Running Sage’s Doctests

Doctesting a function ensures that the function performs as claimed by its documentation. Testing can be performed using one thread or multiple threads. After compiling a source version of Sage, doctesting can be run on the whole Sage library, on all modules under a given directory, or on a specified module only. For the purposes of this chapter, suppose we have compiled Sage from source and the top level directory is:

[jdemeyer@localhost sage]$ pwd
/home/jdemeyer/sage

See the section Running automated doctests for information on Sage’s automated testing process. The general syntax for doctesting is as follows. To doctest a module in the library of a version of Sage, use this syntax:

/path/to/sage_root/sage -t [--long] /path/to/sage_root/path/to/module.py[x]

where --long is an optional argument (see Optional arguments for more options). The version of sage used must match the version of Sage containing the module we want to doctest. A Sage module can be either a Python script (with the file extension “.py”) or it can be a Cython script, in which case it has the file extension “.pyx”.

Testing a module

Say we want to run all tests in the sudoku module sage/games/sudoku.py. In a terminal window, first we cd to the top level Sage directory of our local Sage installation. Now we can start doctesting as demonstrated in the following terminal session:

[jdemeyer@localhost sage]$ ./sage -t src/sage/games/sudoku.py
Running doctests with ID 2012-07-03-03-36-49-d82849c6.
Doctesting 1 file.
sage -t src/sage/games/sudoku.py
    [103 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 4.8 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 3.6 seconds

The numbers output by the test show that testing the sudoku module takes about four seconds, while testing all specified modules took the same amount of time; the total time required includes some startup time for the code that runs the tests. In this case, we only tested one module so it is not surprising that the total testing time is approximately the same as the time required to test only that one module. Notice that the syntax is:

[jdemeyer@localhost sage]$ ./sage -t src/sage/games/sudoku.py
Running doctests with ID 2012-07-03-03-39-02-da6accbb.
Doctesting 1 file.
sage -t src/sage/games/sudoku.py
    [103 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 4.9 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 3.6 seconds

but not:

[jdemeyer@localhost sage]$ ./sage -t sage/games/sudoku.py
Running doctests with ID 2012-07-03-03-40-53-6cc4f29f.
No files matching sage/games/sudoku.py
No files to doctest

We can also first cd to the directory containing the module sudoku.py and doctest that module as follows:

[jdemeyer@localhost sage]$ cd src/sage/games/
[jdemeyer@localhost games]$ ls
__init__.py  hexad.py       sudoku.py           sudoku_backtrack.pyx
all.py       quantumino.py  sudoku_backtrack.c
[jdemeyer@localhost games]$ ../../../../sage -t sudoku.py
Running doctests with ID 2012-07-03-03-41-39-95ebd2ff.
Doctesting 1 file.
sage -t sudoku.py
    [103 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 5.2 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 3.6 seconds

In all of the above terminal sessions, we used a local installation of Sage to test its own modules. Even if we have a system-wide Sage installation, using that version to doctest the modules of a local installation is a recipe for confusion.

You can also run the Sage doctester as follows:

[jdemeyer@localhost sage]$ ./sage -tox -e doctest -- src/sage/games/sudoku.py

See Development and Testing Tools for more information about tox.

Troubleshooting

To doctest modules of a Sage installation, from a terminal window we first cd to the top level directory of that Sage installation, otherwise known as the SAGE_ROOT of that installation. When we run tests, we use that particular Sage installation via the syntax ./sage; notice the “dot-forward-slash” at the front of sage. This is a precaution against confusion that can arise when our system has multiple Sage installations. For example, the following syntax is acceptable because we explicitly specify the Sage installation in the current SAGE_ROOT:

[jdemeyer@localhost sage]$ ./sage -t src/sage/games/sudoku.py
Running doctests with ID 2012-07-03-03-43-24-a3449f54.
Doctesting 1 file.
sage -t src/sage/games/sudoku.py
    [103 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 4.9 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 3.6 seconds
[jdemeyer@localhost sage]$ ./sage -t "src/sage/games/sudoku.py"
Running doctests with ID 2012-07-03-03-43-54-ac8ca007.
Doctesting 1 file.
sage -t src/sage/games/sudoku.py
    [103 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 4.9 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 3.6 seconds

The following syntax is not recommended as we are using a system-wide Sage installation (if it exists):

[jdemeyer@localhost sage]$ sage -t src/sage/games/sudoku.py
sage -t  "src/sage/games/sudoku.py"
**********************************************************************
File "/home/jdemeyer/sage/src/sage/games/sudoku.py", line 515:
    sage: next(h.solve(algorithm='backtrack'))
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/sage/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/usr/local/sage/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/usr/local/sage/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_13[4]>", line 1, in <module>
        next(h.solve(algorithm='backtrack'))###line 515:
    sage: next(h.solve(algorithm='backtrack'))
      File "/home/jdemeyer/.sage/tmp/sudoku.py", line 607, in solve
        for soln in gen:
      File "/home/jdemeyer/.sage/tmp/sudoku.py", line 719, in backtrack
        from sudoku_backtrack import backtrack_all
    ImportError: No module named sudoku_backtrack
**********************************************************************
[...more errors...]
2 items had failures:
   4 of  15 in __main__.example_13
   2 of   8 in __main__.example_14
***Test Failed*** 6 failures.
For whitespace errors, see the file /home/jdemeyer/.sage//tmp/.doctest_sudoku.py
         [21.1 s]

----------------------------------------------------------------------
The following tests failed:


        sage -t  "src/sage/games/sudoku.py"
Total time for all tests: 21.3 seconds

In this case, we received an error because the system-wide Sage installation is a different (older) version than the one we are using for Sage development. Make sure you always test the files with the correct version of Sage.

Parallel testing many modules

So far we have used a single thread to doctest a module in the Sage library. There are hundreds, even thousands of modules in the Sage library. Testing them all using one thread would take a few hours. Depending on our hardware, this could take up to six hours or more. On a multi-core system, parallel doctesting can significantly reduce the testing time. Unless we also want to use our computer while doctesting in parallel, we can choose to devote all the cores of our system for parallel testing.

