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  • pyOpenSci Website diff --git a/_sources/documentation/index.md.txt b/_sources/documentation/index.md.txt index e2507376..23d1aa71 100644 --- a/_sources/documentation/index.md.txt +++ b/_sources/documentation/index.md.txt @@ -43,7 +43,6 @@ Publish Your Docs Website Hosting and Optimization ``` - ```{important} Please note that the tools discussed here are those that we see commonly used in the community. As tools evolve we @@ -104,13 +103,13 @@ Python workflows. They might be new(er) to Python and/or data science. Or expert programmers. But they might not have a background in software development. These users need to know: - * How to install your package - * How to install dependencies that your package requires - * How to get started using the code base - * Information on how to cite your code / give you credit if they are using it - in a research application. - * Information on the license that your code uses so they know how they can - or can't use the code in an operational setting. +- How to install your package +- How to install dependencies that your package requires +- How to get started using the code base +- Information on how to cite your code / give you credit if they are using it + in a research application. +- Information on the license that your code uses so they know how they can + or can't use the code in an operational setting. ### 2. Potential tool contributors @@ -118,16 +117,16 @@ The other subset of users are more experienced and/or more engaged with your package. As such they are potential contributors. These users: -* might have a software development background, -* might also be able to contribute bug fixes to your package or updates to your documentation -* might also just be users who will find spelling errors in your documentation, or bugs in your tutorials. +- might have a software development background, +- might also be able to contribute bug fixes to your package or updates to your documentation +- might also just be users who will find spelling errors in your documentation, or bugs in your tutorials. These users need all of the things that a basic user needs. But, they also need to understand how you'd like for them to contribute to your package. These potential contributors need: -* A development guide to help them understand the infrastructure used in your package repository. -* Contributing guidelines that clarify the types of contributions that you welcome and how you'd prefer those contributions to be submitted. +- A development guide to help them understand the infrastructure used in your package repository. +- Contributing guidelines that clarify the types of contributions that you welcome and how you'd prefer those contributions to be submitted. ```{important} It's important to remember that the definition of what a contribution is can be @@ -136,7 +135,6 @@ spelling issue in your documentation. Or it could be a code fix that includes a new test that covers an edge-case that they discovered. ``` - ## Documentation elements that pyOpenSci looks for reviewing a Python package In the pyOpenSci open peer review, we look for @@ -149,12 +147,12 @@ that you should consider in your package's documentation in more detail. - ```{button-link} https://www.pyopensci.org/software-peer-review/how-to/editor-in-chief-guide.html#editor-checklist-template :color: primary :class: sd-rounded-pill float-left View pyOpenSci peer review check list ``` +

