Merge pull request #20 from lverweijen/package

Modernize package setup

.github/workflows/sphinx.yml

@@ -0,0 +1,25 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Build HTML
+      uses: ammaraskar/sphinx-action@dev
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

.gitignore

@@ -0,0 +1,173 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# Cython debug symbols
+cython_debug/
+
+# 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/
+
+# PyPI configuration file
+.pypirc
+
+.idea

README.md

@@ -45,7 +45,7 @@ print(table_result)
 ```
 
 Change `C:\Users\User\Programs\TauArgus4.2.0b5\TauArgus.exe` to the location where argus is installed.
-See [tutorial](https://github.com/lverweijen/tree/main/tutorial.md) for a general introduction.
+See [tutorial](https://lverweijen.github.io/piargus/tutorial.html) for a general introduction.
 See [Examples](https://github.com/lverweijen/tree/main/examples) for more examples.
 
 ## See also

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/requirements.txt

@@ -0,0 +1,6 @@
+sphinx-rtd-theme>=3.0.2
+myst-parser>=3.0.1
+myst>=1.0.4
+sphinxcontrib-mermaid>=1.0.0
+pandas>=1.5
+littletree>=0.6.2

docs/source/api.rst

@@ -0,0 +1,45 @@
+===
+API
+===
+
+Input Specification
+===================
+
+Input data
+----------
+.. automodule:: piargus.inputspec
+   :members: InputData, MetaData, MicroData, TableData, CodeList
+   :show-inheritance:
+
+Hierarchies
+-----------
+.. automodule:: piargus.inputspec.hierarchy
+   :members: Hierarchy, TreeHierarchy, FlatHierarchy, LevelHierarchy, TreeHierarchyNode
+   :show-inheritance:
+
+Output Specification
+====================
+
+Tables
+------
+.. automodule:: piargus.outputspec
+   :members: Table, Apriori, TreeRecode
+   :show-inheritance:
+
+Safety rule
+-----------
+.. automodule:: piargus
+   :members: dominance_rule, percent_rule, frequency_rule, request_rule, zero_rule, missing_rule, weight_rule, manual_rule, p_rule, nk_rule,
+   :show-inheritance:
+
+Result
+======
+.. automodule:: piargus
+   :members: ArgusReport, TableResult
+   :show-inheritance:
+
+Tau-Argus
+=========
+.. automodule:: piargus
+   :members: TauArgus, BatchWriter, Job, JobSetupError
+   :show-inheritance:

changes.md → docs/source/changes.md

@@ -1,3 +1,5 @@
+# Changelog #
+
 ## Version 1.0.0 ##
 
 - Add alias `Node` for `TreeHierarchyNode`.

docs/source/conf.py

@@ -0,0 +1,41 @@
+# 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 = 'PiArgus'
+copyright = '2025, Laurent Verweijen'
+author = 'Laurent Verweijen'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.viewcode',
+    'myst_parser',
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+myst_enable_extensions = ["colon_fence"]
+
+# Code is in src. Make sure sphinx can find it
+import sys
+from pathlib import Path
+src_folder = Path(__file__).parent.parent.parent / "src"
+sys.path.insert(0, str(src_folder.resolve(strict=True)))

docs/source/index.rst

@@ -0,0 +1,29 @@
+.. PiArgus documentation master file, created by
+   sphinx-quickstart on Tue Jan  7 13:41:10 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PiArgus' documentation!
+==================================
+
+This package provides a python wrapper around `τ-ARGUS <https://research.cbs.nl/casc/tau.htm>`_, a program to protect statistical tables.
+This package takes care of generating all the required metadata and runs τ-ARGUS in the background to do the heavy work.
+
+For this package to work, it is required to install τ-ARGUS locally first.
+It's also recommended to read the `TauArgus manual <https://research.cbs.nl/casc/Software/TauManualV4.1.pdf>`_ to understand some of the underlying concepts used in this package.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   tutorial
+   api
+   changes
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`