Fix repo review

.gitignore

@@ -5,3 +5,5 @@ dist
 __pycache__
 test.yoda
 test.yoda.gz
+docs/build
+.coverage

.pre-commit-config.yaml

@@ -20,8 +20,33 @@ repos:
     - id: trailing-whitespace
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.8"
+    rev: "v0.7.2"
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
+
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"  # replace with latest tag on GitHub
+    hooks:
+    -   id: blacken-docs
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.13.0'  # Use the sha / tag you want to point at
+    hooks:
+    -   id: mypy
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0  # Use the ref you want to point at
+    hooks:
+    -   id: python-use-type-annotations
+-   repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.18  # Use the ref you want to point at
+    hooks:
+    - id: mdformat
+      # Optionally add plugins
+      additional_dependencies:
+      - mdformat-gfm
+      - mdformat-black

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+submodules:
+  include: all
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+
+
+python:
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2018-2024, Eduardo Rodrigues and Henry Schreiner.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the particle package developers nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,32 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "babyyoda"
+copyright = "2024, Alexander Puck Neuwirth"
+author = "Alexander Puck Neuwirth"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = [
+    "**.ipynb_checkpoints",
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. babyyoda documentation master file, created by
+   sphinx-quickstart on Tue Nov  5 13:28:41 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to babyyoda's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyproject.toml

@@ -11,13 +11,15 @@ dynamic = ["version"]
 description = ''
 readme = "README.md"
 requires-python = ">=3.9"
-license = "MIT"
 keywords = []
 authors = [
   { name = "Alexander Puck Neuwirth", email = "[email protected]" },
 ]
 classifiers = [
   "Development Status :: 4 - Beta",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
@@ -26,6 +28,7 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
+  "Topic :: Scientific/Engineering",
 ]
 dependencies = [
   "numpy"
@@ -49,6 +52,9 @@ develop = [
     "pre-commit",
     "tbump>=6.7.0",
 ]
+docs = [
+  "sphinx"
+]
 
 [tool.hatch.envs.develop]
 features = [
@@ -93,12 +99,27 @@ exclude_lines = [
 [tool.hatch.version]
 source = "vcs"
 
+
+
 [tool.hatch.version.raw-options]
 local_scheme = "no-local-version"
 
 [tool.hatch.build.hooks.vcs]
 version-file = "src/babyyoda/_version.py"
 
+[tool.mypy]
+warn_unused_configs = true
+warn_unused_ignores = true
+python_version = "3.9"
+files = "src"
+strict = true
+warn_unreachable = true
+enable_error_code = [
+    "ignore-without-code",
+    "redundant-expr",
+    "truthy-bool",
+]
+
 
 [tool.ruff.lint]
 extend-select = [
@@ -131,3 +152,19 @@ ignore = [
   "RUF012",   # TODO: mutable class attributes
   "SIM115",   # TODO: use context manager for opening files
 ]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+junit_family = "xunit2"
+log_cli_level = "info"
+xfail_strict = true
+addopts = [
+    "-ra",
+    "--strict-markers",
+    "--strict-config",
+]
+filterwarnings = [
+  "error",
+  "ignore:Integer weights indicate poissonian data:UserWarning"
+]

src/babyyoda/analysisobject.py

@@ -1,7 +1,18 @@
 class UHIAnalysisObject:
-    def key(self):
+    ########
+    # Basic needed functions for UHI+YODA
+    ########
+    def path(self) -> str:
+        err = "UHIAnalysisObject.path() must be implemented by subclass"
+        raise NotImplementedError(err)
+
+    def setAnnotation(self, key: str, value: str) -> None:
+        err = "UHIAnalysisObject.setAnnotation() must be implemented by subclass"
+        raise NotImplementedError(err)
+
+    def key(self) -> str:
         return self.path()
 
-    def setAnnotationsDict(self, d: dict):
+    def setAnnotationsDict(self, d: dict[str, str]) -> None:
         for k, v in d.items():
             self.setAnnotation(k, v)