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1, "sphinx": 57}, "alltitles": {"Contributing Guide for the Python open source software packaging book": [[0, "contributing-guide-for-the-python-open-source-software-packaging-book"]], "How this guide structured": [[0, "how-this-guide-structured"]], "Instructions for building the documentation locally on your computer": [[0, "instructions-for-building-the-documentation-locally-on-your-computer"]], "CI and Testing - Coming Soon!": [[1, "ci-and-testing-coming-soon"]], "Tools to Build and Host your Documentation": [[2, "tools-to-build-and-host-your-documentation"]], "Documentation syntax: markdown vs. myST vs. rst syntax to create your docs": [[3, "documentation-syntax-markdown-vs-myst-vs-rst-syntax-to-create-your-docs"]], "How to publish your Python package documentation online": [[4, "how-to-publish-your-python-package-documentation-online"]], "What is Read the Docs ?": [[4, "what-is-read-the-docs"]], "What is GitHub Pages?": [[4, "what-is-github-pages"]], "Read the Docs vs GitHub Pages": [[4, "read-the-docs-vs-github-pages"]], "Using Sphinx to Build Python Package Documentation": [[5, "using-sphinx-to-build-python-package-documentation"]], "Sphinx - a static site generator": [[5, "sphinx-a-static-site-generator"]], "Sphinx sites can be customized using extensions and themes": [[5, "sphinx-sites-can-be-customized-using-extensions-and-themes"]], "Commonly used Sphinx themes": [[5, "commonly-used-sphinx-themes"]], "Optimizing your documentation so search engines (and other users) find it": [[6, "optimizing-your-documentation-so-search-engines-and-other-users-find-it"]], "Google Analytics": [[6, "google-analytics"]], "sphinx-sitemap for search engine optimization": [[6, "sphinx-sitemap-for-search-engine-optimization"]], "sphinxext.opengraph": [[6, "sphinxext-opengraph"]], "Documentation for your Open Source Python Package": [[7, "documentation-for-your-open-source-python-package"]], "Documentation is critical for your Python package\u2019s success": [[7, "documentation-is-critical-for-your-python-package-s-success"]], "Two types of Python package users": [[7, "two-types-of-python-package-users"]], "1. Basic Tool Users": [[7, "basic-tool-users"]], "2. Potential tool contributors": [[7, "potential-tool-contributors"]], "Documentation elements that pyOpenSci looks for reviewing a Python package": [[7, "documentation-elements-that-pyopensci-looks-for-reviewing-a-python-package"]], "What\u2019s next in this Python package documentation section?": [[7, "what-s-next-in-this-python-package-documentation-section"]], "The CODE_OF_CONDUCT.md file In Your Python Open Source Package": [[8, "the-code-of-conduct-md-file-in-your-python-open-source-package"]], "Example Code of Conduct files": [[8, null]], "Why you need a code of conduct": [[8, "why-you-need-a-code-of-conduct"]], "Contributing File in your Python Open Source Package": [[9, "contributing-file-in-your-python-open-source-package"]], "What a CONTRIBUTING.md file should contain": [[9, "what-a-contributing-md-file-should-contain"]], "Example contributing files": [[9, null]], "What the development guide for your Python package should contain": [[10, "what-the-development-guide-for-your-python-package-should-contain"]], "Why a development guide is important": [[10, "why-a-development-guide-is-important"]], "Documentation Files That Should be in your Python Package Repository": [[11, "documentation-files-that-should-be-in-your-python-package-repository"]], "Your repository should have a LICENSE.md file": [[12, "your-repository-should-have-a-license-md-file"]], "Important: make sure that you closely follow the guidelines outlines by the License that you chose": [[12, "important-make-sure-that-you-closely-follow-the-guidelines-outlines-by-the-license-that-you-chose"]], "README File Guidelines and Resources": [[13, "readme-file-guidelines-and-resources"]], "What your README.md file should contain": [[13, "what-your-readme-md-file-should-contain"]], "\u2714\ufe0f Your package\u2019s name": [[13, "your-package-s-name"]], "\u2714\ufe0f Badges for current package version, continuous integration and test coverage": [[13, "badges-for-current-package-version-continuous-integration-and-test-coverage"]], "\u2714\ufe0f A short, easy-to-understand description of what your package does": [[13, "a-short-easy-to-understand-description-of-what-your-package-does"]], "\u2714\ufe0f Installation instructions": [[13, "installation-instructions"]], "\u2714\ufe0f Document any additional setup required": [[13, "document-any-additional-setup-required"]], "\u2714\ufe0f Brief demonstration of how to use the