Let us doctest all modules in a directory, first using a single thread and then using four threads. For this example, suppose we want to test all the modules under sage/crypto/. We can use a syntax similar to that shown above to achieve this:

[jdemeyer@localhost sage]$ ./sage -t src/sage/crypto
Running doctests with ID 2012-07-03-03-45-40-7f837dcf.
Doctesting 24 files.
sage -t src/sage/crypto/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/boolean_function.pyx
    [252 tests, 4.4 s]
sage -t src/sage/crypto/cipher.py
    [10 tests, 0.0 s]
sage -t src/sage/crypto/classical.py
    [718 tests, 11.3 s]
sage -t src/sage/crypto/classical_cipher.py
    [130 tests, 0.5 s]
sage -t src/sage/crypto/cryptosystem.py
    [82 tests, 0.1 s]
sage -t src/sage/crypto/lattice.py
    [1 tests, 0.0 s]
sage -t src/sage/crypto/lfsr.py
    [31 tests, 0.1 s]
sage -t src/sage/crypto/stream.py
    [17 tests, 0.1 s]
sage -t src/sage/crypto/stream_cipher.py
    [114 tests, 0.2 s]
sage -t src/sage/crypto/util.py
    [122 tests, 0.2 s]
sage -t src/sage/crypto/block_cipher/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/block_cipher/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/block_cipher/miniaes.py
    [430 tests, 1.3 s]
sage -t src/sage/crypto/block_cipher/sdes.py
    [290 tests, 0.9 s]
sage -t src/sage/crypto/mq/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/mq/mpolynomialsystem.py
    [320 tests, 9.1 s]
sage -t src/sage/crypto/mq/mpolynomialsystemgenerator.py
    [42 tests, 0.1 s]
sage -t src/sage/crypto/sbox.pyx
    [124 tests, 0.8 s]
sage -t src/sage/crypto/mq/sr.py
    [435 tests, 5.5 s]
sage -t src/sage/crypto/public_key/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/public_key/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/public_key/blum_goldwasser.py
    [135 tests, 0.2 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 38.1 seconds
    cpu time: 29.8 seconds
    cumulative wall time: 35.1 seconds

Now we do the same thing, but this time we also use the optional argument --long:

[jdemeyer@localhost sage]$ ./sage -t --long src/sage/crypto/
Running doctests with ID 2012-07-03-03-48-11-c16721e6.
Doctesting 24 files.
sage -t --long src/sage/crypto/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/boolean_function.pyx
    [252 tests, 4.2 s]
sage -t --long src/sage/crypto/cipher.py
    [10 tests, 0.0 s]
sage -t --long src/sage/crypto/classical.py
    [718 tests, 10.3 s]
sage -t --long src/sage/crypto/classical_cipher.py
    [130 tests, 0.5 s]
sage -t --long src/sage/crypto/cryptosystem.py
    [82 tests, 0.1 s]
sage -t --long src/sage/crypto/lattice.py
    [1 tests, 0.0 s]
sage -t --long src/sage/crypto/lfsr.py
    [31 tests, 0.1 s]
sage -t --long src/sage/crypto/stream.py
    [17 tests, 0.1 s]
sage -t --long src/sage/crypto/stream_cipher.py
    [114 tests, 0.2 s]
sage -t --long src/sage/crypto/util.py
    [122 tests, 0.2 s]
sage -t --long src/sage/crypto/block_cipher/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/block_cipher/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/block_cipher/miniaes.py
    [430 tests, 1.1 s]
sage -t --long src/sage/crypto/block_cipher/sdes.py
    [290 tests, 0.7 s]
sage -t --long src/sage/crypto/mq/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/mq/mpolynomialsystem.py
    [320 tests, 7.5 s]
sage -t --long src/sage/crypto/mq/mpolynomialsystemgenerator.py
    [42 tests, 0.1 s]
sage -t --long src/sage/crypto/sbox.pyx
    [124 tests, 0.7 s]
sage -t --long src/sage/crypto/mq/sr.py
    [437 tests, 82.4 s]
sage -t --long src/sage/crypto/public_key/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/public_key/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/public_key/blum_goldwasser.py
    [135 tests, 0.2 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 111.8 seconds
    cpu time: 106.1 seconds
    cumulative wall time: 108.5 seconds

Notice the time difference between the first set of tests and the second set, which uses the optional argument --long. Many tests in the Sage library are flagged with # long time because these are known to take a long time to run through. Without using the optional --long argument, the module sage/crypto/mq/sr.py took about five seconds. With this optional argument, it required 82 seconds to run through all tests in that module. Here is a snippet of a function in the module sage/crypto/mq/sr.py with a doctest that has been flagged as taking a long time:

def test_consistency(max_n=2, **kwargs):
    r"""
    Test all combinations of ``r``, ``c``, ``e`` and ``n`` in ``(1,
    2)`` for consistency of random encryptions and their polynomial
    systems. `\GF{2}` and `\GF{2^e}` systems are tested. This test takes
    a while.

    INPUT:

    - ``max_n`` -- maximal number of rounds to consider (default: 2)
    - ``kwargs`` -- are passed to the SR constructor

    TESTS:

    The following test called with ``max_n`` = 2 requires a LOT of RAM
    (much more than 2GB).  Since this might cause the doctest to fail
    on machines with "only" 2GB of RAM, we test ``max_n`` = 1, which
    has a more reasonable memory usage. ::

        sage: from sage.crypto.mq.sr import test_consistency
        sage: test_consistency(1)  # long time (80s on sage.math, 2011)
        True
    """

Now we doctest the same directory in parallel using 4 threads:

