Sphinx autodoc - automated api documentation - PyCon.MY 2015

Editor's Notes

• #2: （ここの文字サイズ大きくする、マウスをレーザーポインタにする） Hi everyone. Thank you for coming my session. This session title is: Sphinx autodoc – automated API documentation
• #3: こんにちは
• #4: At first, Let me introduce myself. My name is Takayuki Shimizukawa came from Japan. I do 3 opensource works. 1. Sphinx co-maintainer since the end of 2011. 2. organize Sphinx-users.jp users group in Japan. 3. member of PyCon JP Committee. And I'm working for BePROUD. We develop web applications for business customers with using Django, Pyramid, SQLAlchemy, Sphinx and other python related tools.
• #5: Before my main presentation, I'd like to introduce "PyCon JP 2015" in Tokyo Japan. We will held the event in this October. Registration is opened. Please join us. Anyway.
• #6: Sphinx autodoc. This is a main topic of this session. Autodoc is a feature that is automatic document generation from source code. Autodoc uses the function definitions and also uses docstring of the such functions. Before we jump in the main topic, I want to know how many people know the docstring, and how many people writing the docstring.
• #7: Docstring is a feature of Python. Do you know the docstring? How many people know that? Please raise your hand. 10, 20, 30.. 55 hands. Thanks. Hum, It might be a minor feature of Python.
• #8: OK, This red lines is a docstring. Docstring describe a way of using the function that is written at the first line of the function body. When you type "help(dumps)" in a Python interactive shell, you will get the docstring.
• #9: Have you written API docs as docstrings? Please raise again. 10, 20.. 22.5 hands. Thanks. It's very small number of hands. But some people write a docstrings.
• #10: So, what is the reason you do not write them? Someone would say, * I don't know what/where should I write them. * Are there some specific docstring formats? * It's not beneficial. For example, sometimes docstrings are not updated even the function's behavior is changed. Those opinions are understandable So then, I'll explain you how to write the docstrings.
• #11: Goal of this session. First one is, * How to generate a doc from Python source code. Second one is, * re-discovering the meaning of docstrings. OK, let's move forward.
• #12: Sphinx autodoc is the most useful way to activate docstrings. So, before talking about docstrings, I'll introduce a basic of sphinx and How to Setup it.
• #13: What is Sphinx? Sphinx is a documentation generator. Sphinx generates doc as several output formats from reStructuredText markup that is an extensible. （ポインタでinputとoutputを指す）
• #14: The history of Sphinx. This man, Georg Brandl is the father of Sphinx. （クリック） Until 2007, python official document was written by LaTeX. But, it's too hard to maintenance. Georg was trying to change such situation. （クリック） So then, he created the Sphinx in 2007. The sphinx provides ease of use and maintainability for the Python official document.
• #15: Sphinx before and after. Before There was no standard ways to write documents. One of example is a Python official document. It was written by LaTeX and several some python scripts jungle. And, Sometime, we need converting markups into other formats Since sphinx has been released, * We can generate more multiple output format from single source. * Integrated html themes make read docs easier. * API references can be integrated into narrative docs. * Automated doc building and hosting by ReadTheDocs service.
• #16: Nowadays, sphinx has been used by these libraries and tools. Python libraries/tools: Python, Sphinx, Flask, Jinja2, Django, Pyramid, SQLAlchemy, Numpy, SciPy, scikit-learn, pandas, fabric, ansible, awscli, … And Non python library/tools also using Sphinx for them docs: Chef, CakePHP(2.x), MathJax, Selenium, Varnish
• #17: Nowadays, sphinx has been used by these libraries and tools. Python libraries/tools: Python, Sphinx, Flask, Jinja2, Django, Pyramid, SQLAlchemy, Numpy, SciPy, scikit-learn, pandas, fabric, ansible, awscli, … And Non python library/tools also using Sphinx for them docs: Chef, CakePHP(2.x), MathJax, Selenium, Varnish
• #18: Sphinx provides these extensions to support automated API documentation. sphinx.ext.autodoc sphinx.ext.autosummary sphinx.ext.doctest sphinx.ext.coverage Autodoc is the most important feature of sphinx. Almost python related libraries are using the autodoc feature.
• #19: OK, let's setup a sphinx project for this code, for example. This library will be used in place of your code to explain autodoc feature. The library name is "Deep Thought". This is a structure of the library. The library has three modules: api.py, calc.py and utils.py. Second box is a first lines of program code in utils.py.
• #20: If you don’t have sphinx installation in your environment, you need to install the Sphinx by this command. pip install sphinx Please note that your source code and sphinx should be installed in single python environment. Python version is also important. If you install Sphinx into Python3 environment in spite of your code is written in Python2, autodoc will emit exception to import your Python2 source code.
• #21: Once you installed the sphinx, you can generate your documentation scaffold by using "sphinx-quickstart" command. Then interactive wizard is invoked and it requires Project name, Author name and Project version. The wizard also ask you many questions, but, DON'T PANIC, Usually, all you need is keep pressing Enter key. Note that, -m option is important. If you invoke without the option, you will get a "hard-coded make targets" Makefile, that will annoy you. And my presentation slide stand on this option. This option is introduced since Sphinx-1.3. And -m option will become default from Spihnx-1.5.
