.. highlight:: ipython
.. _chapter-code-basics:
===================
General Conventions
===================
There are many ways to contribute to Sage including sharing scripts
and Sage worksheets that implement new functionality using Sage,
improving to the Sage library, or to working on the many underlying
libraries distributed with Sage [1]_.
This guide focuses on editing the Sage library itself.
Sage is not just about gathering together functionality. It is about
providing a clear, systematic and consistent way to access a large
number of algorithms, in a coherent framework that makes sense
mathematically. In the design of Sage, the semantics of objects, the
definitions, etc., are informed by how the corresponding objects are
used in everyday mathematics.
.. [1]
See https://www.sagemath.org/links-components.html for a full list
of packages shipped with every copy of Sage
To meet the goal of making Sage easy to read, maintain, and improve,
all Python/Cython code that is included with Sage should adhere to the
style conventions discussed in this chapter.
.. _section-coding-python:
Python Code Style
=================
Follow the standard Python formatting rules when writing code for
Sage, as explained at the following URLs:
* :pep:`0008`
* :pep:`0257`
In particular,
- Use 4 spaces for indentation levels. Do not use tabs as they can
result in indentation confusion. Most editors have a feature that
will insert 4 spaces when the tab key is hit. Also, many editors
will automatically search/replace leading tabs with 4 spaces.
- Whitespace before and after assignment and binary operator of the
lowest priority in the expression::
i = i + 1
c = (a+b) * (a-b)
- No whitespace before or after the ``=`` sign if it is used for
keyword arguments::
def complex(real, imag=0.0):
return magic(r=real, i=imag)
- No whitespace immediately inside parenthesis, brackets, and braces::
spam(ham[1], {eggs: 2})
[i^2 for i in range(3)]
- Use all lowercase function names with words separated by
underscores. For example, you are encouraged to write Python
functions using the naming convention::
def set_some_value():
return 1
Note, however, that some functions do have uppercase letters where
it makes sense. For instance, the function for lattice reduction by
the LLL algorithm is called ``Matrix_integer_dense.LLL``.
- Use CamelCase for class names::
class SomeValue(object):
def __init__(self, x):
self._x = 1
and factory functions that mimic object constructors, for example
``PolynomialRing`` or::
def SomeIdentityValue(x):
return SomeValue(1)
.. _chapter-directory-structure:
Files and Directory Structure
=============================
Roughly, the Sage directory tree is layout like this. Note that we use
``SAGE_ROOT`` in the following as a shortcut for the (arbitrary) name
of the directory containing the Sage sources:
.. CODE-BLOCK:: text
SAGE_ROOT/
sage # the Sage launcher
Makefile # top level Makefile
build/ # Sage's build system
deps
install
...
pkgs/ # install, patch, and metadata from spkgs
src/
setup.py
module_list.py
...
sage/ # Sage library
ext_data/ # extra Sage resources (formerly src/ext)
bin/ # the scripts in local/bin that are tracked
upstream/ # tarballs of upstream sources
local/ # installed binaries
Python Sage library code goes into ``src/`` and uses the following
conventions. Directory names may be plural (e.g. ``rings``) and file
names are almost always singular (e.g. ``polynomial_ring.py``). Note
that the file ``polynomial_ring.py`` might still contain definitions
of several different types of polynomial rings.
.. NOTE::
You are encouraged to include miscellaneous notes, emails, design
discussions, etc., in your package. Make these plain text files
(with extension ``.txt``) in a subdirectory called ``notes``.
If you want to create a new directory in the Sage library
``SAGE_ROOT/src/sage`` (say, ``measure_theory``), that directory
should contain a file ``__init__.py`` that contains the single line
``import all`` in addition to whatever
files you want to add (say, ``borel_measure.py`` and
``banach_tarski.py``), and also a file ``all.py`` listing imports from
that directory that are important enough to be in the Sage’s global
namespace at startup.
The file ``all.py`` might look like this::
from borel_measure import BorelMeasure
from banach_tarski import BanachTarskiParadox
but it is generally better to use the lazy import framework::
from sage.misc.lazy_import import lazy_import
lazy_import('sage.measure_theory.borel_measue', 'BorelMeasure')
lazy_import('sage.measure_theory.banach_tarski', 'BanachTarskiParadox')
Then in the file ``SAGE_ROOT/src/sage/all.py``, add a line ::
from sage.measure_theory.all import *
Non-Python Sage source code and supporting files should be placed in
appropriate subdirectories of ``SAGE_ROOT/src/sage/ext_data/``. They will then be
automatically copied to the corresponding subdirectories of
``SAGE_ROOT/local/share/sage/ext/`` during the build process and can be
accessed at runtime using ``SAGE_EXTCODE``. For example, if ``file`` is placed
in ``SAGE_ROOT/src/sage/ext_data/directory/`` it can be accessed with ::
from sage.env import SAGE_EXTCODE
file = os.path.join(SAGE_EXTCODE, 'directory', 'file')
``SAGE_EXTCODE`` is used because not all distributions have ``SAGE_ROOT``.