[jdemeyer@localhost sage]$ ./sage -tp 4 src/sage/crypto/
Running doctests with ID 2012-07-07-00-11-55-9b17765e.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 24 files using 4 threads.
sage -t src/sage/crypto/boolean_function.pyx
    [252 tests, 3.8 s]
sage -t src/sage/crypto/block_cipher/miniaes.py
    [429 tests, 1.1 s]
sage -t src/sage/crypto/mq/sr.py
    [432 tests, 5.7 s]
sage -t src/sage/crypto/sbox.pyx
    [123 tests, 0.8 s]
sage -t src/sage/crypto/block_cipher/sdes.py
    [289 tests, 0.6 s]
sage -t src/sage/crypto/classical_cipher.py
    [123 tests, 0.4 s]
sage -t src/sage/crypto/stream_cipher.py
    [113 tests, 0.1 s]
sage -t src/sage/crypto/public_key/blum_goldwasser.py
    [134 tests, 0.1 s]
sage -t src/sage/crypto/lfsr.py
    [30 tests, 0.1 s]
sage -t src/sage/crypto/util.py
    [121 tests, 0.1 s]
sage -t src/sage/crypto/cryptosystem.py
    [79 tests, 0.0 s]
sage -t src/sage/crypto/stream.py
    [12 tests, 0.0 s]
sage -t src/sage/crypto/mq/mpolynomialsystemgenerator.py
    [40 tests, 0.0 s]
sage -t src/sage/crypto/cipher.py
    [3 tests, 0.0 s]
sage -t src/sage/crypto/lattice.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/block_cipher/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/public_key/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/public_key/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/mq/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/block_cipher/all.py
    [0 tests, 0.0 s]
sage -t src/sage/crypto/mq/mpolynomialsystem.py
    [318 tests, 8.4 s]
sage -t src/sage/crypto/classical.py
    [717 tests, 10.4 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 12.9 seconds
    cpu time: 30.5 seconds
    cumulative wall time: 31.7 seconds
[jdemeyer@localhost sage]$ ./sage -tp 4 --long src/sage/crypto/
Running doctests with ID 2012-07-07-00-13-04-d71f3cd4.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 24 files using 4 threads.
sage -t --long src/sage/crypto/boolean_function.pyx
    [252 tests, 3.7 s]
sage -t --long src/sage/crypto/block_cipher/miniaes.py
    [429 tests, 1.0 s]
sage -t --long src/sage/crypto/sbox.pyx
    [123 tests, 0.8 s]
sage -t --long src/sage/crypto/block_cipher/sdes.py
    [289 tests, 0.6 s]
sage -t --long src/sage/crypto/classical_cipher.py
    [123 tests, 0.4 s]
sage -t --long src/sage/crypto/util.py
    [121 tests, 0.1 s]
sage -t --long src/sage/crypto/stream_cipher.py
    [113 tests, 0.1 s]
sage -t --long src/sage/crypto/public_key/blum_goldwasser.py
    [134 tests, 0.1 s]
sage -t --long src/sage/crypto/lfsr.py
    [30 tests, 0.0 s]
sage -t --long src/sage/crypto/cryptosystem.py
    [79 tests, 0.0 s]
sage -t --long src/sage/crypto/stream.py
    [12 tests, 0.0 s]
sage -t --long src/sage/crypto/mq/mpolynomialsystemgenerator.py
    [40 tests, 0.0 s]
sage -t --long src/sage/crypto/cipher.py
    [3 tests, 0.0 s]
sage -t --long src/sage/crypto/lattice.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/block_cipher/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/public_key/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/mq/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/block_cipher/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/__init__.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/public_key/all.py
    [0 tests, 0.0 s]
sage -t --long src/sage/crypto/mq/mpolynomialsystem.py
    [318 tests, 9.0 s]
sage -t --long src/sage/crypto/classical.py
    [717 tests, 10.5 s]
sage -t --long src/sage/crypto/mq/sr.py
    [434 tests, 88.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 90.4 seconds
    cpu time: 113.4 seconds
    cumulative wall time: 114.5 seconds

As the number of threads increases, the total testing time decreases.

Parallel testing the whole Sage library

The main Sage library resides in the directory SAGE_ROOT/src/. We can use the syntax described above to doctest the main library using multiple threads. When doing release management or patching the main Sage library, a release manager would parallel test the library using 10 threads with the following command:

[jdemeyer@localhost sage]$ ./sage -tp 10 --long src/

Another way is run make ptestlong, which builds Sage (if necessary), builds the Sage documentation (if necessary), and then runs parallel doctests. This determines the number of threads by reading the environment variable MAKE: if it is set to make -j12, then use 12 threads. If MAKE is not set, then by default it uses the number of CPU cores (as determined by the Python function multiprocessing.cpu_count()) with a minimum of 2 and a maximum of 8. (When this runs under the control of the GNU make jobserver, then Sage will request as most this number of job slots.)

In any case, this will test the Sage library with multiple threads:

[jdemeyer@localhost sage]$ make ptestlong

Any of the following commands would also doctest the Sage library or one of its clones:

make test
make check
make testlong
make ptest
make ptestlong

The differences are:

  • make test and make check — These two commands run the same set of tests. First the Sage standard documentation is tested, i.e. the documentation that resides in

    Finally, the commands doctest the Sage library. For more details on these command, see the file SAGE_ROOT/Makefile.

  • make testlong — This command doctests the standard documentation:

    and then the Sage library. Doctesting is run with the optional argument --long. See the file SAGE_ROOT/Makefile for further details.

  • make ptest — Similar to the commands make test and make check. However, doctesting is run with the number of threads as described above for make ptestlong.

  • make ptestlong — Similar to the command make ptest, but using the optional argument --long for doctesting.

The underlying command for running these tests is sage -t --all. For example, make ptestlong executes the command sage -t -p --all --long --logfile=logs/ptestlong.log. So if you want to add extra flags when you run these tests, for example --verbose, you can execute sage -t -p --all --long --verbose --logfile=path/to/logfile. Some of the extra testing options are discussed here; run sage -t -h for a complete list.

Beyond the Sage library

Doctesting also works fine for files not in the Sage library. For example, suppose we have a Python script called my_python_script.py:

[mvngu@localhost sage]$ cat my_python_script.py
from sage.all_cmdline import *   # import sage library

def square(n):
    """
    Return the square of n.

    EXAMPLES::

        sage: square(2)
        4
    """
    return n**2

Then we can doctest it just as with Sage library files:

[mvngu@localhost sage]$ ./sage -t my_python_script.py
Running doctests with ID 2012-07-07-00-17-56-d056f7c0.
Doctesting 1 file.
sage -t my_python_script.py
    [1 test, 0.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 2.2 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

Doctesting can also be performed on Sage scripts. Say we have a Sage script called my_sage_script.sage with the following content:

[mvngu@localhost sage]$ cat my_sage_script.sage
def cube(n):
    r"""
    Return the cube of n.

    EXAMPLES::

        sage: cube(2)
        8
    """
    return n**3

Then we can doctest it just as for Python files:

[mvngu@localhost sage]$ ./sage -t my_sage_script.sage
Running doctests with ID 2012-07-07-00-20-06-82ee728c.
Doctesting 1 file.
sage -t my_sage_script.sage
    [1 test, 0.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 2.5 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

Alternatively, we can preparse it to convert it to a Python script, and then doctest that:

[mvngu@localhost sage]$ ./sage --preparse my_sage_script.sage
[mvngu@localhost sage]$ cat my_sage_script.sage.py
# This file was *autogenerated* from the file my_sage_script.sage.
from sage.all_cmdline import *   # import sage library
_sage_const_3 = Integer(3)
def cube(n):
    r"""
    Return the cube of n.