• #22: So, type "make html" in doc directory to generate html output. You can see the output in _build/html directory.
• #23: Now you can see the directories/files structure, like this. Library files under deep_thought directory. Build output under doc directory. Scaffold files under doc directory. In particular, you will see well utils.py, conf.py and index.rst in this session.
• #24: Now we ready to go. Generate API docs from your python source code.
• #25: Setup sphinx autodoc extension. This is a conf.py file in your sphinx scaffold. What is important is the third and fifth lines. Line-3rd: add your library path to import them from Sphinx autodoc. Line-5th: add 'sphinx.ext.autodoc' to use the extension. Next, let's specify the modules you want to document.
• #26: Add automodule directive to your doc. First box is a utils.py file that is a part of deep_thought example library. Second box is a reST file. You can see the automodule usage in this box. automodule is a sphinx directive syntax that is provided by autodoc extension to generate document. Let's see the second box. （クリック） Line-4th: automodule directive imports specified module and inspect it. In this case, deepthought.utils module will be imported and be inspected. Line-5th: :members: option will inspects all members of module not only just module docstring. OK, we are now all ready. Let's invoke "make html" again.
• #27: So, as a result of "make html", you can get a automatically generated document from .py file. Internally, automodule directive inspects your module and render the function signature, arguments and docstring.
• #28: How does it work? autodoc directive generates intermediate reST, like this. Actually intermediate file is not generated in your filesystem, just created it on memory.
• #29: If you want to see the intermediate reST lines, you can use -vvv option, like this. As you see, automodule directive is replaced with concrete documentation contents.
• #30: But, please take care. Sphinx autodoc import your code to get docstrings. It means autodoc will execute code at module global level. Let me introduce a bad case related to this.
• #31: This module will remove all your files. danger.py was designed as command-line script instead of "import from other module". If you tried to document with using autodoc, delete_world function will be called. Consequence of this, "make html" will destroy all your files.
• #32: On the other hand, safer.py (lower block) using execution guard. It's very famous python's idiom.
• #33: Because of the execution guard, your files will not be removed by make html. As a practical matter,　you shouldn't try to document your setup.py for your package with using autodoc.
• #34: Now let's return to the docstring and its output. This output lacks necessary information. It is the information of the argument. If you are looking for the API reference, and you find it, you will say; "Oh, I can't understand the type of arguments and meanings even reading this!"
• #35: In this case, you can use "info field list" syntax for describing arguments. A real docstring should have descriptions for each function arguments like this. These red parts are special version of "field list" that called "info field lists". The specification of info field lists is described at the URL page.
• #36: Info field lists is rendered as this. The output is quite nice. So, you will say; "Oh, I can understand it!", maybe.
• #37: Cross-reference to functions. You can easily make cross-reference from other location to the dumps function. Of course, the cross-references beyond the pages.
• #38: So far, I introduced the basics of autodoc. Following subject is: Detect deviations of the implementation and document. By using doctest.
• #39: I think good API has a good document that illustrate usages of the API by using code example. If doc has code example, you can grasp the API usage quickly and exactly. I add a code example, such 4 red lines to docstring earlier. （クリック） It's called "doctest block". Obviously, this look is an interactive content of the python interactive shell. Actually, you can copy & paste the red lines from python interactive shell.
• #40: After make html, You can get a syntax highlighted doctest block, like this. Library users can grasp the API usage quickly and exactly. And also users can try out it easily.
• #41: And the point of view from library developers, code example is very close from implementation! We can expect that library developers will update code examples when the interface is changed by themselves. ... Really?
• #42: Sorry, I don't believe it. If the code examples was very close from implementation, developers wouldn't mind to it. Because developers have no spare time to read the implicit rules from the code. Explicit is better than implicit for us.
• #43: OK, let's use the doctest builder to detect deviations of the implementation and documentation.
• #44: To use doctest builder, you need to add sphinx doctest extension to conf.py, like this. Line-5: add 'sphinx.ext.doctest' With only this, you are ready to use the doctest builder. OK, Let's invoke "make doctest" command.
• #45: (OK, Let's invoke "make doctest" command.) After that, you can see the dumps function will provide us different result from the expected one. Expected one is: '{spam: 1, ham: "egg"}' Actual one is: 'to-be-implemented' it is not implemented properly yet. Anyway, by using the doctest builder, it show us differences in implementation and sample code in the documentation. Actually, if your UnitTest also contains doctests, you don't need to do this by Sphinx. However, if you don't write the UnitTest, "make doctest" would be a good place to start.
• #46: Listing APIs automatically with using autosummary. As already noted, autodoc is very useful. However, if you have a lot of function of a lot of modules, ...
• #47: And You want to have individual pages for each modules, you need to prepare many reST files for each modules. （クリック） This box is for utils.py. In this case you should also prepare such .rst files for api module and calc module. If you have 100 modules, you should prepare 100 .rst files.
