Additional development and testing tools

Tox

Tox is a popular package that is used by a large number of Python projects as the standard entry point for testing and linting.

Sage includes tox as a standard package and uses it for three purposes:

  • For portability testing of the Sage distribution, as we explain in Testing on multiple platforms. This is configured in the file SAGE_ROOT/tox.ini.

  • For testing modularized distributions of the Sage library. This is configured in tox.ini files in subdirectories of SAGE_ROOT/pkgs/, such as SAGE_ROOT/pkgs/sagemath-standard/tox.ini. Each distribution’s configuration defines tox environments for testing the distribution with different Python versions and different ways how the dependencies are provided. We explain this in Packaging the Sage Library.

  • As an entry point for testing and linting of the Sage library, as we describe below. This is configured in the file SAGE_ROOT/src/tox.ini.

The tox configuration SAGE_ROOT/src/tox.ini can be invoked by using the command ./sage --tox. (If tox is available in your system installation, you can just type tox instead.)

This configuration provides an entry point for various testing/linting methods, known as “tox environments”. We can type ./sage --advanced to see what is available:

$ ./sage --advanced
SageMath version 9.2
...
Testing files:
...
--tox [options] <files|dirs> -- general entry point for testing
                                and linting of the Sage library
   -e <envlist>     -- run specific test environments
                       (default: run all except full pycodestyle)
      doctest                -- run the Sage doctester
                                (same as "sage -t")
      coverage               -- give information about doctest coverage of files
                                (same as "sage --coverage[all]")
      startuptime            -- display how long each component of Sage takes to start up
                                (same as "sage --startuptime")
      pycodestyle-minimal    -- check against Sage's minimal style conventions
      relint                 -- check whether some forbidden patterns appear
                                (includes all patchbot pattern-exclusion plugins)
      codespell              -- check for misspelled words in source code
      pycodestyle            -- check against the Python style conventions of PEP8
   -p auto          -- run test environments in parallel
   --help           -- show tox help

Doctest

The command ./sage -tox -e doctest requires that Sage has been built already. doctest is a special tox environment that runs the Sage doctester in the normal Sage environment. This is equivalent to using the command ./sage -t; see Running Sage’s doctests.

Coverage

The command ./sage -tox -e coverage requires that Sage has been built already. coverage is a special tox environment that is equivalent to using the command ./sage --coverageall (if no arguments are provided) or ./sage --coverage (if arguments are provided).

Startuptime

The command ./sage -tox -e startuptime requires that Sage has been built already. startuptime is a special tox environment that is equivalent to using the command ./sage --startuptime.

Pycodestyle

Pycodestyle (formerly known as pep8) checks Python code against the style conventions of PEP 8. Tox automatically installs pycodestyle in a separate virtual environment on the first use.

Sage defines two configurations for pycodestyle. The command ./sage -tox -e pycodestyle-minimal uses pycodestyle in a minimal configuration. As of Sage 9.5, the entire Sage library conforms to this configuration:

$ ./sage -tox -e pycodestyle-minimal -- src/sage/
pycodestyle-minimal installed: pycodestyle==2.8.0
pycodestyle-minimal run-test-pre: PYTHONHASHSEED='28778046'
pycodestyle-minimal run-test: commands[0] | pycodestyle --select E401,E70,W605,E711,E712,E721 sage
___________ summary ____________
  pycodestyle-minimal: commands succeeded
  congratulations :)

When preparing a branch for a Sage ticket, developers should verify that ./sage -tox -e pycodestyle-minimal passes. When the Sage patchbot runs on the ticket, it will perform similar coding style checks; but running the check locally reduces the turnaround time from hours to seconds.

The second configuration is used with the command ./sage -tox -e pycodestyle and runs a more thorough check:

$ ./sage -tox -e pycodestyle -- src/sage/quadratic_forms/quadratic_form.py
pycodestyle installed: pycodestyle==2.8.0
pycodestyle run-test-pre: PYTHONHASHSEED='2520226550'
pycodestyle run-test: commands[0] | pycodestyle sage/quadratic_forms/quadratic_form.py
sage/quadratic_forms/quadratic_form.py:135:9: E225 missing whitespace around operator
sage/quadratic_forms/quadratic_form.py:163:64: E225 missing whitespace around operator
sage/quadratic_forms/quadratic_form.py:165:52: E225 missing whitespace around operator
sage/quadratic_forms/quadratic_form.py:173:42: E228 missing whitespace around modulo operator
...
sage/quadratic_forms/quadratic_form.py:1620:9: E266 too many leading '#' for block comment
sage/quadratic_forms/quadratic_form.py:1621:9: E266 too many leading '#' for block comment
25      E111 indentation is not a multiple of 4
2       E117 over-indented
129     E127 continuation line over-indented for visual indent
1       E128 continuation line under-indented for visual indent
4       E201 whitespace after '['
4       E202 whitespace before ']'
2       E222 multiple spaces after operator
7       E225 missing whitespace around operator
1       E228 missing whitespace around modulo operator
25      E231 missing whitespace after ','
1       E262 inline comment should start with '# '
3       E265 block comment should start with '# '
62      E266 too many leading '#' for block comment
2       E272 multiple spaces before keyword
2       E301 expected 1 blank line, found 0
17      E303 too many blank lines (2)
ERROR: InvocationError for command .../pycodestyle sage/quadratic_forms/quadratic_form.py (exited with code 1)
___________ summary ____________
ERROR:   pycodestyle: commands failed

When preparing a branch for a Sage ticket that adds new code, developers should verify that ./sage -tox -e pycodestyle does not issue warnings for the added code. This will avoid later cleanup tickets as the Sage codebase is moving toward full PEP 8 compliance.