    EXAMPLES::

        sage: cube(2)
        8
    """
    return n**_sage_const_3
[mvngu@localhost sage]$ ./sage -t my_sage_script.sage.py
Running doctests with ID 2012-07-07-00-26-46-2bb00911.
Doctesting 1 file.
sage -t my_sage_script.sage.py
    [2 tests, 0.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 2.3 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

Doctesting from within Sage

You can run doctests from within Sage, which can be useful since you don’t have to wait for Sage to start. Use the run_doctests function in the global namespace, passing it either a string or a module:

sage: run_doctests(sage.combinat.affine_permutation)
Running doctests with ID 2018-02-07-13-23-13-89fe17b1.
Git branch: develop
Using --optional=sagemath_doc_html,sage
Doctesting 1 file.
sage -t /opt/sage/sage_stable/src/sage/combinat/affine_permutation.py
    [338 tests, 4.32 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 4.4 seconds
    cpu time: 3.6 seconds
    cumulative wall time: 4.3 seconds

Optional arguments

Run long doctests

Ideally, doctests should not take any noticeable amount of time. If you really need longer-running doctests (anything beyond about one second) then you should mark them as:

sage: my_long_test()  # long time

Even then, long doctests should ideally complete in 5 seconds or less. We know that you (the author) want to show off the capabilities of your code, but this is not the place to do so. Long-running tests will sooner or later hurt our ability to run the testsuite. Really, doctests should be as fast as possible while providing coverage for the code.

Use the --long flag to run doctests that have been marked with the comment # long time. These tests are normally skipped in order to reduce the time spent running tests:

[roed@localhost sage]$ ./sage -t src/sage/rings/tests.py
Running doctests with ID 2012-06-21-16-00-13-40835825.
Doctesting 1 file.
sage -t tests.py
    [18 tests, 1.1 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 2.9 seconds
    cpu time: 0.9 seconds
    cumulative wall time: 1.1 seconds

In order to run the long tests as well, do the following:

[roed@localhost sage]$ ./sage -t --long src/sage/rings/tests.py
Running doctests with ID 2012-06-21-16-02-05-d13a9a24.
Doctesting 1 file.
sage -t tests.py
    [20 tests, 34.7 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 46.5 seconds
    cpu time: 25.2 seconds
    cumulative wall time: 34.7 seconds

To find tests that take longer than a specified amount of CPU time, use the --warn-long flag. Without any options, it will cause a warning to be printed if any tests take longer than one cpu-second. Note that this is a warning, not an error:

[roed@localhost sage]$ ./sage -t --warn-long src/sage/rings/factorint.pyx
Running doctests with ID 2012-07-14-03-27-03-2c952ac1.
Doctesting 1 file.
sage -t --warn-long src/sage/rings/factorint.pyx
**********************************************************************
File "src/sage/rings/factorint.pyx", line 125, in sage.rings.factorint.base_exponent
Failed example:
    base_exponent(-4)
Test ran for 4.09 cpu seconds
**********************************************************************
File "src/sage/rings/factorint.pyx", line 153, in sage.rings.factorint.factor_aurifeuillian
Failed example:
    fa(2^6+1)
Test ran for 2.22 cpu seconds
**********************************************************************
File "src/sage/rings/factorint.pyx", line 155, in sage.rings.factorint.factor_aurifeuillian
Failed example:
    fa(2^58+1)
Test ran for 2.22 cpu seconds
**********************************************************************
File "src/sage/rings/factorint.pyx", line 163, in sage.rings.factorint.factor_aurifeuillian
Failed example:
    fa(2^4+1)
Test ran for 2.25 cpu seconds
**********************************************************************
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 16.1 seconds
    cpu time: 9.7 seconds
    cumulative wall time: 10.9 seconds

You can also pass in an explicit amount of time:

[roed@localhost sage]$ ./sage -t --long --warn-long 2.0 src/sage/rings/tests.py
Running doctests with ID 2012-07-14-03-30-13-c9164c9d.
Doctesting 1 file.
sage -t --long --warn-long 2.0 tests.py
**********************************************************************
File "tests.py", line 240, in sage.rings.tests.test_random_elements
Failed example:
    sage.rings.tests.test_random_elements(trials=1000)  # long time (5 seconds)
Test ran for 13.36 cpu seconds
**********************************************************************
File "tests.py", line 283, in sage.rings.tests.test_random_arith
Failed example:
    sage.rings.tests.test_random_arith(trials=1000)   # long time (5 seconds?)
Test ran for 12.42 cpu seconds
**********************************************************************
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 27.6 seconds
    cpu time: 24.8 seconds
    cumulative wall time: 26.3 seconds

Finally, you can disable any warnings about long tests with --warn-long 0.

Doctests start from a random seed:

[kliem@localhost sage]$ ./sage -t src/sage/doctest/tests/random_seed.rst
Running doctests with ID 2020-06-23-23-22-59-49f37a55.
...
Doctesting 1 file.
sage -t --warn-long 89.5 --random-seed=112986622569797306072457879734474628454 src/sage/doctest/tests/random_seed.rst
**********************************************************************
File "src/sage/doctest/tests/random_seed.rst", line 3, in sage.doctest.tests.random_seed
Failed example:
    randint(5, 10)
Expected:
    9
Got:
    8
**********************************************************************
1 item had failures:
   1 of   2 in sage.doctest.tests.random_seed
    [1 test, 1 failure, 0.00 s]
----------------------------------------------------------------------
sage -t --warn-long 89.5 --random-seed=112986622569797306072457879734474628454 src/sage/doctest/tests/random_seed.rst  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.0 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

This seed can be set explicitly to reproduce possible failures:

[kliem@localhost sage]$ ./sage -t --warn-long 89.5                              \
                          --random-seed=112986622569797306072457879734474628454 \
                          src/sage/doctest/tests/random_seed.rst
Running doctests with ID 2020-06-23-23-24-28-14a52269.
...
Doctesting 1 file.
sage -t --warn-long 89.5 --random-seed=112986622569797306072457879734474628454 src/sage/doctest/tests/random_seed.rst
**********************************************************************
File "src/sage/doctest/tests/random_seed.rst", line 3, in sage.doctest.tests.random_seed
Failed example:
    randint(5, 10)
Expected:
    9
Got:
    8
**********************************************************************
1 item had failures:
   1 of   2 in sage.doctest.tests.random_seed
    [1 test, 1 failure, 0.00 s]
----------------------------------------------------------------------
sage -t --warn-long 89.5 --random-seed=112986622569797306072457879734474628454 src/sage/doctest/tests/random_seed.rst  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.0 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

It can also be set explicitly using the environment variable SAGE_DOCTEST_RANDOM_SEED.

Run optional doctests

You can run tests that require optional packages by using the --optional flag. Obviously, you need to have installed the necessary optional packages in order for these tests to succeed.