Learn by copy/paste
===================
For all of the conventions discussed here, you can find many examples
in the Sage library. Browsing through the code is helpful, but so is
searching: the functions ``search_src``, ``search_def``, and
``search_doc`` are worth knowing about. Briefly, from the "sage:"
prompt, ``search_src(string)`` searches Sage library code for the
string ``string``. The command ``search_def(string)`` does a similar
search, but restricted to function definitions, while
``search_doc(string)`` searches the Sage documentation. See their
docstrings for more information and more options.
Headings of Sage Library Code Files
===================================
The top of each Sage code file should follow this format::
r"""
<Short one-line summary that ends with no period>
<Paragraph description>
EXAMPLES::
<Lots and lots of examples>
AUTHORS:
- YOUR NAME (2005-01-03): initial version
- person (date in ISO year-month-day format): short desc
"""
# ****************************************************************************
# Copyright (C) 2013 YOUR NAME <your email>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
# https://www.gnu.org/licenses/
# ****************************************************************************
As an example, see ``SAGE_ROOT/src/sage/rings/integer.pyx``, which contains the
implementation for `\ZZ`. The names of the people who made major contributions
to the file appear in the ``AUTHORS`` section. You can add your name to the
list if you belong to the people, but refrain from being verbose in the
description. The ``AUTHORS`` section shows very rough overview of the history,
especially if a lot of people have been working on that source file. The
authoritative log for who wrote what is always the git repository (see the
output of ``git blame``).
All code included with Sage must be licensed under the GPLv2+ or a
compatible, that is, less restrictive license (e.g. the BSD license).
.. _section-docstrings:
Documentation Strings
=====================
.. _section-docstring-function:
The docstring of a function: content
-------------------------------------
**Every** function must have a docstring that includes the following
information. You can use the existing functions of Sage as templates.
- A **one-sentence description** of the function.
It must be followed by a blank line and end in a period. It describes the
function or method's effect as a command ("Do this", "Return that"), not as
a description like "Returns the pathname ...".
For methods of a class, it is recommended to refer to the ``self`` argument
in a descriptive way, unless this leads to a confusion. For example, if
``self`` is an integer, then ``this integer`` or ``the integer`` is more
descriptive, and it is preferable to write
.. CODE-BLOCK:: rest
Return whether this integer is prime.
- A **longer description**.
This is optional if the one-sentence description does not need
more explanations.
Start with assumptions of the object, if there are any. For example,
.. CODE-BLOCK:: rest
The poset is expected to be ranked.
if the function raises an exception when called on a non-ranked poset.
Define your terms
.. CODE-BLOCK:: rest
The lexicographic product of `G` and `H` is the graph with vertex set ...
and mention possible aliases
.. CODE-BLOCK:: rest
The tensor product is also known as the categorical product and ...
- An **INPUT** and an **OUTPUT** block describing the input/output of
the function.
The INPUT block describes all arguments that the function accepts.
1. The type names should be descriptive, but do not have to represent
the exact Sage/Python types. For example, use "integer" for
anything that behaves like an integer, rather than ``int``.
2. Mention the default values of the input arguments when applicable.
.. CODE-BLOCK:: rest
INPUT:
- ``n`` -- integer
- ``p`` -- prime integer (default: `2`); coprime with ``n``
The OUTPUT block describes the expected output. This is required if the
one-sentence description of the function needs more explanation.
.. CODE-BLOCK:: rest
OUTPUT: the plaintext decrypted from the ciphertext ``C``
It is often the case that the output consists of several items.
.. CODE-BLOCK:: rest
OUTPUT: a tuple of
- the reduced echelon form `H` of the matrix `A`
- the transformation matrix `U` such that `UA = H`
You are recommended to be verbose enough for complicated outputs.
.. CODE-BLOCK:: rest
OUTPUT:
The decomposition of the free module on which this matrix `A` acts from
the right (i.e., the action is `x` goes to `xA`), along with whether
this matrix acts irreducibly on each factor. The factors are guaranteed
to be sorted in the same way as the corresponding factors of the
characteristic polynomial.
- An **EXAMPLES** block for examples. This is not optional.
These examples are used for documentation, but they are also
tested before each release just like TESTS block.
They should have good coverage of the functionality in question.
- A **SEEALSO** block (highly recommended) with links to related parts of
Sage. This helps users find the features that interest them and discover
the new ones.
.. CODE-BLOCK:: rest
.. SEEALSO::
:ref:`chapter-sage_manuals_links`,
:meth:`sage.somewhere.other_useful_method`,
:mod:`sage.some.related.module`.
See :ref:`chapter-sage_manuals_links` for details on how to setup
links in Sage.
- An **ALGORITHM** block (optional).
It indicates what algorithm and/or what software is used, e.g.
