diff --git a/.gitignore b/.gitignore index 6df7e74..ca8d799 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,13 @@ __pycache__/ # Build artifacts dist/ build/ +*.egg-info/ +.DS_Store +docs/doctrees/ +docs/html/ +docs/_build/ +docs/_source/ +docs/_templates/ # IDE-specific files .idea/ diff --git a/docs/.github/workflows/deploy-docs.yml b/docs/.github/workflows/deploy-docs.yml new file mode 100644 index 0000000..45b2218 --- /dev/null +++ b/docs/.github/workflows/deploy-docs.yml @@ -0,0 +1,29 @@ +name: Deploy Docs + +on: + push: + branches: + - main # or your main branch name + pull_request: + +jobs: + build-and-deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + + - name: Install dependencies + run: | + pip install uv + + - name: Build HTML + run: uv run sphinx-build -b html -c docs docs docs/_build/html + + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v3 + if: github.ref == 'refs/heads/main' + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/_build/html + publish_branch: gh-pages diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(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) diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..784bae5 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,23 @@ +# 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 = 'packio' +copyright = '2024, Zach Kurtz' +author = 'Zach Kurtz' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration +extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"] +templates_path = ["_templates"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv", "dev.py"] + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output +html_static_path = ['_static'] +html_theme = "alabaster" +html_baseurl = 'https://zkurtz.github.io/packio/docs/' \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..5e871f4 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,7 @@ +packio documentation +==================== + +.. automodule:: packio + :members: + :undoc-members: + :show-inheritance: \ No newline at end of file diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/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=. +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 diff --git a/packio.egg-info/PKG-INFO b/packio.egg-info/PKG-INFO deleted file mode 100644 index 141bb65..0000000 --- a/packio.egg-info/PKG-INFO +++ /dev/null @@ -1,96 +0,0 @@ -Metadata-Version: 2.1 -Name: packio -Version: 0.0.4 -Summary: IO for multiple python objects to/from a single file -Author-email: Zach Kurtz -Project-URL: Source, https://github.com/zkurtz/packio -Requires-Python: >=3.10 -Description-Content-Type: text/markdown -License-File: LICENSE - -# packio - -Packio allows you to use a single file to store and retrieve multiple python objects. A typical use case is to define IO methods on an instance of a class that contains multiple types of objects, such as a -- dictionary -- data frame -- string -- trained ML model (for example, lightgbm and xgboost each have built-in serialization methods for trained models) - -When a class contains multiple of these data types, or even multiple instances of the same data type, saving and loading the data associated with a class tends to become unwieldy, requiring the user to either keep track multiple file paths or to fall back to using pickle, which introduces other problems (see below). The goal of packio is to make it as easy as possible to write `save` and `load` methods for such a class while allowing you to keep using all of your favorite object-type-specific serializers (i.e. `to_parquet` for pandas, `json` for dictionaries, `pathlib.Path.write_text` for strings, etc). - - -## Why not pickle? - -The most common approach for serialization of such complex python objects is to use `pickle`. There are many reasons do dislike pickle. As summarized by Gemini, "Python's pickle module, while convenient, has drawbacks. It poses security risks due to potential code execution vulnerabilities when handling untrusted data. Compatibility issues arise because it's Python-specific and version-dependent. Maintaining pickle can be challenging due to refactoring difficulties and complex debugging." See also [Ben Frederickson](https://www.benfrederickson.com/dont-pickle-your-data/). - -## Example - -Here is a toy example of a data class with `save` and `from_file` methods powered by `packio`: - -``` -from dataclasses import dataclass -import json -from pathlib import Path -import pandas as pd -from packio import Reader, Writer - - -@dataclass -class MyData: - """A simple data class for testing. - - Attributes: - documentation: Description of what this class is all about. - df: A data frame. - lookup: A dictionary. - """ - - documentation: str - df: pd.Dataframe - lookup: dict[str, int] - - def save(self, path: Path) -> None: - """Save the data class to disk.""" - with Writer(path) as writer: - writer.file("documentation.txt").write_text(self.documentation) - df.to_parquet(writer.file("df.parquet")) - with writer.file("lookup.json").open("w") as f: - json.dump(self.lookup, f) - - @classmethod - def from_file(cls, path: Path) -> "MyData": - """Load the data class from disk.""" - with Reader(path) as reader: - documentation = reader.file("documentation.txt").read_text() - df = pd.read_parquet(reader.file("df.parquet")) - with reader.file("lookup.json").open() as f: - lookup = json.load(f) - return cls(documentation=documentation, df=df, lookup=lookup) - - -# Create an instance of the class, save it, and re-load it as a new instance: -data = MyData( - documentation="This is an example.", - df=pd.DataFrame({"a": [1, 2], "b": [3, 4]}), - lookup={"a": 1, "b": 2}, -) -data.save(tmp_path / "data.mydata") -loaded = MyData.from_file(tmp_path / "data.mydata") - -# Check that the new class instance matches the old one, at least in terms of it's data attributes: -assert loaded.documentation == data.documentation -pd.testing.assert_frame_equal(loaded.df, data.df) -assert loaded.lookup == data.lookup -``` - -## Development - -Create and activate a virtual env for dev ops: -``` -git clone git@github.com:zkurtz/listwrap.git -cd packio -pip install uv -uv sync -source .venv/bin/activate -pre-commit install -``` diff --git a/packio.egg-info/SOURCES.txt b/packio.egg-info/SOURCES.txt deleted file mode 100644 index 2f17a9a..0000000 --- a/packio.egg-info/SOURCES.txt +++ /dev/null @@ -1,10 +0,0 @@ -LICENSE -README.md -pyproject.toml -packio/__init__.py -packio/io.py -packio.egg-info/PKG-INFO -packio.egg-info/SOURCES.txt -packio.egg-info/dependency_links.txt -packio.egg-info/top_level.txt -tests/test_packio.py diff --git a/packio.egg-info/dependency_links.txt b/packio.egg-info/dependency_links.txt deleted file mode 100644 index e69de29..0000000 diff --git a/packio.egg-info/top_level.txt b/packio.egg-info/top_level.txt deleted file mode 100644 index c9e0d00..0000000 --- a/packio.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -packio diff --git a/packio/__init__.py b/packio/__init__.py index 9cff86b..8ea450e 100644 --- a/packio/__init__.py +++ b/packio/__init__.py @@ -6,3 +6,4 @@ from packio.io import Writer as Writer __version__ = version("packio") +__all__ = ["Reader", "Writer"] diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index dbc3d0f..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1140 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - 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