By default, Sage only runs doctests that are not marked with the optional tag. This is equivalent to running

[roed@localhost sage]$ ./sage -t --optional=sagemath_doc_html,sage \
                              src/sage/rings/real_mpfr.pyx
Running doctests with ID 2012-06-21-16-18-30-a368a200.
Doctesting 1 file.
sage -t src/sage/rings/real_mpfr.pyx
    [819 tests, 7.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 8.4 seconds
    cpu time: 4.1 seconds
    cumulative wall time: 7.0 seconds

If you want to also run tests that require magma, you can do the following:

[roed@localhost sage]$ ./sage -t --optional=sagemath_doc_html,sage,magma \
                              src/sage/rings/real_mpfr.pyx
Running doctests with ID 2012-06-21-16-18-30-a00a7319
Doctesting 1 file.
sage -t src/sage/rings/real_mpfr.pyx
    [823 tests, 8.4 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 9.6 seconds
    cpu time: 4.0 seconds
    cumulative wall time: 8.4 seconds

In order to just run the tests that are marked as requiring magma, omit sage and sagemath_doc_html:

[roed@localhost sage]$ ./sage -t --optional=magma src/sage/rings/real_mpfr.pyx
Running doctests with ID 2012-06-21-16-18-33-a2bc1fdf
Doctesting 1 file.
sage -t src/sage/rings/real_mpfr.pyx
    [4 tests, 2.0 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 3.2 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 2.0 seconds

If you want Sage to detect external software or other capabilities (such as magma, latex, internet) automatically and run all of the relevant tests, then add external:

[roed@localhost sage]$ ./sage -t --optional=external src/sage/rings/real_mpfr.pyx
Running doctests with ID 2016-03-16-14-10-21-af2ebb67.
Using --optional=external
External software to be detected: cplex,gurobi,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,scilab
Doctesting 1 file.
sage -t --warn-long 28.0 src/sage/rings/real_mpfr.pyx
    [5 tests, 0.04 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 0.5 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds
External software detected for doctesting: magma

To run all tests, regardless of whether they are marked optional, pass all as the optional tag:

[roed@localhost sage]$ ./sage -t --optional=all src/sage/rings/real_mpfr.pyx
Running doctests with ID 2012-06-21-16-31-18-8c097f55
Doctesting 1 file.
sage -t src/sage/rings/real_mpfr.pyx
    [865 tests, 11.2 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 12.8 seconds
    cpu time: 4.7 seconds
    cumulative wall time: 11.2 seconds

Running doctests in parallel

If you’re testing many files, you can get big speedups by using more than one thread. To run doctests in parallel use the --nthreads flag (-p is a shortened version). Pass in the number of threads you would like to use (by default Sage just uses 1):

[roed@localhost sage]$ ./sage -tp 2 src/sage/doctest/
Running doctests with ID 2012-06-22-19-09-25-a3afdb8c.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 8 files using 2 threads.
sage -t src/sage/doctest/control.py
    [114 tests, 4.6 s]
sage -t src/sage/doctest/util.py
    [114 tests, 0.6 s]
sage -t src/sage/doctest/parsing.py
    [187 tests, 0.5 s]
sage -t src/sage/doctest/sources.py
    [128 tests, 0.1 s]
sage -t src/sage/doctest/reporting.py
    [53 tests, 0.1 s]
sage -t src/sage/doctest/all.py
    [0 tests, 0.0 s]
sage -t src/sage/doctest/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/doctest/forker.py
    [322 tests, 15.5 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 17.0 seconds
    cpu time: 4.2 seconds
    cumulative wall time: 21.5 seconds

Doctesting all of Sage

To doctest the whole Sage library use the --all flag (-a for short). In addition to testing the code in Sage’s Python and Cython files, this command will run the tests defined in Sage’s documentation as well as testing the Sage notebook:

[roed@localhost sage]$ ./sage -t -a
Running doctests with ID 2012-06-22-19-10-27-e26fce6d.
Doctesting entire Sage library.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 2020 files.
sage -t /Users/roed/sage/src/sage/plot/plot.py
    [304 tests, 69.0 s]
...

Debugging tools

Sometimes doctests fail (that’s why we run them after all). There are various flags to help when something goes wrong. If a doctest produces a Python error, then normally tests continue after reporting that an error occurred. If you use the flag --debug (-d for short) then you will drop into an interactive Python debugger whenever a Python exception occurs. As an example, I modified sage.schemes.elliptic_curves.constructor to produce an error:

[roed@localhost sage]$ ./sage -t --debug \
                             src/sage/schemes/elliptic_curves/constructor.py
Running doctests with ID 2012-06-23-12-09-04-b6352629.
Doctesting 1 file.
**********************************************************************
File "sage.schemes.elliptic_curves.constructor", line 4, in sage.schemes.elliptic_curves.constructor
Failed example:
    EllipticCurve([0,0])
Exception raised:
    Traceback (most recent call last):
      File ".../site-packages/sage/doctest/forker.py", line 573, in _run
        self.execute(example, compiled, test.globs)
      File ".../site-packages/sage/doctest/forker.py", line 835, in execute
        exec compiled in globs
      File "<doctest sage.schemes.elliptic_curves.constructor[0]>", line 1, in <module>
        EllipticCurve([Integer(0),Integer(0)])
      File ".../site-packages/sage/schemes/elliptic_curves/constructor.py", line 346, in EllipticCurve
        return ell_rational_field.EllipticCurve_rational_field(x, y)
      File ".../site-packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 216, in __init__
        EllipticCurve_number_field.__init__(self, Q, ainvs)
      File ".../site-packages/sage/schemes/elliptic_curves/ell_number_field.py", line 159, in __init__
        EllipticCurve_field.__init__(self, [field(x) for x in ainvs])
      File ".../site-packages/sage/schemes/elliptic_curves/ell_generic.py", line 156, in __init__
        "Invariants %s define a singular curve."%ainvs
    ArithmeticError: Invariants [0, 0, 0, 0, 0] define a singular curve.
> .../site-packages/sage/schemes/elliptic_curves/ell_generic.py(156)__init__()
-> "Invariants %s define a singular curve."%ainvs
(Pdb) l
151                 if len(ainvs) == 2:
152                     ainvs = [K(0),K(0),K(0)] + ainvs
153                 self.__ainvs = tuple(ainvs)
154                 if self.discriminant() == 0:
155                     raise ArithmeticError(
156  ->                     "Invariants %s define a singular curve."%ainvs)
157                 PP = projective_space.ProjectiveSpace(2, K, names='xyz');
158                 x, y, z = PP.coordinate_ring().gens()
159                 a1, a2, a3, a4, a6 = ainvs
160                 f = y**2*z + (a1*x + a3*z)*y*z \
161                     - (x**3 + a2*x**2*z + a4*x*z**2 + a6*z**3)
(Pdb) p ainvs
[0, 0, 0, 0, 0]
(Pdb) quit
**********************************************************************
1 items had failures:
   1 of   1 in sage.schemes.elliptic_curves.constructor
***Test Failed*** 1 failures.
sage -t src/sage/schemes/elliptic_curves/constructor.py
    [64 tests, 89.2 s]
------------------------------------------------------------------------
sage -t src/sage/schemes/elliptic_curves/constructor.py # 1 doctest failed
------------------------------------------------------------------------
Total time for all tests: 90.4 seconds
    cpu time: 4.5 seconds
    cumulative wall time: 89.2 seconds