``ALGORITHM: Uses Pari``. Here's a longer example with a
bibliographical reference:
.. CODE-BLOCK:: rest
ALGORITHM:
The following algorithm is adapted from page 89 of [Nat2000]_.
Let `p` be an odd (positive) prime and let `g` be a generator
modulo `p`. Then `g^k` is a generator modulo `p` if and only if
`\gcd(k, p-1) = 1`. Since `p` is an odd prime and positive, then
`p - 1` is even so that any even integer between 1 and `p - 1`,
inclusive, is not relatively prime to `p - 1`. We have now
narrowed our search to all odd integers `k` between 1 and `p - 1`,
inclusive.
So now start with a generator `g` modulo an odd (positive) prime
`p`. For any odd integer `k` between 1 and `p - 1`, inclusive,
`g^k` is a generator modulo `p` if and only if `\gcd(k, p-1) = 1`.
The bibliographical reference should go in Sage's master
bibliography file,
:file:`SAGE_ROOT/src/doc/en/reference/references/index.rst`:
.. CODE-BLOCK:: rest
.. [Nat2000] \M. B. Nathanson. Elementary Methods in Number Theory.
Springer, 2000.
- A **NOTE** block for tips/tricks (optional).
.. CODE-BLOCK:: rest
.. NOTE::
You should note that this sentence is indented at least 4
spaces. Never use the tab character.
- A **WARNING** block for critical information about your code (optional).
For example known situations for which the code breaks, or anything
that the user should be aware of.
.. CODE-BLOCK:: rest
.. WARNING::
Whenever you edit the Sage documentation, make sure that
the edited version still builds. That is, you need to ensure
that you can still build the HTML and PDF versions of the
updated documentation. If the edited documentation fails to
build, it is very likely that you would be requested to
change your patch.
- A **TODO** block for future improvements (optional).
It can contain disabled doctests to demonstrate the desired
feature. Here's an example of a TODO block:
.. CODE-BLOCK:: rest
.. TODO::
Add to ``have_fresh_beers`` an interface with the faster
algorithm "Buy a Better Fridge" (BaBF)::
sage: have_fresh_beers('Bière de l\'Yvette', algorithm="BaBF") # not implemented
Enjoy !
- A **PLOT** block to illustrate with pictures the output of a function.
Generate with Sage code an object ``g`` with a ``.plot`` method, then call
``sphinx_plot(g)``:
.. CODE-BLOCK:: rest
.. PLOT::
g = graphs.PetersenGraph()
sphinx_plot(g)
- A **REFERENCES** block to list related books or papers (optional).
Almost all bibliographic information should be put in the master bibliography
file, see below. Citations will then link to the master bibliography where
the reader can find the bibliographic details (see below for citation
syntax). REFERENCE blocks in individual docstrings are therefore usually not
necessary.
Nevertheless, a REFERENCE block can be useful if there are relevant sources
which are not explicitly mentioned in the docstring or if the docstring is
particularly long. In that case, add the bibliographic information to the
master bibliography file, if not already present, and add a reference block
to your docstring as follows:
.. CODE-BLOCK:: rest
REFERENCES:
For more information, see [Str1969]_, or one of the following references:
- [Sto2000]_
- [Voe2003]_
Note the trailing underscores which makes the citations into hyperlinks. See
below for more about the master bibliography file. For more about citations,
see the `Sphinx/reST markup for citations
<https://www.sphinx-doc.org/rest.html#citations>`_. For links to trac tickets
or wikipedia, see :ref:`chapter-sage_manuals_links`.
- A **TESTS** block (highly recommended).
Formatted just like EXAMPLES, containing tests that are not relevant
to users. In particular, these blocks are not shown when users ask
for help via ``foo?``: they are stripped by the function
:func:`sage.misc.sagedoc.skip_TESTS_block`.
Special and corner cases, like number zero, one-element group etc.
should usually go to this block. This is also right place for most
tests of input validation; for example if the function accepts
``direction='up'`` and ``direction='down'``, you can use this block to check
that ``direction='junk'`` raises an exception.
For the purposes of removal, A "TESTS" block is a block starting
with "TESTS:" (or the same with two colons), on a line on
its own, and ending either with a line indented less than "TESTS",
or with a line with the same level of indentation -- not more --
matching one of the following:
- a Sphinx directive of the form ".. foo:", optionally followed by
other text.
- text of the form "UPPERCASE:", optionally followed by other
text.
- lines which look like a reST header: one line containing
anything, followed by a line consisting only of whitespace,
followed by a string of hyphens, equal signs, or other
characters which are valid markers for reST
headers: ``- = ` : ' " ~ _ ^ * + # < >``.
However, lines only containing double colons `::` do not
end "TESTS" blocks.
Note about Sphinx directives vs. other blocks
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The main Sphinx directives that are used in Sage are:
``.. MATH::``, ``.. NOTE::``, ``.. PLOT::``, ``.. RUBRIC::``,
``.. SEEALSO::``, ``.. TODO::``, ``.. TOPIC::`` and ``.. WARNING::``.
