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# Setting up and using your development environment

## Recommended development setup

Since NumPy contains parts written in C and Cython that need to be compiled before use, make sure you have the necessary compilers and Python development headers installed - see Building from source. Building NumPy as of version `2.0` requires C11 and C++17 compliant compilers.

Having compiled code also means that importing NumPy from the development sources needs some additional steps, which are explained below. For the rest of this chapter we assume that you have set up your git repo as described in Working with scikit-image source code.

Note

If you are having trouble building NumPy from source or setting up your local development environment, you can try to build NumPy with GitHub Codespaces. It allows you to create the correct development environment right in your browser, reducing the need to install local development environments and deal with incompatible dependencies.

If you have good internet connectivity and want a temporary set-up, it is often faster to work on NumPy in a Codespaces environment. For documentation on how to get started with Codespaces, see the Codespaces docs. When creating a codespace for the `numpy/numpy` repository, the default 2-core machine type works; 4-core will build and work a bit faster (but of course at a cost of halving your number of free usage hours). Once your codespace has started, you can run `conda activate numpy-dev` and your development environment is completely set up - you can then follow the relevant parts of the NumPy documentation to build, test, develop, write docs, and contribute to NumPy.

## 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
    $ spin test -p auto # to run tests in parallel threads using pytest-run-parallel

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 type checks

Changes that involve static type declarations are also executed using `spin`. The invocation will look like the following:

> $ spin mypy

This will look in the `typing/tests` directory for sets of operations to test for type incompatibility.

## 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:

    $ spin lint

If there are no errors, the output will look like:

    $ spin lint
    Running Ruff Check...
    All checks passed!

    Running C API borrow-reference linter...
    Scanning 548 C/C++ source files...

    All checks passed! C API borrow-ref linter found no issues.

    Running cython-lint...

In case of errors, check the error message for details:

    $ spin lint
    Running Ruff Check...
    I001 [*] Import block is un-sorted or un-formatted
    --> numpy/matlib.py:12:1
       |
    10 |                 PendingDeprecationWarning, stacklevel=2)
    11 |
    12 | / import numpy as np
    13 | |
    14 | | # Matlib.py contains all functions in the numpy namespace with a few
    15 | | # replacements. See doc/source/reference/routines.matlib.rst for details.
    16 | | # Need * as we're copying the numpy namespace.
    17 | | from numpy import *  # noqa: F403
    18 | | from numpy.matrixlib.defmatrix import matrix, asmatrix
       | |______________________________________________________^
    19 |
    20 |   __version__ = np.__version__
       |
       help: Organize imports
    15 | # replacements. See doc/source/reference/routines.matlib.rst for details.
    16 | # Need * as we're copying the numpy namespace.
    17 | from numpy import *  # noqa: F403
       - from numpy.matrixlib.defmatrix import matrix, asmatrix
    18 + from numpy.matrixlib.defmatrix import asmatrix, matrix
    19 |
    20 | __version__ = np.__version__
    21 |

    E501 Line too long (127 > 88)
    --> numpy/matlib.py:214:89
        |
    212 |     -------
    213 |     I : matrix
    214 |         A `n` x `M` matrix where all elements are equal to zero, except for the `k`-th diagonal, whose values are equal to one.
        |                                                                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    215 |
    216 |     See Also
        |

    Found 2 errors.
    [*] 1 fixable with the `--fix` option.

To automatically fix issues that can be fixed, run:

    $ spin lint --fix
    Running Ruff Check...
    E501 Line too long (127 > 88)
    --> numpy/matlib.py:214:89
        |
    212 |     -------
    213 |     I : matrix
    214 |         A `n` x `M` matrix where all elements are equal to zero, except for the `k`-th diagonal, whose values are equal to one.
        |                                                                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    215 |
    216 |     See Also
        |

    Found 2 errors (1 fixed, 1 remaining).

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:

- Python Style Guide

- NEP 45 — C style guide

## 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!