• #48: As you see, each reST files have just 4 lines. You can get them by repeating copy & paste & modify bit. However ... I believe that you don't want to repeat that, like this.
• #49: Don't Repeat Yourself.
• #50: OK, let's use the autosummary extension to avoid such a boring tasks.
• #51: Setup sphinx autosummary extension. This is your conf.py again. Line-6th: to add 'sphinx.ext.autosummary' to use the extension. Line-8th: to use 'members' option for each autodoc related directives. Line-9th: to generate reST files what you will specify with using autosummary directive. //メモ: 9th to invoke 'sphinx-apidoc' internally. Default is False, in that case, you need to invoke 'sphinx-apidoc' by hand.
• #52: You can use autosummary directive in your reST files as you see. This sample uses autosummary directive and toctree option. The :toctree: option is a directory location of intermediate files that will be generated by autosummary. And contents of autosummary directive, deep_thought.api, calc and utils, are module names you want to document. Thereby the autosummary, you will get 100 intermediate .rst files if you have 100 modules.
• #53: After run "make html" command again. Finally, you can get each documented pages without forcing troublesome simple operations. Additionally, "autosummary" directive you wrote was generating table of contents that linking each module pages.
• #54: Discovering undocumented APIs by using coverage extension.
• #55: So far, we've automated the autodoc by using autosummary. In addition, now you can also find deviation of documents and implementation by using the doctest. But, how do you find a function that is not writing a docstring, at all?
• #56: For such situation, we can use coverage extension to find undocumented functions, classes, methods.
• #57: To use coverage extension, you should setup coverage extension to conf.py. This is your conf.py again. Line-7th: to add 'sphinx.ext.coverage' to use the extension. That's all!
• #58: Let's invoke "make coverage" command. After that, you can get a result of coverage measurement. The coverage report is recorded in "_build/coverage/python.txt" that contains undocumented functions, classes and modules. As you see, you can get the undocumented function name.
• #59: However, please take care that; Command always return 0 Then you can't distinguish the presence or absence of the undocumented function by the return code. IMO, it's fair enough because coverage command shouldn't fail regardless whether coverage is perfect or not. However, unfortunately, "make coverage" also unsupported to generate coverage.xml for Jenkins or some CI tools. As conclusion of this, you can discover the undocumented functions, but you can't integrate the information to a CI tools.
• #60: Sorry for inconvenience. And we are waiting for your contribution to solve the problem.(bow)
• #62: Let's review the reasons for not writing a docstring that was introduced at the beginning. I don't know what/where should I write. Let's write a description, arguments and doctest blocks at the next line of function signature. Are there some docstring format spec? Yes, you can use "info field list" for argument spec and you can use doctest block for code example. It's not beneficial. You can use autodoc, autosummary, doctest and coverage to make it beneficial. I think these reasons are resolved by using sphinx autodoc features, aren't you? Let's write docstrings, and use autodoc!
• #63: At the end, I'd like to introduce some of the tips.
• #64: First one is, Options.
• #65: Options for autodo. :members: blah To document just specified members. If you specify the option without parameter, it means ALL. :undoc-members: ... To document members which doesn't have docstring. If you specify the option without parameter, all undocumented members are rendered. :private-members: ... To document private members which name starts with underscore.:special-members: ... To document starts with underscore underscore. :inherited-members: ... To document inherited from super class. Please refer to sphinx reference for the detail of options.
• #66: Second one is Directives for Web API. It's sphinxcontrib-httpdomain.
• #67: sphinxcontrib-httpdomain 3rd-party extension provides http domain to generate WebAPI doc. As you see, you can use get directive. Httpdomain also provides: Other http related directives "http" syntax highlighter It generates nice WebAPI reference page and well organized WebAPI index page. Httpdmain also contains sphinxcontrib.autohttp extension that support Flask, Bottle and Tornado WAF to document WebAPI methods automatically by using reflection.
• #68: The 3rd one is directives for diagram. It's blockdiag series.
• #69: blockdiag provides block style diagram from text notation. The series of blockdiag; seqdiag, actdiag, nwdiag, packetdiag, rackdiag are also released. These are standalone tool, so it works well without sphinx. And, blockdiag series for sphinx are also released. I'd like to introduce a sphinxcontrib-seqdiag example.
• #70: This is a "sphinxcontrib-seqdiag" example. "seqdiag" provides sequence style diagram from text notation. At first, you need installation to use seqdiag directive in your document. Next, setup extension to your conf.py. And now, you can use seqdiag directive as you see. In this example, Request class docstring has seqdiag directive and notation. Finally, you'll get sequence diagram that is integrated to your documentation. So, you can describe a usage of API, behavior of API, and so on.
• #71: The last one is Document translation.
• #72: You can get translated output w/o editing reST and python code. For that, you can use "make gettext" command that generates gettext style pot files. "make gettext" extract text from reST file and python source file that referenced by autodoc. It means, you can translate them into any language without rewriting the original reST files and python source files. If you are interested, please join my tomorrow session!