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| .. doctest-skip-all | |
| .. _doc-rules: | |
| *********************** | |
| Astropy Docstring Rules | |
| *********************** | |
| The original source for these docstring standards is the NumPy_ project, and | |
| the associated numpydoc_ tools. The most up-to-date version of these standards | |
| can be found at `numpy's github site | |
| <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_. The | |
| guidelines below have been adapted to the Astropy package. | |
| Overview | |
| ======== | |
| In general, we follow the standard Python style conventions as described here: | |
| * `Style Guide for C Code <https://www.python.org/dev/peps/pep-0007/>`_ | |
| * `Style Guide for Python Code <https://www.python.org/dev/peps/pep-0008/>`_ | |
| * `Docstring Conventions <https://www.python.org/dev/peps/pep-0257/>`_ | |
| Additional PEPs of interest regarding documentation of code: | |
| * `Docstring Processing Framework <https://www.python.org/dev/peps/pep-0256/>`_ | |
| * `Docutils Design Specification <https://www.python.org/dev/peps/pep-0258/>`_ | |
| Use a code checker: | |
| * `pylint <https://www.logilab.org/857>`_ | |
| * `pyflakes <https://pypi.python.org/pypi/pyflakes>`_ | |
| * `pycodestyle <https://github.com/PyCQA/pycodestyle>`_ | |
| The following import conventions are used throughout the Astropy source | |
| and documentation:: | |
| import numpy as np | |
| import matplotlib as mpl | |
| import matplotlib.pyplot as plt | |
| Do not abbreviate ``scipy``. There is no motivating use case to abbreviate | |
| it in the real world, so we avoid it in the documentation to avoid | |
| confusion. | |
| It is not necessary to do ``import numpy as np`` at the beginning of | |
| an example. However, some sub-modules, such as ``fft``, are not | |
| imported by default, and you have to include them explicitly:: | |
| import numpy.fft | |
| after which you may use it:: | |
| np.fft.fft2(...) | |
| Docstring Standard | |
| ================== | |
| A documentation string (docstring) is a string that describes a module, | |
| function, class, or method definition. The docstring is a special attribute | |
| of the object (``object.__doc__``) and, for consistency, is surrounded by | |
| triple double quotes, i.e.:: | |
| """ | |
| This is the form of a docstring. | |
| It can be spread over several lines. | |
| """ | |
| NumPy_ and SciPy_ have defined a common convention for docstrings that | |
| provides for consistency, while also allowing our toolchain to produce | |
| well-formatted reference guides. This format should be used for Astropy | |
| docstrings. | |
| This docstring standard uses `re-structured text (reST) | |
| <http://docutils.sourceforge.net/rst.html>`_ syntax and is rendered | |
| using Sphinx_ (a pre-processor that understands the particular | |
| documentation style we are using). While a rich set of markup is | |
| available, we limit ourselves to a very basic subset, in order to | |
| provide docstrings that are easy to read on text-only terminals. | |
| A guiding principle is that human readers of the text are given | |
| precedence over contorting docstrings so our tools produce nice output. | |
| Rather than sacrificing the readability of the docstrings, we have | |
| written pre-processors to assist Sphinx_ in its task. | |
| The length of docstring lines should be kept to 75 characters to | |
| facilitate reading the docstrings in text terminals. | |
| .. _numpydoc-sections: | |
| Sections | |
| ======== | |
| .. highlight:: rst | |
| The sections of the docstring are: | |
| 1. **Short summary** | |
| A one-line summary that does not use variable names or the function | |
| name, e.g. | |
| :: | |
| def add(a, b): | |
| """ | |
| The sum of two numbers. | |
| """ | |
| The function signature is normally found by introspection and | |
| displayed by the help function. For some functions (notably those | |
| written in C) the signature is not available, so we have to specify | |
| it as the first line of the docstring:: | |
| """ | |
| add(a, b) | |
| The sum of two numbers. | |
| """ | |
| 2. **Deprecation warning** | |
| A section (use if applicable) to warn users that the object is deprecated. | |
| Section contents should include: | |
| * In what Astropy version the object was deprecated, and when it will | |
| be removed. | |
| * Reason for deprecation if this is useful information (e.g., object | |
| is superseded, duplicates functionality found elsewhere, etc.). | |
| * New recommended way of obtaining the same functionality. | |
| This section should use the note Sphinx directive instead of an | |
| underlined section header. | |
| :: | |
| .. note:: Deprecated in Astropy 1.2 | |
| `ndobj_old` will be removed in Astropy 2.0, it is replaced by | |
| `ndobj_new` because the latter works also with array subclasses. | |
