Merge pull request #3 from d-v-b/fix/empty-view-regs

fix/empty view regs

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/test.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test V3
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: py=${{ matrix.python-version }}
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install Hatch
+        run: |
+          python -m pip install --upgrade pip 
+          pip install hatch
+      - name: Set Up Hatch Env
+        run: |
+          hatch env create test.py${{ matrix.python-version }}
+      - name: Run Tests
+        run: |
+          hatch env run --env test.py${{ matrix.python-version }} run

.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  autofix_prs: false
+default_stages: [commit, push]
+default_language_version:
+  python: python3
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: ["-L", "ba,ihs,kake,nd,noe,nwo,te,fo,zar", "-S", "fixture"]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        files: src|tests
+        additional_dependencies:
+          - pydantic-xml
+          - pytest
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
+    hooks:
+      - id: sp-repo-review
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "" # replace with latest tag on GitHub
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==22.12.0
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "" # Use the sha / tag you want to point at
+    hooks:
+      - id: prettier

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv
+    - uv pip install .[docs]
+    - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D
+      language=en docs $READTHEDOCS_OUTPUT/html

README.md

@@ -3,7 +3,7 @@
 [![PyPI - Version](https://img.shields.io/pypi/v/pydantic-bigstitcher.svg)](https://pypi.org/project/pydantic-bigstitcher)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pydantic-bigstitcher.svg)](https://pypi.org/project/pydantic-bigstitcher)
 
------
+---
 
 Pydantic models for [bigsticher](https://github.com/PreibischLab/BigStitcher). This is very minimal right now, with features being added only as needed.
 

docs/api/pydantic_bigstitcher.md

@@ -0,0 +1 @@
+::: pydantic_bigstitcher

docs/api/transform.md

@@ -0,0 +1 @@
+::: pydantic_bigstitcher.transform

docs/index.md

@@ -0,0 +1,3 @@
+# pydantic-bigstitcher
+
+pydantic models for bigstitcher xml documents

mkdocs.yml

@@ -0,0 +1,17 @@
+site_name: pydantic-bigstitcher
+site_url: https://d-v-b.github.io/pydantic-bigstitcher/
+theme:
+  name: material
+watch: ["src"]
+plugins:
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            docstring_style: numpy
+            members_order: source
+            separate_signature: true
+            filters: ["!^_"]
+            docstring_options:
+              ignore_init_summary: true
+            merge_init_into_class: true

pyproject.toml

@@ -7,7 +7,7 @@ name = "pydantic-bigstitcher"
 dynamic = ["version"]
 description = ''
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = "MIT"
 keywords = []
 authors = [
@@ -16,8 +16,6 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "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",
@@ -30,21 +28,33 @@ dependencies = [
   ]
 
 [project.urls]
-Documentation = "https://github.com/unknown/pydantic-bigstitcher#readme"
-Issues = "https://github.com/unknown/pydantic-bigstitcher/issues"
-Source = "https://github.com/unknown/pydantic-bigstitcher"
+Documentation = "https://github.com/d-v-b/pydantic-bigstitcher#readme"
+Issues = "https://github.com/d-v-b/pydantic-bigstitcher/issues"
+Source = "https://github.com/d-v-b/pydantic-bigstitcher"
 
-[tool.hatch.version]
-path = "src/pydantic_bigstitcher/__about__.py"
-
-[tool.hatch.envs.test]
-dependencies = [
+[project.optional-dependencies]
+test = [
   "coverage[toml]>=6.5",
   "pytest",
   "xmldiff",
-  "xmltodict"
+  "xmltodict",
+  "deepdiff==8.0.1"
 ]
 
+docs = [
+  "mkdocs-material>=9.5.39", 
+  "mkdocstrings[python]>=0.26.1"
+  ]
+
+[tool.hatch.version]
+path = "src/pydantic_bigstitcher/__about__.py"
+
+[tool.hatch.envs.test]
+features = ["test"]
+
+[[tool.hatch.envs.test.matrix]]
+python = ["3.10", "3.11", "3.12"]
+
 [tool.hatch.envs.test.scripts]
 run = "pytest {args:tests}"
 run-cov = "coverage run -m pytest {args:tests}"
@@ -57,8 +67,16 @@ cov = [
   "cov-report",
 ]
 
+[tool.hatch.envs.docs]
+features = ["docs"]
+
+[tool.hatch.envs.docs.scripts]
+"serve" = "mkdocs serve"
+"build" = "mkdocs build"
+"deploy" = "mkdocs gh-deploy"
+
 [[tool.hatch.envs.all.matrix]]
-python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+python = ["3.10", "3.11", "3.12"]
 
 [tool.hatch.envs.types]
 dependencies = [
@@ -85,3 +103,48 @@ exclude_lines = [
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
+[tool.mypy]
+python_version = "3.11"
+ignore_missing_imports = true
+namespace_packages = false
+strict=true
+warn_unreachable = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+
+[tool.ruff]
+line-length = 100
+force-exclude = true
+extend-exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".ruff_cache",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "notebooks", # temporary, until we achieve compatibility with ruff ≥ 0.6
+    "venv",
+    "docs",
+]
+[tool.ruff.lint]                                                           
+    extend-select = [                                                          
+      "B",  # flake8-bugbear
+      "I",  # isort
+      "UP",  # pyupgrade                                                    
+    ] 
+
+
+[tool.pytest.ini_options]
+minversion = "7"
+testpaths = ["tests"]
+log_cli_level = "INFO"
+xfail_strict = true
+addopts = ["-ra", "--strict-config", "--strict-markers"] 
+filterwarnings = ["error"]