Rubin Observatory / LSST Sphinx documentation tools, extensions, and configurations.
For more information about Documenteer, see the documentation at https://documenteer.lsst.io.
Browse the lsst-doc-engineering GitHub topic for more Rubin Observatory documentation engineering projects.
For technical note projects:
pip install "documenteer[technote]"
For the stack projects (such as the LSST Science Pipelines):
pip install "documenteer[pipelines]"
Documenteer includes preset configurations for common LSST DM Sphinx projects. By using Documenteer, you can also ensure that Sphinx extensions required by these configurations are installed.
From the conf.py for technotes:
from documenteer.conf.technote import *
From the conf.py for a stack package:
from documenteer.conf.pipelinespkg import * project = "example" html_theme_options['logotext'] = project html_title = project html_short_title = project
From the conf.py for the LSST Science Pipelines documentation:
from documenteer.conf.pipelines import *
- Roles for linking to LSST documents and Jira tickets
- The remote-code-block directive
- The module-toctree and package-toctree directives for the LSST Science Pipelines documentation
- Extensions for documenting LSST Science Pipelines tasks
- Support for LSST BibTeX files with sphinxcontrib-bibtex.
- Fixed the “Edit on GitHub” URL string construction in documenteer.conf.technote.
- Add a tstn role for linking to Telescope and Site technical notes.
- Fix type checking by adding stub packages.
- Add new roles for linking to technical notes:
- Link to technical notes, which are hosted on lsst.io, now linking directly to lsst.io rather than going through ls.st. This includes the sqr, dmtn, etc. roles and all the new roles mentioned above.
- Use importlib.metadata for getting the package version, rather than pkg_resources.
- Move to a src/ based package layout for consistency.
- Temporarily disable testing the Doxygen-related Sphinx extensions.
- Support sphinx-jinja 2.0.0 by using the sphinx_jinja extension name in documenteer.conf.pipelines and documenteer.conf.pipelinespkg. Installations that use sphinx-jinja < 2 will continue to use sphinxcontrib.jinja since the sphinx-jinja version is dynamically detected.
- Add support for Sphinx 4.x by switching from sphinx.util.inspect.Signature to sphinx.util.inspect.signature for Sphinx versions 2.4 and later. A minimum Sphinx version 2.4 is now required.
- Updated testing matrix to test against the latest patch versions of Sphinx 2.x, 3.x, and 4.x.
- Document conda-forge based installations.
- Stack documentation builds no longer include meta or build-related files in the HTML site output, such as:
- Build products from sconsUtils-based Doxygen builds, including html and xml.
- The html_extras_path is no longer accidentally reset to [""] in documenteer.conf.pipelines.
- sphinx-automodapi introduces an autodoc enhancement that replace’s autodoc’s attr getter for type with a custom function. However, we’re finding that this enhancement is incompatible with Pybind11 static properties that are part of the LSST Science Pipelines API. This release includes a new extension, documenteer.ext.autodocreset, that resets the attr getter for type to the one built into autodoc. This extension is used by default in documenteer.config.pipelines and documenteer.config.pipelinespkg.
- Updated the documenteer.conf.pipelines (and documenteer.conf.pipelinespkg) configuration modules so that they no longer configure doxylink if the Doxygen tag file is not present. This change is useful for single-package documentation builds of pure-Python packages.
- Updated intersphinx links for Numpy and Astropy in the Pipelines configuration (documenteer.conf.pipelines and documenteer.conf.pipelinespkg).
- Fixed a syntax issue with the package’s long description, and added a linting rule to prevent this issue in the future.
- Documenteer works with the latest version of sphinxcontrib-bibtex. Both the new (documenteer.conf.technote) and old (documenteer.sphinxconfig.technoteconf) versions of the technote configuration use the new bibtex_bibfiles configuration variable. Version 2.0.0 or later of sphinxcontrib-bibtex is now required because of that package’s API.
- The build-stack-docs CLI (replaced by stack-docs build) now defaults to not generating a Doxygen configuration, or running Doxygen. This is consistent with the original behavior of build-stack-docs, which did not perform a Doxygen build.
- The autocppapi directive now works even if the corresponding Doxylink symbol map is unavailable. This feature is useful for any circumstance when a Doxygen subsite that is normally present is unavailable, such as for a single-package documentation build.
