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 http://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.

Python Code Style

Follow the standard Python formatting rules when writing code for Sage, as explained at the following URLs:

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)
    

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:

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 (formerly devel/sage-main/sage)
        ext/      # extra sage resources (formerly devel/ext-main)
        mac-app/  # would no longer have to awkwardly be in extcode
        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. For example, see SAGE_ROOT/src/sage/ext/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 *

An Example Is Worth a Thousand Words

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"""
<Very short 1-line summary>

<Paragraph description>

AUTHORS:

- YOUR NAME (2005-01-03): initial version

- person (date in ISO year-month-day format): short desc

EXAMPLES::

<Lots and lots of examples>
"""

#*****************************************************************************
#       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 3 of the License, or
# (at your option) any later version.
#                  http://www.gnu.org/licenses/
#*****************************************************************************

As an example, see SAGE_ROOT/src/sage/rings/integer.pyx which contains the implementation for \(\ZZ\). The AUTHORS: section is redundant, the authoritative log for who wrote what is always the git repository (see the output of git blame). Nevertheless, it is sometimes useful to have a very rough overview over the history, especially if a lot of people have been working on that source file.

All code included with Sage must be licensed under the GPLv3+ or a compatible, that is, less restrictive license (e.g. GPLv2+ or the BSD license).

Documentation Strings

Docstring Markup With ReST and Sphinx

Every function must have a docstring that includes the following information. Source files in the Sage library contain numerous examples on how to format your documentation, so you could use them as a guide.

  • A one-sentence description of the function, followed by a blank line and ending in a period. It prescribes the function or method’s effect as a command (“Do this”, “Return that”), not as a description; e.g. don’t write “Returns the pathname ...”.

  • An INPUT and an OUTPUT block for input and output arguments (see below for format). 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; you do not have to put a precise type name such as int. The INPUT block describes the expected input to your function or method, while the OUTPUT block describes the expected output of the function/method. If appropriate, you need to describe any default values for the input arguments. For example:

    INPUT:
    
    - ``p`` -- (default: 2) a positive prime integer.
    
    OUTPUT:
    
    A 5-tuple consisting of integers in this order:
    
    1. the smallest primitive root modulo p
    2. the smallest prime primitive root modulo p
    3. the largest primitive root modulo p
    4. the largest prime primitive root modulo p
    5. total number of prime primitive roots modulo p

    Some people prefer to format their OUTPUT section as a block by using a dash. That is acceptable as well:

    OUTPUT:
    
    - The plaintext resulting from decrypting the ciphertext ``C``
      using the Blum-Goldwasser decryption algorithm.
  • An EXAMPLES block for examples. This is not optional. These examples are used both for documentation and for automatic testing before each release so should have good coverage of the functionality in question. New functions without these doctests will not be accepted for inclusion with Sage.

  • A SEEALSO block (optional) with links to related things in Sage. A SEEALSO block should start with .. SEEALSO::. It can also be the lower-case form .. seealso::. However, you are encouraged to use the upper-case form .. SEEALSO::. See Hyperlinks for details on how to setup link in Sage. Here’s an example of a SEEALSO block:

    .. SEEALSO::
    
        :ref:`chapter-sage_manuals_links`
  • An ALGORITHM block (optional) which indicates what algorithm and/or what software is used. For example ALGORITHM: Uses Pari. Here’s a longer example that describes an algorithm used. Note that it also cites the reference where this algorithm can be found:

    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`.
    
    REFERENCES:
    
    .. [Nat2000] M.B. Nathanson. Elementary Methods in Number Theory.
       Springer, 2000.

    You can also number the steps in your algorithm using the hash-dot symbol. This way, the actual numbering of the steps are automatically taken care of when you build the documentation:

    ALGORITHM:
    
    The Blum-Goldwasser decryption algorithm is described in Algorithm
    8.56, page 309 of [MenezesEtAl1996]_. The algorithm works as follows:
    
