html_extras_pathis no longer accidentally reset to
sphinx-automodapi introduces an autodoc enhancement that replace’s autodoc’s attr getter for
typewith 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
typeto the one built into autodoc. This extension is used by default in
documenteer.conf.pipelinespkg) configuration modules so that they no longer configure
doxylinkif 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 (
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_bibfilesconfiguration variable. Version 2.0.0 or later of sphinxcontrib-bibtex is now required because of that package’s API.
build-stack-docsCLI (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.
autocppapidirective 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
_doxygen/htmldirectory is present.
Remove the matplotlib plot extension from the legacy
documenteer.sphinxconfconfiguration because the extension appears to be incompatible with Sphinx 3.x.
breatheextension from the deprecated
documenteer.sphinxconfSphinx configuration for Pipelines documentation. This is because documenteer no longer includes
breathein its dependencies. Though this is backwards incompatible,
breathewas never used in production documentation.
Documenteer now works with Sphinx 2.0+.
Documenteer’s dependencies now cleanly map to each use case:
pip install documenteerinstalls _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
Stack projects now import
Individual Stack packages now import
The previous configuration sub-package,
documenteer.sphinxconfis 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 (
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-apidirectory 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
lsstccrole. Authors can use a new command,
stack-docs listccto find available APIs for linking.
There is a new directive,
autocppapi, part of the
documenteer.ext.autocppapiextension, that helps you list and link to C++ APIs in a namespace. It’s intended to be used equivalently to the
The built-in Doxygen build considers all Stack packages with a
doc/doxygen.conf.infile. Documenteer creates a Doxygen configuration from the contents of each package’s
doxygen.conf.infile, along with built-in defaults appropriate for pipelines.lsst.io. For example, individual packages can add to the
EXCLUDEtag. By default, each package’s
includedirectory is included in the Doxygen build.
Improved Sphinx runner (
Improved packaging, testing, and development environment:
PEP 518-ify the build process by adding a
Removed the deprecated pytest-runner plugin.
Moved most of the packaging configuration to
Adopted black and isort for code formatting.
toxfor running tests.
pre-commitfor 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]
html_domain_indicesconfigurations for Stack documentation projects to enable automatic index generation. The
genindexcontains 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
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.yamlfile 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.
documenteer.sphinxconfig.stackconfmodule sets up a
defaultcontext for the
jinjadirective that includes all module attributes in the Sphinx config module.
documenteer.sphinxconfig.stackconfmodule includes several new configuration attributes that are driven by the presence of an
EUPS_TAGenvironment 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_TAGenvironment variable. The variables are:
These variables are accessible from the
jinjadirective’s context. [DM-17065]
This release also added some new substitutions to the
rst_epilogof stack-based projects:
|eups-tag|— the current EUPS tag, based on the
|eups-tag-mono|— monospace typeface version of
|eups-tag-bold|— bold typeface version of
|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
logotextat the top of the page for stack-based projects. Previously the
logotextwould always be “LSST Science Pipelines.” [DM-17263]
Added the following projects to the intersphinx inventory of stack-based projects:
Added a new
lsorole for linking to LSST Operations documents in DocuShare.
Updated scikit-learn’s intersphinx inventory URL (now available as HTTPS) in the
lsst-task-config-subtasksdirective so that it can introspect items in an
Registrythat are wrapped by a
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-summarydirective. See DM-16102.
documenteer.sphinxext.lssttasksto 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_iodirectory. This directory is created as part of the ci.lsst.codes
sqre/infra/documenteerjob and shouldn’t be part of the documentation build.
New directives and roles for documenting tasks in LSST Science Pipelines.
lsst-config-fieldsdirectives automatically generate documentation for configuration fields and subtasks in Tasks.
lsst-config-topicdirectives mark pages that document a given task or configuration class.
lsst-config-fieldroles create references to task topics or configuration fields.
lsst-task-api-summarydirective 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.
lsst-configsdirectives 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-config-topicdirectives. These directives also generate a toctree.
Added Astropy to the intersphinx configuration.
automodsumm_inherited_membersin 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.abcclass) won’t have any of their members documented. See DM-16102 for discussion.
tododirectives 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.
remote-code-block, which works like the
literalincludedirective, but allows you to include content from a URL over the web. You can use this directive after adding
documenteer.sphinxextto the extensions list in a project’s
package-toctreedirectives. 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.rstfile in https://github.com/lsst/pipelines_lsst_io each time new packages are added or removed. You can use this directive after adding
documenteer.sphinxextto the extensions list in a project’s
conf.py. These directives include
skipoptions for skipping certain packages and modules.
stack-docscommand-line app. This replaces
build-stack-docs, and now provides a subcommand interface:
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.
package-docscommand-line app. This CLI complements
stack-docs, but is intended for single-package documentation. This effectively lets us replace the Sphinx Makefile (including the
cleancommand). 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.build_pipelines_lsst_io_configsto 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
"class", fitting the LSST DM standards for writing class docstrings, and not filling out
pandasto the intersphinx configuration; removed h5py from intersphinx since it was never needed and conflicted with
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
Recognize a new field in the
metadata.yamlfiles 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_datefor 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
Updated to lsst-sphinx-bootstrap-theme 0.3.x for pipelines docs.
setuptools_scmfor managing version strings.
Improved the Travis CI-based PyPI release process.
build_package_configsan optional keyword argument. This is the way it should have always been to work with templated
astropy_helpersversion to >=3.0, <4.0 to get improved Sphinx extensions.
tests_requireto let us run tests without installing dependencies in the Python environment.
python setup.py testto run pytest.
Update to lsst-dd-rtd-theme 0.2.1
edit_urlto 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:
Links made by the
documenteer.sphinxext.lsstdocushareextension are now HTTPS.
Pin the flake8 developer dependency to 3.3.0. Flake8 version 3.4 has changed how
noqacomments are treated.
documenteer.sphinxext.bibtexextension to support LSST BibTeX entries that include a
docusharefield. Originally from lsst-texmf. This extension is active in the technote Sphinx configuration.
refresh-lsst-bibcommand 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:
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-docscommand 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_requirefeature 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.
ddconfig.pymodule for technical note Sphinx project configuration to the
documenteer.sphinxconfig.technoteconfnamespace for similarity with the
Now using versioneer for version management.
documenteer.sphinxconfi.utils.form_ltd_edition_nameto 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:
documenteer.sphinxconfig.stackconfmodule 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).
versionmetadata change from v0.1.8 to work on Travis CI, by using the
versionmetadata in technote projects can now be set automatically from Git context if those fields are not explicitly set in
Dependencies are now specified solely in
requirements.txtbeing 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.
documenteer.sphinxextin the default extensions for technote projects.
Fix rendering bug with
Add roles for making mock references to code objects that don’t have API references yet. E.g.
Add roles for linking to ls.st links:
Add roles for linking to JIRA tickets:
Include sphinxcontrib-bibtex to Sphinx extensions available in technote projects. DM-6033.