- The Doxygen subsite is only added to html_extras_path if the _doxygen/html directory is present.
- Remove the matplotlib plot extension from the legacy documenteer.sphinxconf configuration because the extension appears to be incompatible with Sphinx 3.x.
- Removed the breathe extension from the deprecated documenteer.sphinxconf Sphinx configuration for Pipelines documentation. This is because documenteer no longer includes breathe in its dependencies. Though this is backwards incompatible, breathe was never used in production documentation.
Documenteer now works with Sphinx 2.0+.
Documenteer’s dependencies now cleanly map to each use case:
- pip install documenteer installs _only_ the dependencies required to use Documenteer’s own Sphinx extensions. The dependencies are not strictly pinned (aside from Sphinx >= 2.0).
- pip install documenteer[technote] installs the core dependencies required by Documenteer, as well as the pinned Sphinx theme and extensions used by all technote projects.
- pip install documenteer[pipelines] installs the core dependencies required by Documenteer, as well as the Sphinx theme and extensions used by pipelines.lsst.io. These extensions no longer have pinned versions.
Development and test dependencies are no longer pinned.
Python 3.6 is no longer officially supported. Documenteer is tested with Python 3.7 and 3.8.
New Sphinx configuration facilities should prevent recursion issues by more cleanly populating the Python attributes in the configuration module:
- Technote projects now import documenteer.conf.technote in their conf.py files.
- Stack projects now import documenteer.conf.pipelines in their conf.py files.
- Individual Stack packages now import documenteer.conf.pipelinespkg in their conf.py files.
The previous configuration sub-package, documenteer.sphinxconf is deprecated. [DM-20866]
Overall, the configurations are compatible with these exceptions:
- ReStructuredText source files are no longer copied into the built site for Pipelines projects (html_copy_source is False). This change reduces the upload site of the pipelines.lsst.io site.
- Updated the MathJax CDN URL to point to cdnjs.
The stack documentation build (stack-docs build) can now run a Doxygen build to generate an HTML site and tag file of the C++ API. The HTML site is copied into the cpp-api directory of the Sphinx site, during the Sphinx build. This Doxygen build replaces, and is independent of, the Doxygen build tooling in sconsUtils, lsstDoxygen, and the base package.
ReStructuredText content can now link into the embedded Doxygen-generate site using the sphinxcontrib-doxylink extension with the new lsstcc role. Authors can use a new command, stack-docs listcc to find available APIs for linking.
There is a new directive, autocppapi, part of the documenteer.ext.autocppapi extension, that helps you list and link to C++ APIs in a namespace. It’s intended to be used equivalently to the automodapi extension.
The built-in Doxygen build considers all Stack packages with a doc/doxygen.conf.in file. Documenteer creates a Doxygen configuration from the contents of each package’s doxygen.conf.in file, along with built-in defaults appropriate for pipelines.lsst.io. For example, individual packages can add to the EXCLUDE tag. By default, each package’s include directory is included in the Doxygen build.
Improved Sphinx runner (documenteer.sphinxrunner). [DM-26768]
Improved packaging, testing, and development environment:
- PEP 518-ify the build process by adding a pyproject.toml file.
- Removed the deprecated pytest-runner plugin.
- Moved most of the packaging configuration to setup.cfg.
- Adopted black and isort for code formatting.
- Migrated to tox for running tests.
- Migrated to pre-commit for running linters and code formatters.
- Migrated to GitHub Actions from Travis CI.
- Added a new Developer guide and Release procedure guide.
- Added an installation page.
- Moved the Python API reference to its own page.
- Improved the README to list features.
Added GitHub community health features: contributing, support, and code of conduct files.
- This new version of the technote sphinx theme should fix the edition link in the sidebar for non-main editions. [DM-20839]
- Enabled the html_use_index and html_domain_indices configurations for Stack documentation projects to enable automatic index generation. The genindex contains links to all command-line options and Python objects (Sphinx’s domains). This also opens us up to a more general content index by way of the index directive. [DM-20850]
- Fixed compatibility with docutils 0.15. Now Sphinx will control which version of docutils is used, which should now be 0.15.