package": [[13, "brief-demonstration-of-how-to-use-the-package"]], "\u2714\ufe0f Descriptive links to package documentation, short tutorials": [[13, "descriptive-links-to-package-documentation-short-tutorials"]], "Too Much Of A Good Thing": [[13, null]], "\u2714\ufe0f A Community Section with Links to Contributing Guide, Code of Conduct": [[13, "a-community-section-with-links-to-contributing-guide-code-of-conduct"]], "\u2714\ufe0f Citation information": [[13, "citation-information"]], "Create tutorials in your Python package documentation": [[14, "create-tutorials-in-your-python-package-documentation"]], "Create Python package tutorials that run when you build your docs": [[14, "create-python-package-tutorials-that-run-when-you-build-your-docs"]], "sphinx gallery:": [[14, "sphinx-gallery"]], "Sphinx Gallery benefits": [[14, "sphinx-gallery-benefits"]], "Sphinx gallery challenges": [[14, "sphinx-gallery-challenges"]], "nbsphinx - tutorials using Jupyter Notebooks": [[14, "nbsphinx-tutorials-using-jupyter-notebooks"]], "Document the code in your package\u2019s API using docstrings": [[15, "document-the-code-in-your-package-s-api-using-docstrings"]], "What is an API?": [[15, "what-is-an-api"]], "What is a docstring and how does it relate to documentation?": [[15, "what-is-a-docstring-and-how-does-it-relate-to-documentation"]], "Python package API documentation": [[15, "python-package-api-documentation"]], "Three Python docstring formats and why we like NumPy style": [[15, "three-python-docstring-formats-and-why-we-like-numpy-style"]], "Docstring examples Better and Best": [[15, "docstring-examples-better-and-best"]], "Best: a docstring with example use of the function": [[15, "best-a-docstring-with-example-use-of-the-function"]], "Using doctest to run docstring examples in your package\u2019s methods and functions": [[15, "using-doctest-to-run-docstring-examples-in-your-package-s-methods-and-functions"]], "Adding type hints to your docstrings": [[15, "adding-type-hints-to-your-docstrings"]], "Why use type hints": [[15, "why-use-type-hints"]], "Beware of too much type hinting": [[15, null]], "Gradually adding type hints": [[15, "gradually-adding-type-hints"]], "Create User Facing Documentation for your Python Package": [[16, "create-user-facing-documentation-for-your-python-package"]], "Core components of user-facing Python package documentation": [[16, "core-components-of-user-facing-python-package-documentation"]], "Write usable documentation": [[16, "write-usable-documentation"]], "Four elements of a good open source documentation landing page": [[16, "four-elements-of-a-good-open-source-documentation-landing-page"]], "Writing user-facing documentation for your Python package": [[17, "writing-user-facing-documentation-for-your-python-package"]], "pyOpenSci Python Open Source Package Development Guide": [[18, "pyopensci-python-open-source-package-development-guide"]], "Welcome, Python open source enthusiast!": [[18, "welcome-python-open-source-enthusiast"]], "pyOpenSci\u2019s packaging goals": [[18, "pyopensci-s-packaging-goals"]], "How this guide is created": [[18, "how-this-guide-is-created"]], "Who this guidebook is for": [[18, "who-this-guidebook-is-for"]], "What you will find in this guidebook": [[18, "what-you-will-find-in-this-guidebook"]], "Where this guide is headed": [[18, "where-this-guide-is-headed"]], "Python Package Code Style, Format and Linters": [[19, "python-package-code-style-format-and-linters"]], "Use a code format tool (or tools) to make your life easier": [[19, "use-a-code-format-tool-or-tools-to-make-your-life-easier"]], "Linting vs format and style": [[19, "linting-vs-format-and-style"]], "Code Linting": [[19, "code-linting"]], "Code Formatters (and stylers)": [[19, "code-formatters-and-stylers"]], "Code format and style": [[19, "code-format-and-style"]], "Black and Blue": [[19, "black-and-blue"]], "flake8 for linting code in Python packages": [[19, "flake8-for-linting-code-in-python-packages"]], "Isort": [[19, "isort"]], "Example application of isort": [[19, "example-application-of-isort"]], "How to use code formatter in your