| 3. **Extended summary** | |
| A few sentences giving an extended description. This section should be used | |
| to clarify *functionality*, not to discuss implementation detail or | |
| background theory, which should rather be explored in the **notes** section | |
| below. You may refer to the parameters and the function name, but parameter | |
| descriptions still belong in the **parameters** section. | |
| At the end of the extended summary one may optionally include one or more | |
| links to section(s) in the narrative documentation which provide additional | |
| usage information. This is most commonly the case for major classes | |
| or functions which have complex behavior that is not fully described | |
| by the docstring itself. The format is shown in the two examples | |
| below. | |
| One link:: | |
| See also: http://docs.astropy.org/en/stable/table/ | |
| Two or more links:: | |
| See also: | |
| - http://docs.astropy.org/en/stable/table/ | |
| - http://docs.astropy.org/en/stable/table/mixin_columns.html | |
| 4. **Parameters** | |
| Description of the function arguments, keywords and their respective types. | |
| :: | |
| Parameters | |
| ---------- | |
| x : type | |
| Description of parameter `x`. | |
| Enclose variables in single backticks. | |
| For the parameter types, be as precise as possible. Below are a few | |
| examples of parameters and their types. | |
| :: | |
| Parameters | |
| ---------- | |
| filename : str | |
| copy : bool | |
| dtype : data-type | |
| iterable : iterable object | |
| shape : int or tuple of int | |
| files : list of str | |
| If it is not necessary to specify a keyword argument, use ``optional``:: | |
| x : int, optional | |
| Optional keyword parameters have default values, which are displayed as | |
| part of the function signature. They can also be detailed in the | |
| description:: | |
| Description of parameter `x` (the default is -1, which implies summation | |
| over all axes). | |
| When a parameter can only assume one of a fixed set of values, those values | |
| can be listed in braces:: | |
| order : {'C', 'F', 'A'} | |
| Description of `order`. | |
| When two or more input parameters have exactly the same type, shape and | |
| description, they can be combined:: | |
| x1, x2 : array-like | |
| Input arrays, description of `x1`, `x2`. | |
| 5. **Returns** | |
| Explanation of the returned values and their types, of the same format as | |
| **parameters**. | |
| 6. **Other parameters** | |
| An optional section used to describe infrequently used parameters. It | |
| should only be used if a function has a large number of keyword parameters, | |
| to prevent cluttering the **parameters** section. | |
| 7. **Raises** | |
| An optional section detailing which errors get raised and under what | |
| conditions:: | |
| Raises | |
| ------ | |
| InvalidWCSException | |
| If the WCS information is invalid. | |
| This section should be used judiciously, i.e only for errors that are | |
| non-obvious or have a large chance of getting raised. | |
| 8. **See Also** | |
| An optional section used to refer to related code. This section can be very | |
| useful, but should be used judiciously. The goal is to direct users to | |
| other functions they may not be aware of, or have easy means of discovering | |
| (by looking at the module docstring, for example). Routines whose | |
| docstrings further explain parameters used by this function are good | |
| candidates. | |
| As an example, for a hypothetical function ``astropy.wcs.world2pix`` | |
| converting sky to pixel coordinates, we would have:: | |
| See Also | |
| -------- | |
| pix2world : Convert pixel to sky coordinates | |
| When referring to functions in the same sub-module, no prefix is needed, | |
| and the tree is searched upwards for a match. | |
| Prefix functions from other sub-modules appropriately. E.g., whilst | |
| documenting a hypothetical ``astropy.vo`` module, refer to a function in | |
| ``table`` by | |
| :: | |
| table.read : Read in a VO table | |
| When referring to an entirely different module:: | |
| astropy.coords : Coordinate handling routines | |
| Functions may be listed without descriptions, and this is preferable if the | |
| functionality is clear from the function name:: | |
| See Also | |
| -------- | |
| func_a : Function a with its description. | |
| func_b, func_c_, func_d | |
| func_e | |
| 9. **Notes** | |
| An optional section that provides additional information about the code, | |
| possibly including a discussion of the algorithm. This section may include | |
| mathematical equations, written in `LaTeX <http://www.latex-project.org/>`_ | |
| format:: | |
| The FFT is a fast implementation of the discrete Fourier transform: | |
| .. math:: X(e^{j\omega } ) = x(n)e^{ - j\omega n} | |
