Setting up and using your development environment#

Using virtual environments#

A frequently asked question is “How do I set up a development version of NumPy in parallel to a released version that I use to do my job/research?”.

One simple way to achieve this is to install the released version in site-packages, by using pip or conda for example, and set up the development version in a virtual environment.

If you use conda, we recommend creating a separate virtual environment for numpy development using the environment.yml file in the root of the repo (this will create the environment and install all development dependencies at once):

$ conda env create -f environment.yml  # `mamba` works too for this command
$ conda activate numpy-dev

If you installed Python some other way than conda, first install virtualenv (optionally use virtualenvwrapper), then create your virtualenv (named numpy-dev here), activate it, and install all project dependencies with:

$ virtualenv numpy-dev
$ source numpy-dev/bin/activate # activate virtual environment
$ python -m pip install -r requirements/all_requirements.txt

Now, whenever you want to switch to the virtual environment, you can use the command source numpy-dev/bin/activate, and deactivate to exit from the virtual environment and back to your previous shell.

Building from source#

See Building from source.

Testing builds#

Before running the tests, first install the test dependencies:

$ python -m pip install -r requirements/test_requirements.txt
$ python -m pip install asv # only for running benchmarks

To build the development version of NumPy and run tests, spawn interactive shells with the Python import paths properly set up etc., use the spin utility. To run tests, do one of:

$ spin test -v
$ spin test numpy/random  # to run the tests in a specific module
$ spin test -v -t numpy/_core/tests/test_nditer.py::test_iter_c_order

This builds NumPy first, so the first time it may take a few minutes.

You can also use spin bench for benchmarking. See spin --help for more command line options.

Note

If the above commands result in RuntimeError: Cannot parse version 0+untagged.xxxxx, run git pull upstream main --tags.

Additional arguments may be forwarded to pytest by passing the extra arguments after a bare --. For example, to run a test method with the --pdb flag forwarded to the target, run the following:

$ spin test -t numpy/tests/test_scripts.py::test_f2py -- --pdb

You can also match test names using python operators by passing the -k argument to pytest:

$ spin test -v -t numpy/_core/tests/test_multiarray.py -- -k "MatMul and not vector"

To run “doctests” – to check that the code examples in the documentation is correct – use the check-docs spin command. It relies on the scipy-docs package, which provides several additional features on top of the standard library doctest package. Install scipy-doctest and run one of:

$ spin check-docs -v
$ spin check-docs numpy/linalg
$ spin check-docs -v -- -k 'det and not slogdet'

Note

Remember that all tests of NumPy should pass before committing your changes.

Note

Some of the tests in the test suite require a large amount of memory, and are skipped if your system does not have enough.

Other build options#

For more options including selecting compilers, setting custom compiler flags and controlling parallelism, see Compiler selection and customizing a build (from the SciPy documentation.)

Running tests#

Besides using spin, there are various ways to run the tests. Inside the interpreter, tests can be run like this:

>>> np.test()  
>>> np.test('full')   # Also run tests marked as slow
>>> np.test('full', verbose=2)   # Additionally print test name/file

An example of a successful test :
``4686 passed, 362 skipped, 9 xfailed, 5 warnings in 213.99 seconds``

Or a similar way from the command line:

$ python -c "import numpy as np; np.test()"

Tests can also be run with pytest numpy, however then the NumPy-specific plugin is not found which causes strange side effects.

Running individual test files can be useful; it’s much faster than running the whole test suite or that of a whole module (example: np.random.test()). This can be done with:

$ python path_to_testfile/test_file.py

That also takes extra arguments, like --pdb which drops you into the Python debugger when a test fails or an exception is raised.

Running tests with tox is also supported. For example, to build NumPy and run the test suite with Python 3.9, use:

$ tox -e py39

For more extensive information, see Testing guidelines.

Note: do not run the tests from the root directory of your numpy git repo without spin, that will result in strange test errors.

Running linting#

Lint checks can be performed on newly added lines of Python code.

Install all dependent packages using pip:

$ python -m pip install -r requirements/linter_requirements.txt

To run lint checks before committing new code, run:

$ python tools/linter.py

To check all changes in newly added Python code of current branch with target branch, run:

$ python tools/linter.py --branch main

If there are no errors, the script exits with no message. In case of errors, check the error message for details:

$ python tools/linter.py --branch main
./numpy/_core/tests/test_scalarmath.py:34:5: E303 too many blank lines (3)
1       E303 too many blank lines (3)

It is advisable to run lint checks before pushing commits to a remote branch since the linter runs as part of the CI pipeline.