local workflow": [[19, "how-to-use-code-formatter-in-your-local-workflow"]], "Linters, code formatters and your favorite coding tools": [[19, "linters-code-formatters-and-your-favorite-coding-tools"]], "Use pre-commit hooks to run code formatters and linters on commits": [[19, "use-pre-commit-hooks-to-run-code-formatters-and-linters-on-commits"]], "Pre-commit hook example workflow": [[19, "pre-commit-hook-example-workflow"]], "General pre commit checks": [[19, "general-pre-commit-checks"]], "Pre-commit.ci": [[19, "pre-commit-ci"]], "Setting up a git pre-commit hook": [[19, "setting-up-a-git-pre-commit-hook"]], "Summary": [[19, "summary"]], "Complex Python package builds": [[20, "complex-python-package-builds"]], "Pure Python Packages vs. packages with extensions in other languages": [[20, "pure-python-packages-vs-packages-with-extensions-in-other-languages"]], "Python package structure information": [[21, "python-package-structure-information"]], "What you will learn here": [[21, "what-you-will-learn-here"]], "Guidelines for pyOpenSci\u2019s packaging recommendations": [[21, "guidelines-for-pyopensci-s-packaging-recommendations"]], "Suggestions in this guide are not pyOpenSci review requirements": [[21, null]], "Publishing Your Package In A Community Repository: PyPI or Anaconda Cloud": [[22, "publishing-your-package-in-a-community-repository-pypi-or-anaconda-cloud"]], "What is PyPI": [[22, "what-is-pypi"]], "What is Anaconda Cloud and Conda?": [[22, "what-is-anaconda-cloud-and-conda"]], "Conda channels": [[22, "conda-channels"]], "Conda channels, PyPI, conda, pip - Where to publish your package": [[22, "conda-channels-pypi-conda-pip-where-to-publish-your-package"]], "Managing Python package dependency conflicts": [[22, "managing-python-package-dependency-conflicts"]], "Take-aways: If you can, publish on both PyPI and conda-forge to accommodate more users of your package": [[22, "take-aways-if-you-can-publish-on-both-pypi-and-conda-forge-to-accommodate-more-users-of-your-package"]], "How to submit to conda-forge": [[22, "how-to-submit-to-conda-forge"]], "Maintaining your conda-forge package repository": [[22, "maintaining-your-conda-forge-package-repository"]], "Use a pyproject.toml file for your package configuration & metadata": [[23, "use-a-pyproject-toml-file-for-your-package-configuration-metadata"]], "Benefits of using a pyproject.toml file": [[23, "benefits-of-using-a-pyproject-toml-file"]], "Setup.py is still useful for complex package builds": [[23, null]], "Example pyproject.toml for building using PDM": [[23, "example-pyproject-toml-for-building-using-pdm"]], "Example pyproject.toml for building using setuptools": [[23, "example-pyproject-toml-for-building-using-setuptools"]], "Python Package Build Tools": [[24, "python-package-build-tools"]], "Tools that we review here": [[24, "tools-that-we-review-here"]], "Summary of tools Hatch vs. PDM vs. Poetry (and setuptools)": [[24, "summary-of-tools-hatch-vs-pdm-vs-poetry-and-setuptools"]], "Build front-end vs. build back-end tools": [[24, "build-front-end-vs-build-back-end-tools"]], "Build back-ends": [[24, "build-back-ends"]], "Python package build front-ends": [[24, "python-package-build-front-ends"]], "Example build steps that can be simplified using a front-end tool": [[24, "example-build-steps-that-can-be-simplified-using-a-front-end-tool"]], "Choosing a build back-end": [[24, "choosing-a-build-back-end"]], "Build back-end support for non pure-python packages": [[24, "build-back-end-support-for-non-pure-python-packages"]], "An ecosystem of Python build tools": [[24, "an-ecosystem-of-python-build-tools"]], "We do not suggest using setuptools": [[24, null]], "Chose a build workflow tool": [[24, "chose-a-build-workflow-tool"]], "Python packaging tools summary": [[24, "python-packaging-tools-summary"]], "Package tool features table": [[24, "package-tool-features-table"]], "PDM": [[24, "pdm"]], "PDM support for C and C++ extensions": [[24, null]], "PDM Features": [[24, "pdm-features"]], "PDM vs. Poetry": [[24, null]], "Challenges with