- Also updated the intersphinx URL for Pandas to use https.
- Add sphinxcontrib.autoprogram to enable automated reference documentation of argparse-based command-line scripts. This extension is available with the documenteer[pipelines] installation extra and enabled by default for LSST Science Pipelines projects. [DM-20767]
- Update the official list of tested and supported Python versions to Python 3.6 and 3.7.
- Pin docutils temporarily to 0.14. The latest release, 0.15, is currently incompatible with the :jira: role.
The stack documentation build now requires that packages be explicitly required by the main documentation project’s EUPS table file. Before, a package only needed a doc/manifest.yaml file and to be currently set up in the EUPS environment to be linked into the documentation build. This would lead to packages being included in a documentation build despite not being a part of that stack product. [DM-17765]
This release adds the sphinx-jinja extension for documenteer[pipelines] installations. This extension makes it possible to dynamically create content with Jinja templating.
The documenteer.sphinxconfig.stackconf module sets up a default context for the jinja directive that includes all module attributes in the Sphinx config module.
The documenteer.sphinxconfig.stackconf module includes several new configuration attributes that are driven by the presence of an EUPS_TAG environment variable. The overall intent of these variables is to make it possible to render installation documentation for the https://pipelines.lsst.io documentation project from the EUPS_TAG environment variable. The variables are:
These variables are accessible from the jinja directive’s context. [DM-17065]
This release also added some new substitutions to the rst_epilog of stack-based projects:
- |eups-tag| — the current EUPS tag, based on the EUPS_TAG environment variable.
- |eups-tag-mono| — monospace typeface version of |eups-tag|.
- |eups-tag-bold| — bold typeface version of |eups-tag|.
The |current-release| substitution is no longer available.
Fixed some bugs with the display of copyrights in stack-based projects.
The project’s name is also used as the logotext at the top of the page for stack-based projects. Previously the logotext would always be “LSST Science Pipelines.” [DM-17263]
Added the following projects to the intersphinx inventory of stack-based projects:
- Added a new lso role for linking to LSST Operations documents in DocuShare.
- Updated scikit-learn’s intersphinx inventory URL (now available as HTTPS) in the documenteer.sphinxconfig.stackconf.
- Fixed the lsst-task-config-subtasks directive so that it can introspect items in an lsst.pex.config Registry that are wrapped by a ConfigurableWrapper. [DM-17661]
- Handle cases where an object does not have a docstring in documenteer.sphinxext.lssttasks.taskutils.get_docstring. This improves the reliability of the lsst-task-api-summary directive. See DM-16102.
- Add documenteer.sphinxext.lssttasks to the Sphinx extensions available for pipelines.lsst.io documentation builds.
- For pipelines.lsst.io builds, Documenteer ignores the home/ directory that’s created at the root of the pipelines_lsst_io directory. This directory is created as part of the ci.lsst.codes sqre/infra/documenteer job and shouldn’t be part of the documentation build.
- New directives and roles for documenting tasks in LSST Science Pipelines.
- The lsst-task-config-fields, lsst-task-config-subtasks, and lsst-config-fields directives automatically generate documentation for configuration fields and subtasks in Tasks.
- The lsst-task-topic and lsst-config-topic directives mark pages that document a given task or configuration class.
- The lsst-task, lsst-config, and lsst-config-field roles create references to task topics or configuration fields.
- The lsst-task-api-summary directive autogenerates a summary of the of a task’s key APIs. This directive does not replace the autodoc-generated documentation for the task’s class, but instead provides an affordance that creates a bridge from the task topic to the API reference topic.
- The lsst-tasks, lsst-cmdlinetasks, lsst-pipelinetasks, lsst-configurables, and lsst-configs directives create listings of topics. These listings not only link to the topic, but also show a summary that’s either extracted from the corresponding docstring or set through the lsst-task-topic or lsst-config-topic directives. These directives also generate a toctree.
- Added Astropy to the intersphinx configuration.
- Enabled automodsumm_inherited_members in the stackconf for stack documentation.
This configuration is critical:
- It is actually responsible for ensuring that inherited members of classes appear in our docs.
- Without this, classes that have a __slots__ attribute (typically through inheritance of a collections.abc class) won’t have any of their members documented. See DM-16102 for discussion.