Sometimes an error might be so severe that it causes Sage to segfault or hang. In such a situation you have a number of options. The doctest framework will print out the output so far, so that at least you know what test caused the problem (if you want this output to appear in real time use the --verbose flag). To have doctests run under the control of gdb, use the --gdb flag:

[roed@localhost sage]$ ./sage -t --gdb \
                              src/sage/schemes/elliptic_curves/constructor.py
exec gdb --eval-commands="run" --args /home/roed/sage/local/var/lib/sage/venv-python3.9/bin/python3 sage-runtests --serial --timeout=0 --stats-path=/home/roed/.sage/timings2.json --optional=pip,sage,sage_spkg src/sage/schemes/elliptic_curves/constructor.py
GNU gdb 6.8-debian
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu"...
[Thread debugging using libthread_db enabled]
[New Thread 0x7f10f85566e0 (LWP 6534)]
Running doctests with ID 2012-07-07-00-43-36-b1b735e7.
Doctesting 1 file.
sage -t src/sage/schemes/elliptic_curves/constructor.py
    [67 tests, 5.8 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 15.7 seconds
    cpu time: 4.4 seconds
    cumulative wall time: 5.8 seconds

Program exited normally.
(gdb) quit

Sage also includes valgrind, and you can run doctests under various valgrind tools to track down memory issues: the relevant flags are --valgrind (or --memcheck), --massif, --cachegrind and --omega. See http://wiki.sagemath.org/ValgrindingSage for more details.

Once you’re done fixing whatever problems where revealed by the doctests, you can rerun just those files that failed their most recent test by using the --failed flag (-f for short):

[roed@localhost sage]$ ./sage -t -fa
Running doctests with ID 2012-07-07-00-45-35-d8b5a408.
Doctesting entire Sage library.
Only doctesting files that failed last test.
No files to doctest

Miscellaneous options

There are various other options that change the behavior of Sage’s doctesting code.

Show only first failure

The first failure in a file often causes a cascade of others, as NameErrors arise from variables that weren’t defined and tests fail because old values of variables are used. To only see the first failure in each doctest block use the --initial flag (-i for short).

Show skipped optional tests

To print a summary at the end of each file with the number of optional tests skipped, use the --show-skipped flag:

[roed@localhost sage]$ ./sage -t --show-skipped \
                              src/sage/rings/finite_rings/integer_mod.pyx
Running doctests with ID 2013-03-14-15-32-05-8136f5e3.
Doctesting 1 file.
sage -t sage/rings/finite_rings/integer_mod.pyx
    2 axiom tests not run
    1 cunningham test not run
    2 fricas tests not run
    1 long test not run
    3 magma tests not run
    [440 tests, 4.0 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 4.3 seconds
    cpu time: 2.4 seconds
    cumulative wall time: 4.0 seconds

Running tests with iterations

Sometimes tests fail intermittently. There are two options that allow you to run tests repeatedly in an attempt to search for Heisenbugs. The flag --global-iterations takes an integer and runs the whole set of tests that many times serially:

[roed@localhost sage]$ ./sage -t --global-iterations 2 src/sage/sandpiles
Running doctests with ID 2012-07-07-00-59-28-e7048ad9.
Doctesting 3 files (2 global iterations).
sage -t src/sage/sandpiles/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/all.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/sandpile.py
    [711 tests, 14.7 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 17.6 seconds
    cpu time: 13.2 seconds
    cumulative wall time: 14.7 seconds
sage -t src/sage/sandpiles/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/all.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/sandpile.py
    [711 tests, 13.8 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 14.3 seconds
    cpu time: 26.4 seconds
    cumulative wall time: 28.5 seconds

You can also iterate in a different order: the --file-iterations flag runs the tests in each file N times before proceeding:

[roed@localhost sage]$ ./sage -t --file-iterations 2 src/sage/sandpiles
Running doctests with ID 2012-07-07-01-01-43-8f954206.
Doctesting 3 files (2 file iterations).
sage -t src/sage/sandpiles/__init__.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/all.py
    [0 tests, 0.0 s]
sage -t src/sage/sandpiles/sandpile.py
    [1422 tests, 13.3 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 29.6 seconds
    cpu time: 12.7 seconds
    cumulative wall time: 13.3 seconds

Note that the reported results are the average time for all tests in that file to finish. If a failure in a file occurs, then the failure is reported and testing proceeds with the next file.

Using a different timeout

On a slow machine the default timeout of 5 minutes may not be enough for the slowest files. Use the --timeout flag (-T for short) to set it to something else:

[roed@localhost sage]$ ./sage -tp 2 --all --timeout 1
Running doctests with ID 2012-07-07-01-09-37-deb1ab83.
Doctesting entire Sage library.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 2067 files using 2 threads.
sage -t src/sage/schemes/elliptic_curves/ell_rational_field.py
    Timed out!
...

Using absolute paths

By default filenames are printed using relative paths. To use absolute paths instead pass in the --abspath flag:

[roed@localhost sage]$ ./sage -t --abspath src/sage/doctest/control.py
Running doctests with ID 2012-07-07-01-13-03-a023e212.
Doctesting 1 file.
sage -t /home/roed/sage/src/sage/doctest/control.py
    [133 tests, 4.7 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 7.1 seconds
    cpu time: 0.2 seconds
    cumulative wall time: 4.7 seconds

Testing changed files

If you are working on some files in the Sage library it can be convenient to test only the files that have changed. To do so use the --new flag, which tests files that have been modified or added since the last commit:

[roed@localhost sage]$ ./sage -t --new
Running doctests with ID 2012-07-07-01-15-52-645620ee.
Doctesting files changed since last git commit.
Doctesting 1 file.
sage -t src/sage/doctest/control.py
    [133 tests, 3.7 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 3.8 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 3.7 seconds

Running tests in a random order

By default, tests are run in the order in which they appear in the file. To run tests in a random order (which can reveal subtle bugs), use the --randorder flag and pass in a random seed:

[roed@localhost sage]$ ./sage -t --new --randorder 127
Running doctests with ID 2012-07-07-01-19-06-97c8484e.
Doctesting files changed since last git commit.
Doctesting 1 file.
sage -t src/sage/doctest/control.py
    [133 tests, 3.6 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 3.7 seconds
    cpu time: 0.2 seconds
    cumulative wall time: 3.6 seconds

Note that even with this option, the tests within a given doctest block are still run in order.