For more details on Style Guidelines:

Rebuilding & cleaning the workspace#

Rebuilding NumPy after making changes to compiled code can be done with the same build command as you used previously - only the changed files will be re-built. Doing a full build, which sometimes is necessary, requires cleaning the workspace first. The standard way of doing this is (note: deletes any uncommitted files!):

$ git clean -xdf

When you want to discard all changes and go back to the last commit in the repo, use one of:

$ git checkout .
$ git reset --hard

Debugging#

Another frequently asked question is “How do I debug C code inside NumPy?”. First, ensure that you have gdb installed on your system with the Python extensions (often the default on Linux). You can see which version of Python is running inside gdb to verify your setup:

(gdb) python
>import sys
>print(sys.version_info)
>end
sys.version_info(major=3, minor=7, micro=0, releaselevel='final', serial=0)

Most python builds do not include debug symbols and are built with compiler optimizations enabled. To get the best debugging experience using a debug build of Python is encouraged, see Advanced debugging tools.

In terms of debugging, NumPy also needs to be built in a debug mode. You need to use debug build type and disable optimizations to make sure -O0 flag is used during object building. Note that NumPy should NOT be installed in your environment before you build with the spin build command.

To generate source-level debug information within the build process run:

$ spin build --clean -- -Dbuildtype=debug -Ddisable-optimization=true

Note

In case you are using conda environment be aware that conda sets CFLAGS and CXXFLAGS automatically, and they will include the -O2 flag by default. You can safely use unset CFLAGS && unset CXXFLAGS to avoid them or provide them at the beginning of the spin command: CFLAGS="-O0 -g" CXXFLAGS="-O0 -g". Alternatively, to take control of these variables more permanently, you can create env_vars.sh file in the <path-to-conda-envs>/numpy-dev/etc/conda/activate.d directory. In this file you can export CFLAGS and CXXFLAGS variables. For complete instructions please refer to https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#saving-environment-variables.

Next you need to write a Python script that invokes the C code whose execution you want to debug. For instance mytest.py:

import numpy as np
x = np.arange(5)
np.empty_like(x)

Note that your test file needs to be outside the NumPy clone you have. Now, you can run:

$ spin gdb /path/to/mytest.py

In case you are using clang toolchain:

$ spin lldb /path/to/mytest.py

And then in the debugger:

(gdb) break array_empty_like
(gdb) run

lldb counterpart:

(lldb) breakpoint set --name array_empty_like
(lldb) run

The execution will now stop at the corresponding C function and you can step through it as usual. A number of useful Python-specific commands are available. For example to see where in the Python code you are, use py-list, to see the python traceback, use py-bt. For more details, see DebuggingWithGdb. Here are some commonly used commands:

  • list: List specified function or line.

  • next: Step program, proceeding through subroutine calls.

  • step: Continue program being debugged, after signal or breakpoint.

  • print: Print value of expression EXP.

Rich support for Python debugging requires that the python-gdb.py script distributed with Python is installed in a path where gdb can find it. If you installed your Python build from your system package manager, you likely do not need to manually do anything. However, if you built Python from source, you will likely need to create a .gdbinit file in your home directory pointing gdb at the location of your Python installation. For example, a version of python installed via pyenv needs a .gdbinit file with the following contents:

add-auto-load-safe-path ~/.pyenv

Building NumPy with a Python built with debug support (on Linux distributions typically packaged as python-dbg) is highly recommended.

Understanding the code & getting started#

The best strategy to better understand the code base is to pick something you want to change and start reading the code to figure out how it works. When in doubt, you can ask questions on the mailing list. It is perfectly okay if your pull requests aren’t perfect, the community is always happy to help. As a volunteer project, things do sometimes get dropped and it’s totally fine to ping us if something has sat without a response for about two to four weeks.

So go ahead and pick something that annoys or confuses you about NumPy, experiment with the code, hang around for discussions or go through the reference documents to try to fix it. Things will fall in place and soon you’ll have a pretty good understanding of the project as a whole. Good Luck!

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