- todo directives are now hidden when using build_pipelines_lsst_io_configs. They are still shown, by default, for standalone package documentation builds, which are primarily developer-facing.
- New remote-code-block, which works like the literalinclude directive, but allows you to include content from a URL over the web. You can use this directive after adding documenteer.sphinxext to the extensions list in a project’s conf.py.
- New module-toctree and package-toctree directives. These create toctrees for modules and packages, respectively, in Stack documentation sites like pipelines.lsst.io. With these directives, we don’t need to modify the index.rst file in https://github.com/lsst/pipelines_lsst_io each time new packages are added or removed. You can use this directive after adding documenteer.sphinxext to the extensions list in a project’s conf.py. These directives include skip options for skipping certain packages and modules.
- New stack-docs command-line app. This replaces build-stack-docs, and now provides a subcommand interface: stack-docs build and stack-docs clean. This CLI is nice to use since it’ll discover the root conf.py as long as you’re in the root documentation repository.
- New package-docs command-line app. This CLI complements stack-docs, but is intended for single-package documentation. This effectively lets us replace the Sphinx Makefile (including the clean command). Using a packaged app lets us avoid SIP issues, as well as Makefile drift in individual packages. This CLI is nice to use since it’ll discover the doc/ directory of a package as long as you’re in the package’s root directory, the doc/ directory, or a subdirectory of doc/.
- Refactored the Sphinx interface into documenteer.sphinxrunner.run_sphinx. This change lets multiple command-line front-ends to drive Sphinx.
- Various improvements to the configuration for LSST Stack-based documentation projects (documenteer.sphinxconf.stackconf):
- Add documenteer.sphinxconf.stackconf.build_pipelines_lsst_io_configs to configure the Sphinx build of the https://github.com/lsst/pipelines_lsst_io repo. This pattern lets us share configurations between per-package documentation builds and the “stack” build in pipelines_lsst_io.
- Replaced the third-party astropy_helpers package with the numpydoc and sphinx-automodapi packages. This helps reduce the number of extraneous dependencies needed for Stack documentation.
- autoclass_content is now "class", fitting the LSST DM standards for writing class docstrings, and not filling out __init__ docstrings.
- Added scikit-learn and pandas to the intersphinx configuration; removed h5py from intersphinx since it was never needed and conflicted with daf_butler documentation.
- Removed the viewcode extension since that won’t scale well with the LSST codebase. Ultimately we want to link to source on GitHub.
- _static/ directories are not needed and won’t produce warnings if not present in a package.
- Other internal cleanups for documenteer.sphinxconf.stackconf.
- Recognize a new field in the metadata.yaml files of Sphinx technotes called exclude_patterns. This is an array of file or directory paths that will be ignored by Sphinx during its build, as well as extensions like our get_project_content_commit_date for looking up commit date of content files.
- Updated to Sphinx >1.7.0, <1.8.0. Sphinx 1.8.0 is known to be incompatible with documenteer.sphinxrunner.
- Updated to lsst-sphinx-bootstrap-theme 0.3.x for pipelines docs.
- Switched to setuptools_scm for managing version strings.
- Improved the Travis CI-based PyPI release process.
- Make copyright in build_package_configs an optional keyword argument. This is the way it should have always been to work with templated conf.py files.
- Bump astropy_helpers version to >=3.0, <4.0 to get improved Sphinx extensions.
- Use setuptools tests_require to let us run tests without installing dependencies in the Python environment.
- Enable python setup.py test to run pytest.
- Update to lsst-dd-rtd-theme 0.2.1
- Add edit_url to the Jinja context for technotes. This enables “Edit on GitHub” functionality.
- Use lsst-dd-rtd-theme 0.2.0 for new branding, Edit on GitHub, and edition switching features for technotes.
- Add support for additional DocuShare linking roles with documenteer.sphinxext.lsstdocushare. Supported handles now include: ldm, lse, lpm, lts, lep, lca, lsstc, lcr, lcn, dmtr, spt, document, report, minutes, collection, sqr, dmtn, smtn.
- Links made by the documenteer.sphinxext.lsstdocushare extension are now HTTPS.