They must be written exactly as above, so for example
``WARNING::`` or ``.. WARNING ::`` will not work.
Some other directives are also available, but less frequently used, namely:
``.. MODULEAUTHOR::``, ``.. automethod::``, ``.. autofunction::``,
``.. image::``, ``.. figure::``.
Other blocks shall not be used as directives; for example
``.. ALGORITHM::`` will not be shown at all.
Sage documentation style
^^^^^^^^^^^^^^^^^^^^^^^^
All Sage documentation is written in reStructuredText (reST) and is
processed by Sphinx. See https://www.sphinx-doc.org/rest.html for an
introduction. Sage imposes these styles:
- Lines should be shorter than 80 characters. If in doubt, read `PEP8: Maximum
Line Length <https://www.python.org/dev/peps/pep-0008/#maximum-line-length>`_.
- All reST and Sphinx directives (like ``.. WARNING::``, ``.. NOTE::``,
``.. MATH::``, etc.) are written in uppercase.
- Code fragments are quoted with double backticks. This includes function
arguments and the Python literals like ````True````, ````False```` and
````None````. For example:
.. CODE-BLOCK:: rest
If ``check`` is ``True``, then ...
Sage's master **BIBLIOGRAPHY** file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
All bibliographical references should be stored in the master
bibliography file,
:file:`SAGE_ROOT/src/doc/en/reference/references/index.rst`, in the
format
.. CODE-BLOCK:: rest
.. [Gau1801] \C. F. Gauss, *Disquisitiones Arithmeticae*, 1801.
.. [RSA1978] \R. Rivest, A. Shamir, L. Adleman,
"A Method for Obtaining Digital Signatures and
Public-Key Cryptosystems".
Communications of the ACM **21** (February 1978),
120–126. :doi:`10.1145/359340.359342`.
The part in brackets is the citation key: given these examples, you
could then use ``[Gau1801]_`` in a docstring to provide a link to the
first reference. Note the trailing underscore which makes the citation a
hyperlink.
When possible, the key should have this form: for a single author, use the
first three letters of the family name followed by the year; for multiple
authors, use the first letter of each of the family names followed by the
year. Note that the year should be four digits, not just the last two -- Sage
already has references from both 1910 and 2010, for example.
When abbreviating the first name of an author in a bibliography
listing, be sure to put a backslash in front of it. This ensures
that the letter (``C.`` in the example above) will not be
interpreted as a list enumerator.
For more about citations, see the `Sphinx/reST markup for citations
<https://www.sphinx-doc.org/rest.html#citations>`_.
Template
^^^^^^^^
Use the following template when documenting functions. Note the
indentation:
.. skip # do not doctest
.. CODE-BLOCK:: python
def point(self, x=1, y=2):
r"""
Return the point `(x^5,y)`.
INPUT:
- ``x`` -- integer (default: `1`); the description of the
argument ``x`` goes here. If it contains multiple lines, all
the lines after the first need to begin at the same indentation
as the backtick.
- ``y`` -- integer (default: `2`); the description of the
argument ``y``
OUTPUT: the point as a tuple
EXAMPLES:
This example illustrates ... ::
sage: A = ModuliSpace()
sage: A.point(2,3)
xxx
We now ... ::
sage: B = A.point(5,6)
sage: xxx
It is an error to ... ::
sage: C = A.point('x',7)
Traceback (most recent call last):
...
TypeError: unable to convert 'r' to an integer
.. NOTE::
This function uses the algorithm of [BCDT2001]_ to determine
whether an elliptic curve `E` over `Q` is modular.
...
.. SEEALSO::
:func:`line`
TESTS::
sage: A.point(42, 0) # Check for corner case y=0
xxx
"""
<body of the function>
The master bibliography file would contain
.. CODE-BLOCK:: rest
.. [BCDT2001] Breuil, Conrad, Diamond, Taylor,
"Modularity ...."
You are strongly encouraged to:
- Use LaTeX typesetting (see :ref:`section-latex-typeset`).
- Liberally describe what the examples do.
.. NOTE::
There must be a blank line after the example code and before the
explanatory text for the next example (indentation is not enough).
- Illustrate the exceptions raised by the function with examples (as
given above: "It is an error to [..]", ...)
- Include many examples.
They are helpful for the users, and are crucial for the quality and
adaptability of Sage. Without such examples, small changes to one part
of Sage that break something else might not go seen until much later
when someone uses the system, which is unacceptable.
Private functions
^^^^^^^^^^^^^^^^^
Functions whose names start with an underscore are considered
private. They do not appear in the reference manual, and their docstring
should not contain any information that is crucial for Sage users. You
can make their docstrings be part of the documentation of another
method. For example::
class Foo(SageObject):
def f(self):
"""
<usual docstring>
.. automethod:: _f
"""
return self._f()
def _f(self):
"""
This would be hidden without the ``.. automethod::``
"""
Private functions should contain an EXAMPLES (or TESTS) block.