    #. Let `C` be the ciphertext `C = (c_1, c_2, \dots, c_t, x_{t+1})`.
       Then `t` is the number of ciphertext sub-blocks and `h` is the
       length of each binary string sub-block `c_i`.
    #. Let `(p, q, a, b)` be the private key whose corresponding
       public key is `n = pq`. Note that `\gcd(p, q) = ap + bq = 1`.
    #. Compute `d_1 = ((p + 1) / 4)^{t+1} \bmod{(p - 1)}`.
    #. Compute `d_2 = ((q + 1) / 4)^{t+1} \bmod{(q - 1)}`.
    #. Let `u = x_{t+1}^{d_1} \bmod p`.
    #. Let `v = x_{t+1}^{d_2} \bmod q`.
    #. Compute `x_0 = vap + ubq \bmod n`.
    #. For `i` from 1 to `t`, do:
    
       #. Compute `x_i = x_{t-1}^2 \bmod n`.
       #. Let `p_i` be the `h` least significant bits of `x_i`.
       #. Compute `m_i = p_i \oplus c_i`.
    
    #. The plaintext is `m = m_1 m_2 \cdots m_t`.
  • A NOTE block for special notes (optional). Include information such as purpose etc. A NOTE block should start with .. NOTE::. You can also use the lower-case version .. note::, but do not mix lower-case with upper-case. However, you are encouraged to use the upper-case version .. NOTE::. If you want to put anything within the NOTES block, you should indent it at least 4 spaces (no tabs). Here’s an example of a NOTE block:

    .. NOTE::
    
        You should note that this sentence is indented at least 4
        spaces. Avoid tab characters as much as possible when
        writing code or editing the Sage documentation. You should
        follow Python conventions by using spaces only.
  • A WARNING block for critical information about your code. For example, the WARNING block might include information about when or under which conditions your code might break, or information that the user should be particularly aware of. A WARNING block should start with .. WARNING::. It can also be the lower-case form .. warning::. However, you are encouraged to use the upper-case form .. WARNING::. Here’s an example of a WARNING block:

    .. 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 room for improvements. The TODO block might contains disabled doctests to demonstrate the desired feature. A TODO block should start with .. TODO::. It can also be the lower-case form .. todo::. However, you are encouraged to use the upper-case form .. TODO::. Here’s an example of a TODO block:

    .. TODO::
    
        Improve further function ``have_fresh_beers`` using algorithm
        ``buy_a_better_fridge``::
    
            sage: have_fresh_beers('Bière de l\'Yvette') # todo: not implemented
            Enjoy !
  • A REFERENCES block to list books or papers (optional). This block serves a similar purpose to a list of references in a research paper, or a bibliography in a monograph. If your method, function or class uses an algorithm that can be found in a standard reference, you should list that reference under this block. The Sphinx/ReST markup for citations is described at http://sphinx.pocoo.org/rest.html#citations. See below for an example. Sage also add specific markup for links to sage trac tickets and Wikipedia. See Hyperlinks. Here’s an example of a REFERENCES block:

    This docstring is referencing [SC]_. Just remember that references
    are global, so we can also reference to [Nat2000]_ in the ALGORITHM
    block, even if it is in a separate file. However we would not
    include the reference here since it would cause a conflict.
    
    REFERENCES:
    
    .. [SC] Conventions for coding in sage.
       http://www.sagemath.org/doc/developer/conventions.html.
  • A TESTS block (optional), formatted just like EXAMPLES, for additional tests which should be part of the regression suite but are not illustrative enough to merit placement in EXAMPLES.

Use the following template when documenting functions. Note the indentation

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 ...

    OUTPUT:

    The point as a tuple.

    .. SEEALSO::

        :func:`line`

    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 x (=r) to an integer

    .. NOTE::

        This function uses the algorithm of [BCDT]_ to determine
        whether an elliptic curve `E` over `Q` is modular.

    ...

    REFERENCES:

    .. [BCDT] Breuil, Conrad, Diamond, Taylor,
       "Modularity ...."
    """
    <body of the function>

You are strongly encouraged to:

  • Use nice LaTeX formatting everywhere, see LaTeX Typesetting.
  • Liberally describe what the examples do. Note that there must be a blank line after the example code and before the explanatory text for the next example (indentation is not enough).
  • Illustrate any exceptions raised by the function with examples, as given above. (It is an error to ...; In particular, use ...)
  • Include many examples. These are automatically tested on a regular basis, 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. Note that new functions without doctests will not be accepted for inclusion in Sage.

