
+    -   id: upgrade-type-hints
+        args: [--futures=true]
+-   repo: https://github.com/asottile/add-trailing-comma
+    rev: v3.1.0
+    hooks:
+    -   id: add-trailing-comma
+-   repo: https://github.com/myint/unify
+    rev: v0.5
+    hooks:
+    -   id: unify
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: detect-private-key
+    -   id: check-ast
+    -   id: check-docstring-first
+    -   id: end-of-file-fixer
+    -   id: check-added-large-files
+    -   id: mixed-line-ending
+        args: [--fix=lf]
+        exclude: ^docs/make.bat$
+    -   id: trailing-whitespace
+        exclude: ^.bumpversion.cfg$
+    -   id: check-merge-conflict
+    -   id: check-case-conflict
+    -   id: check-symlinks
+    -   id: check-yaml
+        args: [--unsafe]
+    -   id: check-ast
+    -   id: fix-encoding-pragma
+        args: [--remove] # for Python3 codebase, it's not necessary
+    -   id: requirements-txt-fixer
+-   repo: https://github.com/john-hen/Flake8-pyproject
+    rev: 1.2.3
+    hooks:
+    -   id: Flake8-pyproject
+        additional_dependencies:
+        -   flake8-docstrings
+        -   flake8-comprehensions
+        -   flake8-bugbear
+        -   git+https://github.com/saezlab/flake8-kwargs-spaces.git
+-   repo: https://github.com/rstcheck/rstcheck
+    rev: v6.2.0
+    hooks:
+    -   id: rstcheck
+        exclude: docs
+-   repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+    -   id: blacken-docs
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.16.0
+    hooks:
+    -   id: pyupgrade
+        args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.13.0
+    hooks:
+    -   id: pretty-format-yaml
+        args: [--autofix, --indent, '4']
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+    -   id: python-no-eval
+    -   id: python-use-type-annotations
+    -   id: python-check-blanket-noqa
+    -   id: rst-backticks
+    -   id: rst-directive-colons
+    -   id: rst-inline-touching-normal

.readthedocs.yaml

@@ -0,0 +1,22 @@
+version: 2
+
+sphinx:
+    builder: html
+    configuration: docs/source/conf.py
+    fail_on_warning: true
+
+formats:
+-   htmlzip
+-   pdf
+
+build:
+    os: ubuntu-22.04
+    tools:
+        python: 3.10
+
+python:
+    install:
+    -   method: pip
+        path: .
+        extra_requirements:
+        -   docs