A special case is the constructor ``__init__``: due to its special
status the ``__init__`` docstring is used as the class docstring if
there is not one already. That is, you can do the following:
.. CODE-BLOCK:: ipycon
sage: class Foo(SageObject):
....: # no class docstring
....: def __init__(self):
....: """Construct a Foo."""
sage: foo = Foo()
sage: from sage.misc.sageinspect import sage_getdoc
sage: sage_getdoc(foo) # class docstring
'Construct a Foo.\n'
sage: sage_getdoc(foo.__init__) # constructor docstring
'Construct a Foo.\n'
.. _section-latex-typeset:
LaTeX Typesetting
-----------------
In Sage's documentation LaTeX code is allowed and is marked with **backticks or
dollar signs**:
```x^2 + y^2 = 1``` and ``$x^2 + y^2 = 1$`` both yield `x^2 + y^2 = 1`.
**Backslashes:** For LaTeX commands containing backslashes, either use double
backslashes or begin the docstring with a ``r"""`` instead of ``"""``. Both of
the following are valid::
def cos(x):
"""
Return `\\cos(x)`.
"""
def sin(x):
r"""
Return $\sin(x)$.
"""
**MATH block:** This is similar to the LaTeX syntax ``\[<math expression>\]``
(or ``$$<math expression>$$``). For instance:
.. CODE-BLOCK:: rest
.. MATH::
\sum_{i=1}^{\infty} (a_1 a_2 \cdots a_i)^{1/i}
\leq
e \sum_{i=1}^{\infty} a_i
.. MATH::
\sum_{i=1}^{\infty} (a_1 a_2 \cdots a_i)^{1/i}
\leq
e \sum_{i=1}^{\infty} a_i
The **aligned** environment works as it does in LaTeX:
.. CODE-BLOCK:: rest
.. MATH::
\begin{aligned}
f(x) & = x^2 - 1 \\
g(x) & = x^x - f(x - 2)
\end{aligned}
.. MATH::
\begin{aligned}
f(x) & = x^2 - 1 \\
g(x) & = x^x - f(x - 2)
\end{aligned}
When building the PDF documentation, everything is translated to LaTeX
and each MATH block is automatically wrapped in a math environment --
in particular, it is turned into ``\begin{gather} block
\end{gather}``. So if you want to use a LaTeX environment (like
``align``) which in ordinary LaTeX would not be wrapped like this, you
must add a **:nowrap:** flag to the MATH mode. See also `Sphinx's
documentation for math blocks
<http://sphinx-doc.org/latest/ext/math.html?highlight=nowrap#directive-math>`_. :
.. CODE-BLOCK:: rest
.. MATH::
:nowrap:
\begin{align}
1+...+n &= n(n+1)/2\\
&= O(n^2)\\
\end{align}
.. MATH::
:nowrap:
\begin{align}
1+...+n &= n(n+1)/2\\
&= O(n^2)\\
\end{align}
**Readability balance:** in the interactive console, LaTeX formulas contained
in the documentation are represented by their LaTeX code (with backslashes
stripped). In this situation ``\\frac{a}{b}`` is less readable than ``a/b`` or
``a b^{-1}`` (some users may not even know LaTeX code). Make it pleasant for
everybody as much as you can manage.
**Commons rings** `(\Bold{Z},\Bold{N},...)`: The Sage LaTeX style is to typeset
standard rings and fields using the locally-defined macro ``\\Bold`` (e.g.
``\\Bold{Z}`` gives `\Bold{Z}`).
**Shortcuts** are available which preserve readability, e.g. ``\\ZZ`` (`\ZZ`),
``\\RR`` (`\RR`), ``\\CC`` (`\CC`), and ``\\QQ`` (`\QQ`). They appear as
LaTeX-formatted ``\\Bold{Z}`` in the html manual, and as ``Z`` in the
interactive help. Other examples: ``\\GF{q}`` (`\GF{q}`) and ``\\Zmod{p}``
(`\Zmod{p}`).
See the file ``SAGE_ROOT/src/sage/misc/latex_macros.py`` for a full list and
for details about how to add more macros.
.. _section-doctest-writing:
Writing Testable Examples
-------------------------
The examples from Sage's documentation have a double purpose:
- They provide **illustrations** of the code's usage to the users
- They are **tests** that are checked before each release, helping us avoid
new bugs.
All new doctests added to Sage should **pass all tests** (see
:ref:`chapter-doctesting`), i.e. running ``sage -t your_file.py`` should not
give any error messages. Below are instructions about how doctests should be
written.