Testing external files

When testing a file which is not part of a package (which is not in a directory containing an __init__.py file), the testing code loads the globals from that file into the namespace before running tests. To disable this behaviour (and require imports to be explicitly specified), use the --force-lib option.

Auxiliary files

To specify a logfile (rather than use the default which is created for sage -t --all), use the --logfile flag:

[roed@localhost sage]$ ./sage -t --logfile test1.log src/sage/doctest/control.py
Running doctests with ID 2012-07-07-01-25-49-e7c0e52d.
Doctesting 1 file.
sage -t src/sage/doctest/control.py
    [133 tests, 4.3 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 6.7 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 4.3 seconds
[roed@localhost sage]$ cat test1.log
Running doctests with ID 2012-07-07-01-25-49-e7c0e52d.
Doctesting 1 file.
sage -t src/sage/doctest/control.py
    [133 tests, 4.3 s]
------------------------------------------------------------------------
All tests passed!
------------------------------------------------------------------------
Total time for all tests: 6.7 seconds
    cpu time: 0.1 seconds
    cumulative wall time: 4.3 seconds

To give a json file storing the timings and pass/fail status for each file, use the --stats-path flag; the default location of this file is ~/.sage/timings2.json. The doctester reads it if it exists, for the purpose of sorting the files so that slower tests are run first (and thus multiple processes are utilized most efficiently):

[roed@localhost sage]$ ./sage -tp 2 --stats-path ~/.sage/timings2.json --all
Running doctests with ID 2012-07-07-01-28-34-2df4251d.
Doctesting entire Sage library.
Sorting sources by runtime so that slower doctests are run first....
Doctesting 2067 files using 2 threads.
...

At the end of the doctest run, Sage updates the json file if it exists or creates a new one.

The recorded pass/fail status of the files can be used for running only those files that failed their most recent test by using the --failed flag (-f for short).

Using the option --baseline-stats-path known-test-failures.json, it is possible to distinguish files with known doctest failures from new failures. The file known-test-failures.json should be prepared in the same format as timings2.json.

Source files marked as failed there will be marked as “[failed in baseline]” failures in the doctest report; and if there are only baseline failures, no new failures, then sage -t will exit with status code 0 (success).

Options for testing in virtual environments

The distribution packages of the modularized Sage library can be tested in virtual environments. Sage has infrastructure to create such virtual environments using tox, which is explained in detail in Testing distribution packages. Our examples in this section refer to this setting, but it applies the same to any user-created virtual environments.

The virtual environments, set up in directories such as pkgs/sagemath-standard/.tox/sagepython-sagewheels-nopypi-norequirements contain installations of built (non-editable) wheels.

To test all modules of Sage that are installed in a virtual environment, use the option --installed (instead of --all):

[mkoeppe@localhost sage]$ pkgs/sagemath-standard/.tox/sagepython-.../sage -t   \
                            -p4 --installed

This tests against the doctests as they appear in the installed copies of the files (in site-packages/sage/...). Note that these installed copies should never be edited, as they can be overwritten without warning.

When testing a modularized distribution package other than sagemath-standard, the top-level module sage.all is not available. Use the option --environment to select an appropriate top-level module:

[mkoeppe@localhost sage]$ pkgs/sagemath-categories/.tox/sagepython-.../sage -t \
                            -p4 --environment sage.all__sagemath_categories    \
                            --installed

To test the installed modules against the doctests as they appear in the source tree (src/sage/...):

[mkoeppe@localhost sage]$ pkgs/sagemath-categories/.tox/sagepython-.../sage -t \
                            -p4 --environment sage.all__sagemath_categories    \
                            src/sage/structure

Note that testing all doctests as they appear in the source tree does not make sense because many of the source files may not be installed in the virtual environment. Use the option --if-installed to skip the source files of all Python/Cython modules that are not installed in the virtual environment:

[mkoeppe@localhost sage]$ pkgs/sagemath-categories/.tox/sagepython-.../sage -t \
                            -p4 --environment sage.all__sagemath_categories    \
                            --if-installed src/sage/schemes

This option can also be combined with --all:

[mkoeppe@localhost sage]$ pkgs/sagemath-categories/.tox/sagepython-.../sage -t \
                            -p4 --environment sage.all__sagemath_categories    \
                            --if-installed --all

The doctest fixer

Sage provides a development tool that assists with updating doctests.

Updating doctest outputs

By default, ./sage --fixdoctests runs the doctester and replaces the expected outputs of all examples by the actual outputs from the current version of Sage:

[mkoeppe@localhost sage]$ ./sage --fixdoctests \
                            --overwrite src/sage/arith/weird.py

For example, when applied to this Python file:

| r"""
| ...
|
| EXAMPLES::
|
|     sage: 2 + 2
|     5
|     sage: factor("91")
|     "7" * "13"
| ...

the doctest fixer edits the file as follows:

| r"""
| ...
|
| EXAMPLES::
|
|     sage: 2 + 2
|     4
|     sage: factor("91")
|     Traceback (most recent call last):
|     ...
|     TypeError: unable to factor '91'
| ...

As this command edits the source file, it may be a good practice to first use git commit to save any changes made in the file.

After running the doctest fixer, it is a good idea to use git diff to check all edits that the automated tool made.

An alternative to this workflow is to use the option --keep-both. When expected and actual output of an example differ, it duplicates the example, marking the two copies # optional - EXPECTED and # optional - GOT. (Thus, when re-running the doctester, neither of the two copies is run; this makes ./sage --fixdoctests idempotent.)

When exceptions are expected by an example, it is standard practice to abbreviate the tracebacks using .... The doctest fixer uses this abbreviation automatically when formatting the actual output, as shown in the above example. To disable it so that the details of the exception can be inspected, use the option --full-tracebacks. This is particularly useful in combination with --keep-both:

[mkoeppe@localhost sage]$ ./sage --fixdoctests --keep-both --full-tracebacks \
                            --overwrite src/sage/arith/weird.py

This will give the following result on the above example:

| r"""
| ...
|
| EXAMPLES::
|
|     sage: 2 + 2                                 # optional - EXPECTED
|     5
|     sage: 2 + 2                                 # optional - GOT
|     4
|     sage: factor("91")                          # optional - EXPECTED
|     "7" * "13"
|     sage: factor("91")                          # optional - GOT
|     Traceback (most recent call last):
|     ...
|     File "<doctest...>", line 1, in <module>
|     factor("91")
|     File ".../src/sage/arith/misc.py", line 2680, in factor
|     raise TypeError("unable to factor {!r}".format(n))
|     TypeError: unable to factor '91'
| ...
| """

To make sure that all doctests are updated, you may have to use the option --long:

[mkoeppe@localhost sage]$ ./sage --fixdoctests --long \
                            --overwrite src/sage/arith/weird.py

If you are not comfortable with allowing this tool to edit your source files, you can use the option --no-overwrite, which will create a new file with the extension .fixed instead of overwriting the source file:

[mkoeppe@localhost sage]$ ./sage --fixdoctests \
                            --no-overwrite src/sage/arith/weird.py

Managing # optional and # needs tags

When a file uses a # sage.doctest: optional/needs FEATURE directive, the doctest fixer automatically removes the redundant # optional/needs FEATURE tags from all sage: lines. Likewise, when a block-scoped tag sage: # optional/needs FEATURE is used, then the doctest fixer removes redundant tags from all doctests in this scope. For example:

| # sage.doctest: optional - sirocco, needs sage.rings.number_field
| r"""
| ...
|
| EXAMPLES::
|
|     sage: # needs sage.modules sage.rings.number_field
|     sage: Q5 = QuadraticField(5)
|     sage: V = Q5^42                                 # needs sage.modules
|     sage: T = transmogrify(V)           # optional - bliss sirocco

is automatically transformed to:

| # sage.doctest: optional - sirocco, needs sage.rings.number_field
| r"""
| ...
|
| EXAMPLES::
|
|     sage: # needs sage.modules
|     sage: Q5 = QuadraticField(5)
|     sage: V = Q5^42
|     sage: T = transmogrify(V)               # optional - bliss

The doctest fixer also aligns the # optional/needs FEATURE tags on individual doctests at a fixed set of tab stops.

The doctester may issue style warnings when # optional/needs tags are repeated on a whole block of doctests, suggesting to use a block-scoped tag instead. The doctest fixer makes these changes automatically.

There are situations in which the doctester and doctest fixer show too much restraint and a manual intervention would improve the formatting of the doctests. In the example below, the doctester does not issue a style warning because the first doctest line does not carry the # needs tag:

| EXAMPLES::
|
|     sage: set_verbose(-1)
|     sage: P.<x,y,z> = ProjectiveSpace(QQbar, 2)     # needs sage.rings.number_field
|     sage: C = Curve([x^3*y + 2*x^2*y^2 + x*y^3      # needs sage.rings.number_field
|     ....:             + x^3*z + 7*x^2*y*z
|     ....:             + 14*x*y^2*z + 9*y^3*z], P)
|     sage: Q = P([0,0,1])                            # needs sage.rings.number_field
|     sage: C.tangents(Q)                             # needs sage.rings.number_field
|     [x + 4.147899035704788?*y,
|      x + (1.426050482147607? + 0.3689894074818041?*I)*y,
|      x + (1.426050482147607? - 0.3689894074818041?*I)*y]

To change this example, there are two approaches:

  1. Just add the line sage: # needs sage.rings.number_field at the beginning and run the doctest fixer, which will remove the tags on the individual doctests that have now become redundant.

  2. Insert a blank line after the first doctest line, splitting the block into two. Now the # needs tag is repeated on the whole second block, so running the doctest fixer will add a block-scoped tag and remove the individual tags:

    | EXAMPLES::
|
|     sage: set_verbose(-1)
|
|     sage: # needs sage.rings.number_field
|     sage: P.<x,y,z> = ProjectiveSpace(QQbar, 2)
|     sage: C = Curve([x^3*y + 2*x^2*y^2 + x*y^3
|     ....:             + x^3*z + 7*x^2*y*z
|     ....:             + 14*x*y^2*z + 9*y^3*z], P)
|     sage: Q = P([0,0,1])
|     sage: C.tangents(Q)
|     [x + 4.147899035704788?*y,
|      x + (1.426050482147607? + 0.3689894074818041?*I)*y,
|      x + (1.426050482147607? - 0.3689894074818041?*I)*y]

In places where the doctester issues a doctest dataflow warning (Variable ... referenced here was set only in doctest marked '# optional - FEATURE'), the doctest fixer automatically adds the missing # optional/needs tags.

Sometimes code changes can make existing # optional/needs FEATURE tags unnecessary. In an installation or virtual environment where FEATURE is not available, you can invoke the doctest fixer with the option --probe FEATURE. Then it will run examples marked # optional/needs - FEATURE silently, and if the example turns out to work anyway, the tag is automatically removed.

Note

Probing works best when the doctests within a docstring do not reuse the same variable for different values.

To have the doctest fixer take care of the # optional/needs tags, but not change the expected results of examples, use the option --only-tags. This mode is suitable for mostly unattended runs on many files.

With the option --verbose, the doctest fixer shows the doctester’s messages one by one and reports the changes made.

Warning

While the doctest fixer guarantees to preserve any comments that appear before # optional/needs and all parenthesized comments of the form # optional - FEATURE (EXPLANATION), any free-form comments that may be mixed with the doctest tags will be lost.

If you don’t want to update any doctests, you can use the option --no-test. In this mode, the doctest fixer does not run the doctester and only normalizes the style of the # optional tags.

Use in virtual environments

The doctest fixer can also run tests using the Sage doctester installed in a virtual environment:

[mkoeppe@localhost sage]$ ./sage --fixdoctests --overwrite                      \
                            --distribution sagemath-categories                  \
                            src/sage/geometry/schemes/generic/*.py

This command, using --distribution, is equivalent to a command that uses the more specific options --venv and --environment:

[mkoeppe@localhost sage]$ ./sage --fixdoctests --overwrite                      \
                            --venv pkgs/sagemath-categories/.tox/sagepython-... \
                            --environment sage.all__sagemath_categories
                            src/sage/geometry/schemes/generic/*.py

Either way, the options --keep-both, --full-tracebacks, and --if-installed are implied.

In this mode of operation, when the doctester encounters a global name that is unknown in its virtual environment (NameError), the doctest fixer will look up the name in its own environment (typically a full installation of the Sage library) and add a # needs ... tag to the doctest.

Likewise, when the doctester runs into a ModuleNotFoundError, the doctest fixer will automatically add a # needs ... tag.

The switch --distribution can be repeated; the given distributions will be tested in sequence. Using --distribution all is equivalent to a preset list of --distribution switches. With the switch --fixed-point, the doctest fixer runs the given distributions until no more changes are made.

Updating baseline files

The modularized distribution packages pkgs/sagemath-categories and pkgs/sagemath-repl contain files known-test-failures*.json for use with the option --baseline-stats-path, see section Auxiliary files.

After running the doctesters of the distributions, for example, via sage --fixdoctests, you can use the test results stored in timings2.json files to update the known-test-failures*.json files. This update can be done using the command:

[mkoeppe@localhost sage]$ ./sage --fixdoctests --no-test                        \
                            --update-known-test-failures --distribution all