Functions whose names start with an underscore are considered private. Hence they do not appear in the reference manual, and their docstring should not contain any information that is crucial for Sage users. Having said that, you can explicitly enable their docstrings to be shown as 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::``
         """

An EXAMPLES or TESTS block is still required for these private functions.

A special case is the constructor __init__, which clearly starts with an underscore. However, 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:

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'

LaTeX Typesetting

In ReST documentation, you use backticks ` to mark LaTeX code to be typeset. In Sage docstrings, you may also use dollar signs instead. Thus `x^2 + y^2 = 1` and $x^2 + y^2 = 1$ should produce identical output. If you use TeX commands containing backslashes in docstrings, then either use double backslashes or place an “r” right before the first triple opening quote. For example, both of the following are valid:

def cos(x):
    """
    Return `\\cos(x)`.
    """

def sin(x):
    r"""
    Return $\sin(x)$.
    """

You can also use the MATH block to format complicated mathematical expressions:

.. MATH::

    \sum_{i=1}^{\infty} (a_1 a_2 \cdots a_i)^{1/i}
    \leq
    e \sum_{i=1}^{\infty} a_i

Note that the MATH block is automatically wrapped in a latex math environment (i.e. in \[ \] or $$, etc.). To use aligned equations, use the aligned environment:

.. MATH::

    \begin{aligned}
     f(x) & = x^2 - 1 \\
     g(x) & = x^x - f(x - 2)
    \end{aligned}

If you wish to explicitly not wrap the MATH block, make the first line of the indented block :nowrap::

.. MATH::
    :nowrap:

    This is now plain text so I can do things like $x = 5$.

Warning

With or without :nowrap:, the html documentation output currently will work if you use environments such as align which wrap their contents in math mode. However, :nowrap: is necessary for the pdf documentation to build correctly.

The Sage LaTeX style is to typeset standard rings and fields like the integers and the real numbers using the locally-defined macro \\Bold, as in \\Bold{Z} for the integers. This macro is defined to be ordinary bold-face \\mathbf by default, but users can switch to blackboard-bold \\mathbb and back on-the-fly by using latex.blackboard_bold(True) and latex.blackboard_bold(False).

The docstring will be available interactively (for the “def point...” example above, by typing “point?” at the “sage:” prompt) and also in the reference manual. When viewed interactively, LaTeX code has the backslashes stripped from it, so “\cos” will appear as “cos”.

Because of the dual role of the docstring, you need to strike a balance between readability (for interactive help) and using perfect LaTeX code (for the reference manual). For instance, instead of using “\frac{a}{b}”, use “a/b” or maybe “a b^{-1}”. Also keep in mind that some users of Sage are not familiar with LaTeX; this is another reason to avoid complicated LaTeX expressions in docstrings, if at all possible: “\frac{a}{b}” will be obscure to someone who doesn’t know any LaTeX.

Finally, a few non-standard LaTeX macros are available to help achieve this balance, including “\ZZ”, “\RR”, “\CC”, and “\QQ”. These are names of Sage rings, and they are typeset using a single boldface character; they allow the use of “\ZZ” in a docstring, for example, which will appear interactively as “ZZ” while being typeset as “\Bold{Z}” in the reference manual. Other examples are “\GF” and “\Zmod”, each of which takes an argument: “\GF{q}” is typeset as “\Bold{F}_{q}” and “\Zmod{n}” is typeset as “\Bold{Z}/n\Bold{Z}”. See the file $SAGE_ROOT/src/sage/misc/latex_macros.py for a full list and for details about how to add more macros.

Writing Testable Examples

The code in the examples should pass automatic testing. This means that if the above code is in the file f.py (or f.sage), then sage -t f.py should not give any error messages. Testing occurs with full Sage preparsing of input within the standard Sage shell environment, as described in Sage Preparsing. Important: The file f.py is not imported when running tests unless you have arranged that it be imported into your Sage environment, i.e. unless its functions are available when you start Sage using the sage command. 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.

When writing documentation, keep the following points in mind:

  • All input is preparsed before being passed to Python, e.g. 2/3 is replaced by Integer(2)/Integer(3), which evaluates to 2/3 as a rational instead of the Python int 0. For more information on preparsing, see Sage Preparsing.