.. highlight:: ipycon
**What doctests should test:**
- **Interesting examples** of what the function can do. This will be the
most helpful to a lost user. It is also the occasion to check famous
theorems (just in case)::
sage: is_prime(6) # 6 is not prime
False
sage: 2 * 3 # and here is a proof
6
- All **meaningful combinations** of input arguments. For example a function
may accept an ``algorithm="B"`` argument, and doctests should involve both
``algorithm="A"`` and ``algorithm="B"``.
- **Corner cases:** the code should be able to handle a 0 input, or an empty
set, or a null matrix, or a null function, ... All corner cases should be
checked, as they are the most likely to be broken, now or in the future. This
probably belongs to the TESTS block (see :ref:`section-docstring-function`).
- **Systematic tests** of all small-sized inputs, or tests of **random**
instances if possible.
.. NOTE::
Note that **TestSuites** are an automatic way to generate some of these
tests in specific situations. See
``SAGE_ROOT/src/sage/misc/sage_unittest.py``.
**The syntax:**
- **Environment:** doctests should work if you copy/paste them in Sage's
interactive console. For example, the function ``AA()`` in the file
``SAGE_ROOT/src/sage/algebras/steenrod/steenrod_algebra.py`` includes an
EXAMPLES block containing the following::
sage: from sage.algebras.steenrod.steenrod_algebra import AA as A
sage: A()
mod 2 Steenrod algebra, milnor basis
Sage does not know about the function ``AA()`` by default, so it needs to be
imported before it is tested. Hence the first line in the example.
- **Preparsing:** As in Sage's console, `4/3` returns `4/3` and not
`1.3333333333333333` as in Python 3.8. Testing occurs with full Sage
preparsing of input within the standard Sage shell environment, as
described in :ref:`section-preparsing`.
- **Writing files:** If a test outputs to a file, the file should be a
temporary file. Use :func:`tmp_filename` to get a temporary filename, or
:func:`tmp_dir` to get a temporary directory. An example from
``SAGE_ROOT/src/sage/plot/graphics.py``)::
sage: plot(x^2 - 5, (x, 0, 5), ymin=0).save(tmp_filename(ext='.png'))
- **Multiline doctests:** You may write tests that span multiple lines, using
the line continuation marker ``....:`` ::
sage: for n in srange(1,10):
....: if n.is_prime():
....: print(n)
2
3
5
7
- **Python3 print:** Python3 syntax for print must be used in Sage
code and doctests. If you use an old-style print in doctests, it
will raise a SyntaxError::
sage: print "not like that"
Traceback (most recent call last):
...
SyntaxError: ...
sage: print("but like this")
but like this
- **Split long lines:** You may want to split long lines of code with a
backslash. Note: this syntax is non-standard and may be removed in the
future::
sage: n = 123456789123456789123456789\
....: 123456789123456789123456789
sage: n.is_prime()
False
- **Doctests flags:** flags are available to change the behaviour of doctests:
see :ref:`section-further_conventions`.
.. _section-further_conventions:
Special Markup to Influence Doctests
------------------------------------
Overly complicated output in the example code can be shortened
by an ellipsis marker ``...``::
sage: [ZZ(n).ordinal_str() for n in range(25)]
['0th',
'1st',
'2nd',
'3rd',
'4th',
'5th',
...
'21st',
'22nd',
'23rd',
'24th']
sage: ZZ('sage')
Traceback (most recent call last):
...
TypeError: unable to convert 'sage' to an integer
On the proper usage of the ellipsis marker, see :python:`Python's documentation
<library/doctest.html#doctest.ELLIPSIS>`.
There are a number of magic comments that you can put into the example
code that change how the output is verified by the Sage doctest
framework. Here is a comprehensive list:
- **random:** The line will be executed, but its output will not be checked with
the output in the documentation string::
sage: c = CombinatorialObject([1,2,3])
sage: hash(c) # random
1335416675971793195
sage: hash(c) # random
This doctest passes too, as the output is not checked
Doctests are expected to pass with any state of the pseudorandom number
generators (PRNGs).
When possible, avoid the problem, e.g.: rather than checking the value of the
hash in a doctest, one could illustrate successfully using it as a key in a
dict.
One can also avoid the ``random``-tag by checking basic properties::
sage: QQ.random_element().parent() is QQ
True
sage: QQ.random_element() in QQ
True
sage: a = QQ.random_element()
sage: b = QQ._random_nonzero_element()
sage: c = QQ._random_nonzero_element()
sage: (a/c) / (b/c) == a/b
True
Distribution can be checked with loops::
sage: found = {i: False for i in range(-2, 3)}
sage: while not all(found.values()):
....: found[ZZ.random_element(-2, 3)] = True
This is mathematically correct, as it is
guaranteed to terminate. However, there is a
nonzero probability of a timout.
- **long time:** The line is only tested if the ``--long`` option is given, e.g.
``sage -t --long f.py``.