On the other hand, it is usually not advisable to mix coding-style fixes with productive changes on the same ticket because this would makes it harder for reviewers to evaluate the changes.

By passing the options --count -qq we can reduce the output to only show the number of style violation warnings. This can be helpful for planning work on coding-style clean-up tickets that focus on one or a few related issues:

$ ./sage -tox -e pycodestyle -- --count -qq src/sage
pycodestyle installed: pycodestyle==2.8.0
pycodestyle run-test-pre: PYTHONHASHSEED='3166223974'
pycodestyle run-test: commands[0] | pycodestyle --count -qq sage
557     E111 indentation is not a multiple of 4
1       E112 expected an indented block
194     E114 indentation is not a multiple of 4 (comment)
...
7       E743 ambiguous function definition 'l'
335     W291 trailing whitespace
4       W292 no newline at end of file
229     W293 blank line contains whitespace
459     W391 blank line at end of file
97797
ERROR: InvocationError for command .../pycodestyle --count -qq sage (exited with code 1)
___________ summary ____________
ERROR:   pycodestyle: commands failed

Installation: (for manual use:) pip install -U pycodestyle --user

Usage:

  • With tox: See above.

  • Manual: Run pycodestyle path/to/the/file.py.

  • VS Code: Activate by adding the setting "python.linting.pycodestyleEnabled": true, see official VS Code documentation for details.

Configuration: [pycodestyle] block in SAGE_ROOT/src/tox.ini

Documentation: https://pycodestyle.pycqa.org/en/latest/index.html

Relint

Relint checks all source files for forbidden text patterns specified by regular expressions.

Our configuration of relint flags some outdated Python constructions, plain TeX commands when equivalent LaTeX commands are available, common mistakes in documentation markup, and modularization anti-patterns.

Configuration: SAGE_ROOT/src/.relint.yml

Documentation: https://pypi.org/project/relint/

Codespell

Codespell uses a dictionary to check for misspelled words in source code.

Sage defines a configuration for codespell:

$ ./sage -tox -e codespell -- src/sage/homology/
codespell installed: codespell==2.1.0
codespell run-test-pre: PYTHONHASHSEED='1285169064'
codespell run-test: commands[0] | codespell '--skip=*.png,*.jpg,*.JPG,*.inv,*.dia,*.pdf,*.ico,*#*,*~*,*.bak,*.orig,*.log,*.sobj,*.tar,*.gz,*.pyc,*.o,*.sws,*.so,*.a,.DS_Store' --skip=doc/ca,doc/de,doc/es,doc/hu,doc/ja,doc/ru,doc/fr,doc/it,doc/pt,doc/tr --skip=src/doc/ca,src/doc/de,src/doc/es,src/doc/hu,src/doc/ja,src/doc/ru,src/doc/fr,src/doc/it,src/doc/pt,src/doc/tr '--skip=.git,.tox,worktree*,dist,upstream,logs,local,cythonized,scripts-3,autom4te.cache,tmp,lib.*,*.egg-info' --dictionary=- --dictionary=/Users/mkoeppe/s/sage/sage-rebasing/src/.codespell-dictionary.txt --ignore-words=/Users/mkoeppe/s/sage/sage-rebasing/src/.codespell-ignore.txt sage/homology
sage/homology/hochschild_complex.py:271: mone ==> mono, money, none
sage/homology/hochschild_complex.py:277: mone ==> mono, money, none
sage/homology/hochschild_complex.py:280: mone ==> mono, money, none
sage/homology/chain_complex.py:2185: mor ==> more
sage/homology/chain_complex.py:2204: mor ==> more
sage/homology/chain_complex.py:2210: mor ==> more
sage/homology/chain_complex.py:2211: mor ==> more
sage/homology/chain_complex.py:2214: mor ==> more
sage/homology/chain_complex.py:2215: mor ==> more
ERROR: InvocationError for command .../codespell '--skip=*.png,...' --dictionary=- --dictionary=/Users/mkoeppe/s/sage/sage-rebasing/src/.codespell-dictionary.txt --ignore-words=/Users/mkoeppe/s/sage/sage-rebasing/src/.codespell-ignore.txt sage/homology (exited with code 65)
___________ summary ____________
ERROR:   codespell: commands failed

Configuration:

  • [testenv:codespell] block in SAGE_ROOT/src/tox.ini

  • SAGE_ROOT/src/.codespell-dictionary.txt and SAGE_ROOT/src/.codespell-ignore.txt

Pytest

Pytest is a testing framework. It is included in the Sage distribution as an optional package.

Currently, Sage only makes very limited use of pytest, for testing the package sage.numerical.backends and some modules in sage.manifolds.

Installation:

  • ./sage -i pytest.

Usage:

  • Tox, Sage doctester: At the end of ./sage -t (or ./sage --tox -e doctest), Pytest is automatically invoked.

  • Manual: Run ./sage -pytest path/to/the/test_file.py or ./sage -pytest to run all tests.

  • VS Code: Install the Python extension and follow the offical VS Code documentation.

Configuration: SAGE_ROOT/src/conftest.py

Documentation: https://docs.pytest.org/en/stable/index.html

Pyright

Pyright is static type checker.

Installation:

  • (for manual use:) npm install -g pyright, see documentation for details.

Usage:

  • Tox: Run ./sage -tox -e pyright path/to/the/file.py

  • Manual: Run pyright path/to/the/file.py

  • VS Code: Install the Pylance extension.

Configuration: SAGE_ROOT/pyrightconfig.json

Documentation: https://github.com/microsoft/pyright#documentation

Pyflakes

Pyflakes checks for common coding errors.