| Equations can also be typeset underneath the math directive:: | |
| The discrete-time Fourier time-convolution property states that | |
| .. math:: | |
| x(n) * y(n) \Leftrightarrow X(e^{j\omega } )Y(e^{j\omega } )\\ | |
| another equation here | |
| Math can furthermore be used inline, i.e. | |
| :: | |
| The value of :math:`\omega` is larger than 5. | |
| Variable names are displayed in typewriter font, obtained by using | |
| ``\mathtt{var}``:: | |
| We square the input parameter `alpha` to obtain | |
| :math:`\mathtt{alpha}^2`. | |
| Note that LaTeX is not particularly easy to read, so use equations | |
| sparingly. | |
| Images are allowed, but should not be central to the explanation; users | |
| viewing the docstring as text must be able to comprehend its meaning | |
| without resorting to an image viewer. These additional illustrations are | |
| included using:: | |
| .. image:: filename | |
| where filename is a path relative to the reference guide source directory. | |
| 10. **References** | |
| References cited in the **notes** section may be listed here, | |
| e.g. if you cited the article below using the text ``[1]_``, | |
| include it as in the list as follows:: | |
| .. [1] O. McNoleg, "The integration of GIS, remote sensing, | |
| expert systems and adaptive co-kriging for environmental habitat | |
| modeling of the Highland Haggis using object-oriented, fuzzy-logic | |
| and neural-network techniques," Computers & Geosciences, vol. 22, | |
| pp. 585-588, 1996. | |
| which renders as [1]_ | |
| .. [1] O. McNoleg, "The integration of GIS, remote sensing, | |
| expert systems and adaptive co-kriging for environmental habitat | |
| modeling of the Highland Haggis using object-oriented, fuzzy-logic | |
| and neural-network techniques," Computers & Geosciences, vol. 22, | |
| pp. 585-588, 1996. | |
| Referencing sources of a temporary nature, like web pages, is discouraged. | |
| References are meant to augment the docstring, but should not be required | |
| to understand it. References are numbered, starting from one, in the order | |
| in which they are cited. | |
| 11. **Examples** | |
| An optional section for examples, using the `doctest | |
| <https://docs.python.org/3/library/doctest.html>`_ format. This section | |
| is meant to illustrate usage, not to provide a testing framework -- for | |
| that, use the ``tests/`` directory. While optional, this section is very | |
| strongly encouraged. | |
| When multiple examples are provided, they should be separated by blank | |
| lines. Comments explaining the examples should have blank lines both above | |
| and below them:: | |
| >>> astropy.wcs.world2pix(233.2, -12.3) | |
| (134.5, 233.1) | |
| Comment explaining the second example | |
| >>> astropy.coords.fk5_to_gal("00:42:44.33 +41:16:07.5") | |
| (121.1743, -21.5733) | |
| For tests with a result that is random or platform-dependent, mark the | |
| output as such:: | |
| >>> astropy.coords.randomize_position(244.9, 44.2, radius=0.1) | |
| (244.855, 44.13) # random | |
| It is not necessary to use the doctest markup ``<BLANKLINE>`` to indicate | |
| empty lines in the output. The examples may assume that ``import numpy as | |
| np`` is executed before the example code. | |
| .. We need to consider whether to add a doctest= option to astropy.test to | |
| .. enable automated testing of the examples as in Numpy. | |
| Documenting classes | |
| =================== | |
| Class docstrings | |
| ---------------- | |
| Use the same sections as outlined above (all except ``Returns`` are | |
| applicable). The constructor (``__init__``) should also be documented here, | |
| the ``Parameters`` section of the docstring details the constructors | |
| parameters. | |
| An ``Attributes`` section, located below the ``Parameters`` section, may be | |
| used to describe class variables:: | |
| Attributes | |
| ---------- | |
| x : float | |
| The X coordinate. | |
| y : float | |
| The Y coordinate. | |
| Attributes that are properties and have their own docstrings can be simply | |
| listed by name:: | |
| Attributes | |
| ---------- | |
| real | |
| imag | |
| x : float | |
| The X coordinate | |
| y : float | |
| The Y coordinate | |
| .. highlight:: python | |
| In general, it is not necessary to list class methods. Those that are not part | |
| of the public API have names that start with an underscore. In some cases, | |
| however, a class may have a great many methods, of which only a few are | |
| relevant (e.g., subclasses of ndarray). Then, it becomes useful to have an | |
| additional ``Methods`` section:: | |
| class Table(ndarray): | |
| """ | |
| A class to represent tables of data | |
| ... | |
| Attributes | |
| ---------- | |
| columns : list | |
| List of columns | |
| Methods | |
| ------- | |
| read(filename) | |
| Read a table from a file | |