PDM": [[24, "challenges-with-pdm"]], "Flit": [[24, "flit"]], "Flit Features": [[24, "flit-features"]], "Learn more about flit": [[24, null]], "Why you might not want to use Flit": [[24, "why-you-might-not-want-to-use-flit"]], "Hatch": [[24, "hatch"]], "Hatch features": [[24, "hatch-features"]], "Why you might not want to use Hatch": [[24, "why-you-might-not-want-to-use-hatch"]], "Poetry": [[24, "poetry"]], "Poetry features": [[24, "poetry-features"]], "Challenges with Poetry": [[24, "challenges-with-poetry"]], "Challenges with Poetry dependency pinning": [[24, null]], "Using Setuptools Back-end for Python Packaging with Build Front-end": [[24, "using-setuptools-back-end-for-python-packaging-with-build-front-end"]], "Setuptools Features": [[24, "setuptools-features"]], "Challenges using setuptools": [[24, "challenges-using-setuptools"]], "The Python Package Source and Wheel Distributions": [[25, "the-python-package-source-and-wheel-distributions"]], "Source Distribution (sdist)": [[25, "source-distribution-sdist"]], "GitHub archive vs SDist": [[25, null]], "Wheel (.whl files):": [[25, "wheel-whl-files"]], "Python Package Structure for Scientific Python Projects": [[26, "python-package-structure-for-scientific-python-projects"]], "pyOpenSci will never require a specific package structure for peer review": [[26, null]], "Example scientific packages that use src/package layout": [[26, null]], "The src/ layout and testing": [[26, "the-src-layout-and-testing"]], "How Python discovers and prioritizes importing modules": [[26, null]], "Sometimes tests are needed in a distribution": [[26, "sometimes-tests-are-needed-in-a-distribution"]], "Challenges with including tests and data in a package wheel": [[26, null]], "Don\u2019t include test suite datasets in your package": [[26, "don-t-include-test-suite-datasets-in-your-package"]], "About the flat Python package layout": [[26, "about-the-flat-python-package-layout"]], "Why most scientific Python packages do not use source": [[26, null]], "What does the flat layout structure look like?": [[26, "what-does-the-flat-layout-structure-look-like"]], "Benefits of using the flat layout in your Python package": [[26, "benefits-of-using-the-flat-layout-in-your-python-package"]], "Core scientific Python packages that use the flat layout": [[26, null]], "Creating New Versions of Your Python Package": [[27, "creating-new-versions-of-your-python-package"]], "SemVer rules": [[27, "semver-rules"]], "Avoid manually updating Python package version numbers if you can": [[27, "avoid-manually-updating-python-package-version-numbers-if-you-can"]], "Tools to manage versions for your Python package": [[27, "tools-to-manage-versions-for-your-python-package"]], "Semantic release, vs version control based vs manual version bumping": [[27, "semantic-release-vs-version-control-based-vs-manual-version-bumping"]], "Tools for bumping Python package versions": [[27, "tools-for-bumping-python-package-versions"]], "Tool 1: Hatch and other build tools that offer incremental versioning": [[27, "tool-1-hatch-and-other-build-tools-that-offer-incremental-versioning"]], "Hatch (or other tools like PDM) Pros": [[27, "hatch-or-other-tools-like-pdm-pros"]], "Hatch (or other tools like PDM) Cons": [[27, "hatch-or-other-tools-like-pdm-cons"]], "Tool 2: Hatch_vcs & hatchling build back-end": [[27, "tool-2-hatch-vcs-hatchling-build-back-end"]], "Hatch example setup in your pyproject.toml": [[27, "hatch-example-setup-in-your-pyproject-toml"]], "hatch_vcs Pros": [[27, "hatch-vcs-pros"]], "hatch_vcs Cons": [[27, "hatch-vcs-cons"]], "Tool 3: setuptools-scm versioning using git tags": [[27, "tool-3-setuptools-scm-versioning-using-git-tags"]], "setuptools_scm Cons": [[27, "setuptools-scm-cons"]], "Tool 4: Python semantic release": [[27, "tool-4-python-semantic-release"]], "Python Semantic Release Pros": [[27, "python-semantic-release-pros"]], "Python Semantic Release Cons": [[27, "python-semantic-release-cons"]], "Python Packaging Tools\u2026 Coming soon\u2026": [[28, "python-packaging-tools-coming-soon"]]}, "indexentries": {}}) \ No newline at end of file