  • If a test outputs to a file, the file should be a temporary file. Use tmp_filename() to get a temporary filename, or tmp_dir() to get a temporary directory. For example (taken from the file SAGE_ROOT/src/sage/plot/graphics.py):

    sage: plot(x^2 - 5, (x, 0, 5), ymin=0).save(tmp_filename(ext='.png'))
    
  • You may write tests that span multiple lines. The best way to do so is to use the line continuation marker ....:

    sage: for n in srange(1,10):
    ....:     if n.is_prime():
    ....:         print n,
    2 3 5 7
    

    If you have a long line of code, you may want to consider adding a backslash to the end of the line, which tells the doctesting framework to join that current line with the next. This syntax is non-standard so may be removed in a future version of Sage, but in the mean time it can be useful for breaking up large integers across multiple lines:

    sage: n = 123456789123456789123456789\
    ....:     123456789123456789123456789
    sage: n.is_prime()
    False
    

Special Markup to Influence Tests

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:

  • If a test line contains the comment random, it is executed but it is not checked that the output agrees with the output in the documentation string. For example, the docstring for the __hash__ method for CombinatorialObject in SAGE_ROOT/src/sage/combinat/combinat.py includes the lines:

    sage: c = CombinatorialObject([1,2,3])
    sage: hash(c)   # random
    1335416675971793195
    sage: c.__hash__()   # random
    1335416675971793195
    

    However, most functions generating pseudorandom output do not need this tag since the doctesting framework guarantees the state of the pseudorandom number generators (PRNGs) used in Sage for a given doctest. See Randomized Testing for details on this framework. It is preferable to write tests that do not expose this non-determinism, for example rather than checking the value of the hash in a dockets, one could illustrate successfully using it as a key in a dict.

  • If a line contains the comment long time then that line is not tested unless the --long option is given, e.g. sage -t --long f.py. Use this to include examples that take more than about a second to run. These will not be run regularly during Sage development, but will get run before major releases. No example should take more than about 30 seconds.

    For instance, here is part of the docstring from the regulator method for rational elliptic curves, from the file SAGE_ROOT/devel/sage/sage/schemes/elliptic_curves/ell_rational.py:

    sage: E = EllipticCurve([0, 0, 1, -1, 0])
    sage: E.regulator()        # long time (1 second)
    0.0511114082399688
    
  • If a comment contains tol or tolerance, numerical results are only verified to the given tolerance. This may be prefixed by abs[olute] or rel[ative] to specify whether to measure absolute or relative error; this defaults to relative error except when the expected value is exactly zero:

    sage: RDF(pi)                               # abs tol 1e-5
    3.14159
    sage: [10^n for n in [0.0 .. 4]]            # rel tol 2e-4
    [0.9999, 10.001, 100.01, 999.9, 10001]
    

    This can be useful when the exact output is subject to rounding error and/or processor floating point arithmetic variation. Here are some more examples.

    A singular value decomposition of a matrix will produce two unitary matrices. Over the reals, this means the inverse of the matrix is equal to its transpose. We test this result by applying the norm to a matrix difference. The result will usually be a “small” number, distinct from zero:

    sage: A = matrix(RDF, 8, range(64))
    sage: U, S, V = A.SVD()
    sage: (U.transpose()*U-identity_matrix(8)).norm(p=2)    # abs tol 1e-10
    0.0
    

    The 8-th cyclotomic field is generated by the complex number \(e^\frac{i\pi}{4}\). Here we compute a numerical approximation:

    sage: K.<zeta8> = CyclotomicField(8)
    sage: N(zeta8)                             # absolute tolerance 1e-10
    0.7071067812 + 0.7071067812*I
    

    A relative tolerance on a root of a polynomial. Notice that the root should normally print as 1e+16, or something similar. However, the tolerance testing causes the doctest framework to use the output in a computation, so other valid text representations of the predicted value may be used. However, they must fit the pattern defined by the regular expression float_regex in sage.doctest.parsing:

    sage: y = polygen(RDF, 'y')
    sage: p = (y - 10^16)*(y-10^(-13))*(y-2); p
    y^3 - 1e+16*y^2 + 2e+16*y - 2000.0
    sage: p.roots(multiplicities=False)[2]     # relative tol 1e-10
    10000000000000000
    
  • If a comment contains not implemented or not tested, it is never tested. It is good to include lines like this to make clear what we want Sage to eventually implement:

    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.