Use it for doctests that take more than a second to run. No example should
take more than about 30 seconds::
sage: E = EllipticCurve([0, 0, 1, -1, 0])
sage: E.regulator() # long time (1 second)
0.0511114082399688
- **tol** or **tolerance:** The numerical values returned by the line are only
verified to the given tolerance. It is useful when the output is subject to
numerical noise due to system-dependent (floating point arithmetic, math
libraries, ...) or non-deterministic algorithms.
- This may be prefixed by ``abs[olute]`` or ``rel[ative]`` to specify whether
to measure **absolute** or **relative** error (see the
:wikipedia:`Approximation_error`).
- If none of ``abs/rel`` is specified, the error is considered to be
``absolute`` when the expected value is **zero**, and is ``relative`` for
**nonzero** values.
::
sage: n(pi) # abs tol 1e-9
3.14159265358979
sage: n(pi) # rel tol 2
6
sage: n(pi) # abs tol 1.41593
2
sage: K.<zeta8> = CyclotomicField(8)
sage: N(zeta8) # absolute tolerance 1e-10
0.7071067812 + 0.7071067812*I
**Multiple numerical values:** the representation of complex numbers,
matrices, or polynomials usually involves several numerical values. If a
doctest with tolerance contains several numbers, each of them is checked
individually::
sage: print("The sum of 1 and 1 equals 5") # abs tol 1
The sum of 2 and 2 equals 4
sage: e^(i*pi/4).n() # rel tol 1e-1
0.7 + 0.7*I
sage: ((x+1.001)^4).expand() # rel tol 2
x^4 + 4*x^3 + 6*x^2 + 4*x + 1
sage: M = matrix.identity(3) + random_matrix(RR,3,3)/10^3
sage: M^2 # abs tol 1e-2
[1 0 0]
[0 1 0]
[0 0 1]
The values that the doctesting framework involves in the error computations
are defined by the regular expression ``float_regex`` in
:mod:`sage.doctest.parsing`.
- **not implemented** or **not tested:** The line is never tested.
Use it for very long doctests that are only meant as documentation. It can
also be used for todo notes of what will eventually be implemented::
sage: factor(x*y - x*z) # todo: not implemented
It is also immediately clear to the user that the indicated example
does not currently work.
.. NOTE::
Skip all doctests of a file/directory
- **file:** If one of the first 10 lines of a file starts with any of
``r""" nodoctest`` (or ``""" nodoctest`` or ``# nodoctest`` or ``%
nodoctest`` or ``.. nodoctest``, or any of these with different spacing),
then that file will be skipped.
- **directory:** If a directory contains a file ``nodoctest.py``, then that
whole directory will be skipped.
Neither of this applies to files or directories which are explicitly given
as command line arguments: those are always tested.
- **optional:** A line flagged with ``optional - keyword`` is not tested unless
the ``--optional=keyword`` flag is passed to ``sage -t`` (see
:ref:`section-optional-doctest-flag`). The main applications are:
- **optional packages:** When a line requires an optional package to be
installed (e.g. the ``sloane_database`` package)::
sage: SloaneEncyclopedia[60843] # optional - sloane_database
- **internet:** For lines that require an internet connection::
sage: oeis(60843) # optional - internet
A060843: Busy Beaver problem: a(n) = maximal number of steps that an
n-state Turing machine can make on an initially blank tape before
eventually halting.
- **bug:** For lines that describe bugs. Alternatively, use ``# known bug``
instead: it is an alias for ``optional bug``.
.. CODE-BLOCK:: rest
The following should yield 4. See :trac:`2`. ::
sage: 2+2 # optional: bug
5
sage: 2+2 # known bug
5
.. NOTE::
- Any words after ``# optional`` are interpreted as a list of
package names, separated by spaces.
- Any punctuation (periods, commas, hyphens, semicolons, ...) after the
first word ends the list of packages. Hyphens or colons between the
word ``optional`` and the first package name are allowed. Therefore,
you should not write ``optional: needs package CHomP`` but simply
``optional: CHomP``.
- Optional tags are case-insensitive, so you could also write ``optional:
chOMP``.
- **indirect doctest:** in the docstring of a function ``A(...)``, a line
calling ``A`` and in which the name ``A`` does not appear should have this
flag. This prevents ``sage --coverage <file>`` from reporting the docstring as
"not testing what it should test".
Use it when testing special functions like ``__repr__``, ``__add__``,
etc. Use it also when you test the function by calling ``B`` which
internally calls ``A``:
.. CODE-BLOCK:: rest
This is the docstring of an ``__add__`` method. The following
example tests it, but ``__add__`` is not written anywhere::
sage: 1+1 # indirect doctest
2
- **32-bit** or **64-bit:** for tests that behave differently on 32-bit or
64-bit machines. Note that this particular flag is to be applied on the
**output** lines, not the input lines::
sage: hash(2^31 + 2^13)
8193 # 32-bit
2147491840 # 64-bit
Using ``search_src`` from the Sage prompt (or ``grep``), one can
easily find the aforementioned keywords. In the case of ``todo: not
implemented``, one can use the results of such a search to direct
further development on Sage.