| sort(column, order='ascending') | |
| Sort by `column` | |
| """ | |
| If it is necessary to explain a private method (use with care!), it can be | |
| referred to in the **extended summary** or the **notes**. Do not list private | |
| methods in the Methods section. | |
| Do not list ``self`` as the first parameter of a method. | |
| Method docstrings | |
| ----------------- | |
| Document these as you would any other function. Do not include ``self`` in | |
| the list of parameters. If a method has an equivalent function, the function | |
| docstring should contain the detailed documentation, and the method | |
| docstring should refer to it. Only put brief ``Summary`` and ``See Also`` | |
| sections in the method docstring. | |
| Documenting class instances | |
| =========================== | |
| Instances of classes that are part of the Astropy API may require some care. | |
| To give these instances a useful docstring, we do the following: | |
| * Single instance: If only a single instance of a class is exposed, document | |
| the class. Examples can use the instance name. | |
| * Multiple instances: If multiple instances are exposed, docstrings for each | |
| instance are written and assigned to the instances' ``__doc__`` attributes | |
| at run time. The class is documented as usual, and the exposed instances can | |
| be mentioned in the Notes and See Also sections. | |
| Documenting constants | |
| ===================== | |
| Use the same sections as outlined for functions where applicable:: | |
| 1. summary | |
| 2. extended summary (optional) | |
| 3. see also (optional) | |
| 4. references (optional) | |
| 5. examples (optional) | |
| Docstrings for constants will not be visible in text terminals | |
| (constants are of immutable type, so docstrings can not be assigned | |
| to them like for for class instances), but will appear in the | |
| documentation built with Sphinx. | |
| Documenting modules | |
| =================== | |
| Each module should have a docstring with at least a summary line. Other | |
| sections are optional, and should be used in the same order as for documenting | |
| functions when they are appropriate:: | |
| 1. summary | |
| 2. extended summary | |
| 3. routine listings | |
| 4. see also | |
| 5. notes | |
| 6. references | |
| 7. examples | |
| Routine listings are encouraged, especially for large modules, for which it is | |
| hard to get a good overview of all functionality provided by looking at the | |
| source file(s) or the ``__all__`` dict. | |
| Note that license and author info, while often included in source files, do not | |
| belong in docstrings. | |
| Other points to keep in mind | |
| ============================ | |
| * Notes and Warnings : If there are points in the docstring that deserve | |
| special emphasis, the reST directives for a note or warning can be used | |
| in the vicinity of the context of the warning (inside a section). Syntax: | |
| .. code-block:: rst | |
| .. warning:: Warning text. | |
| .. note:: Note text. | |
| Use these sparingly, as they do not look very good in text terminals | |
| and are not often necessary. One situation in which a warning can | |
| be useful is for marking a known bug that is not yet fixed. | |
| * ``array-like`` : For functions that take arguments which can have not only | |
| a type ``ndarray``, but also types that can be converted to an ndarray | |
| (i.e. scalar types, sequence types), those arguments can be documented | |
| with type ``array-like``. | |
| Common reST concepts | |
| ==================== | |
| For paragraphs, indentation is significant and indicates indentation in the | |
| output. New paragraphs are marked with a blank line. | |
| Use *italics*, **bold**, and ``courier`` if needed in any explanations (but | |
| not for variable names and doctest code or multi-line code). Variable, module | |
| and class names should be written between single back-ticks (```astropy```). | |
| A more extensive example of reST markup can be found in `this example document | |
| <http://docutils.sourceforge.net/docs/user/rst/demo.txt>`_; the `quick | |
| reference <http://docutils.sourceforge.net/docs/user/rst/quickref.html>`_ is | |
| useful while editing. | |
| Line spacing and indentation are significant and should be carefully followed. | |
| Conclusion | |
| ========== | |
| `An example <https://github.com/numpy/numpy/blob/master/doc/example.py>`_ of the | |
| format shown here is available. | |
| Refer to How to Build API/Reference | |
| Documentation :ref:`astropy-doc-building` | |
| on how to use Sphinx_ to build the manual. | |
| .. _NumPy: http://www.numpy.org/ | |
| .. _numpydoc: https://pypi.python.org/pypi/numpydoc/0.3.1 | |
| .. _Matplotlib: http://matplotlib.sourceforge.net/ | |
| .. _SciPy: https://www.scipy.org/ | |
| .. _Sphinx: http://sphinx.pocoo.org | |