  • If one of the first 10 lines of a file starts with r""" nodoctest (or """ nodoctest or # nodoctest or % nodoctest or .. nodoctest, or any of these with different spacing), then that file will be skipped. 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.

  • If a comment contains optional - PKGNAME, it is not tested unless the --optional=PKGNAME flag is passed to sage -t. Mark a doctest as optional if it requires optional packages. Running sage -t --optional=all f.py executes all doctests, including all optional tests. Running sage -t --optional=sage,sloane_database f.py runs the normal tests (because of --optional=sage), as well as those marked as # optional - sloane_database. For example, the file SAGE_ROOT/src/sage/databases/sloane.py contains the lines:

    sage: sloane_sequence(60843)       # optional - internet
    

    and:

    sage: SloaneEncyclopedia[60843]    # optional - sloane_database
    

    The first of these just needs internet access, while the second requires that the “sloane_database” package be installed. Calling sage -t --optional=all on this file runs both of these tests, while calling sage -t --optional=sage,internet on it will only run the first test. A test requiring several packages should be marked # optional - pkg1 pkg2 and executed by sage -t --optional=sage,pkg1,pkg2 f.py.

    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.

  • If you are documenting a known bug in Sage, mark it as known bug or optional: bug. For example:

    The following should yield 4.  See :trac:`2`. ::
    
        sage: 2+2  # optional: bug
        5

    Then the doctest will be skipped by default, but could be revealed by running sage -t --optional=sage,bug .... (A doctest marked as known bug gets automatically converted to optional bug).

  • Some tests (hashing for example) behave differently on 32-bit and 64-bit platforms. You can mark a line (generally the output) with either # 32-bit or # 64-bit and the testing framework will remove any lines that don’t match the current architecture. For example:

    sage: z = 32
    sage: z.powermodm_ui(2^32-1, 14)
    ...                                                             # 32-bit
    OverflowError: exp (=4294967295) must be <= 4294967294          # 32-bit
    8              # 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.

Running Automated Tests

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 Documentation Strings for a discussion on how to include examples in documentation strings and what conventions to follow. The chapter Doctesting the Sage Library contains a tutorial on doctesting modules in the Sage library.

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:

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 Doctesting the Sage Library.

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:

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/devel/sage/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/devel/sage/doc/en/tutorial/ for many examples of how to include automated testing in ReST documentation for Sage.

The Pickle Jar

Sage maintains a pickle jar at SAGE_ROOT/src/ext/pickle_jar/pickle_jar.tar.bz2 which is a tar file of “standard” pickles created by sage. This pickle jar is used to ensure that sage maintains backward compatibility by have having sage.structure.sage_object.unpickle_all() check that sage can always unpickle all of the pickles in the pickle jar as part of the standard doc testing framework.

Most people first become aware of the pickle_jar when their patch breaks the unpickling of one of the “standard” pickles in the pickle jar due to the failure of the doctest:

sage -t devel/sage-main/sage/structure/sage_object.pyx

When this happens an error message is printed which contains the following hints for fixing the uneatable pickle:

----------------------------------------------------------------------
** This error is probably due to an old pickle failing to unpickle.
** See sage.structure.sage_object.register_unpickle_override for
** how to override the default unpickling methods for (old) pickles.
** NOTE: pickles should never be removed from the pickle_jar!
----------------------------------------------------------------------

For more details about how to fix unpickling errors in the pickle jar see sage.structure.sage_object.register_unpickle_override()

Warning

Sage’s pickle jar helps to ensure backward compatibility in sage. Pickles should only be removed from the pickle jar after the corresponding objects have been properly deprecated. Any proposal to remove pickles from the pickle jar should first be discussed on sage-devel.

Randomized Testing

In addition to all the examples in your docstrings, which serve as both demonstrations and tests of your code, you should consider creating a test suite. Think of this as a program that will run for a while and “tries” to crash your code using randomly generated input. Your test code should define a class Test with a random() method that runs random tests. These are all assembled together later, and each test is run for a certain amount of time on a regular basis.

For an example, see the file SAGE_ROOT/src/sage/modular/modsym/tests.py.

Global Options

Global options for classes can be defined in Sage using GlobalOptions.