.. _chapter-testing:
Running Automated Doctests
==========================
This section describes Sage's automated testing of test files of the
following types: ``.py``, ``.pyx``, ``.sage``, ``.rst``. Briefly, use
``sage -t <file>`` to test that the examples in ``<file>`` behave
exactly as claimed. See the following subsections for more
details. See also :ref:`section-docstrings` for a discussion on how to
include examples in documentation strings and what conventions to
follow. The chapter :ref:`chapter-doctesting` contains a tutorial on
doctesting modules in the Sage library.
.. _section-testpython:
Testing .py, .pyx and .sage Files
---------------------------------
Run ``sage -t <filename.py>`` to test all code examples in
``filename.py``. Similar remarks apply to ``.sage`` and ``.pyx``
files:
.. CODE-BLOCK:: shell-session
$ sage -t [--verbose] [--optional] [files and directories ... ]
The Sage doctesting framework is based on the standard Python doctest
module, but with many additional features (such as parallel testing,
timeouts, optional tests). The Sage doctester recognizes ``sage:``
prompts as well as ``>>>`` prompts. It also preparses the doctests,
just like in interactive Sage sessions.
Your file passes the tests if the code in it will run when entered
at the ``sage:`` prompt with no extra imports. Thus users are
guaranteed to be able to exactly copy code out of the examples you
write for the documentation and have them work.
For more information, see :ref:`chapter-doctesting`.
Testing reST Documentation
--------------------------
Run ``sage -t <filename.rst>`` to test the examples in verbatim
environments in reST documentation.
Of course in reST files, one often inserts explanatory texts between
different verbatim environments. To link together verbatim
environments, use the ``.. link`` comment. For example:
.. CODE-BLOCK:: rest
EXAMPLES::
sage: a = 1
Next we add 1 to ``a``.
.. link::
sage: 1 + a
2
If you want to link all the verbatim environments together, you can
put ``.. linkall`` anywhere in the file, on a line by itself. (For
clarity, it might be best to put it near the top of the file.) Then
``sage -t`` will act as if there were a ``.. link`` before each
verbatim environment. The file
``SAGE_ROOT/src/doc/en/tutorial/interfaces.rst`` contains a
``.. linkall`` directive, for example.
You can also put ``.. skip`` right before a verbatim environment to
have that example skipped when testing the file. This goes in the
same place as the ``.. link`` in the previous example.
See the files in ``SAGE_ROOT/src/doc/en/tutorial/`` for many
examples of how to include automated testing in reST documentation for
Sage.
.. _section-coding-general-whitespace:
General Coding Style Regarding Whitespace
=========================================
Use spaces instead of tabs for indentation. The only exception is for
makefiles, in which tabs have a syntactic meaning different from
spaces.
Do not add trailing whitespace.
Sage provides editor configuration for Emacs, using the file
``.dir-locals.el``, to use spaces instead of tabs. Regarding trailing
whitespace, see https://www.emacswiki.org/emacs/DeletingWhitespace
for various solutions.
If you use another editor, we recommend to configure it so you do not
add tabs to files.
Global Options
==============
Global options for classes can be defined in Sage using
:class:`~sage.structure.global_options.GlobalOptions`.
Miscellaneous minor things
==========================
Some decisions are arbitrary, but common conventions make life easier.
* Non-ASCII names in identifiers:
* Translate *ä* and *ö* to *ae* and *oe*, like ``moebius_function``
for Möbius function.
* Translate *á* to *a*, like ``lovasz_number`` for Lovász number.
* Common function keyword arguments:
This is a list of some keyword arguments that many functions and
methods take. For consistency, you should use the keywords from the
list below with the meaning as explained here. Do not use a
different keyword with the same meaning (for example, do not use
``method``; use ``algorithm`` instead).
* ``algorithm``, a string or ``None``: choose between various
implementation or algorithm. Use ``None`` as a default that
selects a sensible default, which could depend on installed
optional packages.
* ``certificate``, a Boolean with ``False`` as default: whether the
function should return some kind of certificate together with the
result. With ``certificate=True`` the return value should be a
pair `(r, c)` where `r` is the result that would be given with
``certificate=False`` and `c` is the certificate or ``None`` if
there is no meaningful certificate.
* ``proof``, a Boolean with ``True`` as default: if ``True``,
require a mathematically proven computation. If ``False``, a
probabilistic algorithm or an algorithm relying to non-proved
hypothesis like RH can be used.
* ``check``, a Boolean: do some additional checks to verify the
input parameters. This should not otherwise influence the
functioning of the code: if code works with ``check=True``, it should
also work with ``check=False``.
* ``coerce``, a Boolean: convert the input parameters to a suitable
parent. This is typically used in constructors. You can call a
method with ``coerce=False`` to skip some checks if the parent is
known to be correct.
* ``inplace``, a Boolean: whether to modify the object in-place or
to return a copy.