- Pin the flake8 developer dependency to 3.3.0. Flake8 version 3.4 has changed how noqa comments are treated.
- Add documenteer.sphinxext.bibtex extension to support LSST BibTeX entries that include a docushare field. Originally from lsst-texmf. This extension is active in the technote Sphinx configuration.
- Add a refresh-lsst-bib command line program that downloads the latest LSST bib files from the lsst-texmf GitHub repository. This program can be used by technote authors to update a technote’s local bibliography set at any time.
- Added graceful defaults when a technote is being built without an underlying Git repository (catches exceptions from functions that seek Git metadata).
- Add a dependency upon the Requests library.
- Rename configuration function for technotes: documenteer.sphinxconfig.technoteconfig.configure_sphinx_design_doc is now documenteer.sphinxconfig.technoteconf.configure_technote.
- Sphinx is no longer in the default intersphinx object list for technotes. This will speed up builds for documents that don’t refer to Python APIs, and it still straightforward to configure on a per-project basis.
- The default revision timestamp for technotes is now derived from the most recent Git commit that modified a technote’s content (‘rst’, and common image file formats). This is implemented with the new documenteer.sphinxconfig.utils.get_project_content_commit_date() function. This feature allows us to change technote infrastructure without automatically bumping the default revision date of the technote.
- Add a new build-stack-docs command line executable. This executable links stack package documentation directories into a root documentation project and runs a Sphinx build. This is how we will build the https://pipelines.lsst.io documentation site. See DMTN-030 for design details.
- New system for installing project-specific dependencies. We’re using setuptools’s extras_require feature to install different dependencies for technote and stack documentation projects. To install documenteer for a technote project, the new command is pip install documenteer[technote]. For stack documentation projects: pip install documenteer[pipelines]. Developers may use pip install -e .[technote,pipelines,dev]. This will allow us to install different Sphinx themes for different types of projects, for example.
- Pin Sphinx to >=1.5.0,<1.6.0 and docutils to 0.13.1. This is due to an API change in Sphinx’s application Config.init_values(), which is used for making mock applications in Documenteer’s unit tests.
- Move the ddconfig.py module for technical note Sphinx project configuration to the documenteer.sphinxconfig.technoteconf namespace for similarity with the stackconf module.
- Now using versioneer for version management.
- Add documenteer.sphinxconfi.utils.form_ltd_edition_name to form LSST the Docs-like edition names for Git refs.
- Configure automated PyPI deployments with Travis.
Includes prototype support for LSST Science Pipelines documentation, as part of DM-6199:
- Added dependencies to breathe, astropy-helpers and the lsst-sphinx-bootstrap-theme to generally coordinate LSST Science Pipelines documentation dependencies.
- Created documenteer.sphinxconfig.stackconf module to centrally coordinate Science Pipelines documentation configuration. Much of the configuration is based on astropy-helper’s Sphinx configuration since the LSST Science Pipelines documentation is heavily based upon Astropy’s Sphinx theme and API reference generation infrastructure. Also includes prototype configuration for breathe (the doxygen XML bridge).
- Updated test harness (pytest and plugin versions).
- Enhanced the version metadata change from v0.1.8 to work on Travis CI, by using the TRAVIS_BRANCH.
- last_revised and version metadata in technote projects can now be set automatically from Git context if those fields are not explicitly set in metadata.yaml. DM-6916.
- Dependencies are now specified solely in setup.py, with requirements.txt being used for development dependencies only. This is consistent with advice from https://caremad.io/2013/07/setup-vs-requirement/.
- Fix separator logic in JIRA tickets interpreted as lists.
- Include documenteer.sphinxext in the default extensions for technote projects.
- Fix rendering bug with lpm, ldm, and lse links.
- Add roles for making mock references to code objects that don’t have API references yet. E.g. lclass, lfunc. DM-6326.
- Add roles for linking to ls.st links: lpm, ldm, and lse. DM-6181.
- Add roles for linking to JIRA tickets: jira, jirab, and jirap. DM-6181.
- Include sphinxcontrib-bibtex to Sphinx extensions available in technote projects. DM-6033.
- Initial version
The MIT License (MIT)
Copyright (c) 2015-2021 Association of Universities for Research in Astronomy, Inc. (AURA)
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