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520 lines
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=====================
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Contributing to SciPy
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=====================
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This document aims to give an overview of how to contribute to SciPy. It
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tries to answer commonly asked questions, and provide some insight into how the
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community process works in practice. Readers who are familiar with the SciPy
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community and are experienced Python coders may want to jump straight to the
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`git workflow`_ documentation.
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There are a lot of ways you can contribute:
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- Contributing new code
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- Fixing bugs and other maintenance work
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- Improving the documentation
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- Reviewing open pull requests
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- Triaging issues
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- Working on the `scipy.org`_ website
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- Answering questions and participating on the scipy-dev and scipy-user
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`mailing lists`_.
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Contributing new code
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=====================
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If you have been working with the scientific Python toolstack for a while, you
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probably have some code lying around of which you think "this could be useful
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for others too". Perhaps it's a good idea then to contribute it to SciPy or
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another open source project. The first question to ask is then, where does
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this code belong? That question is hard to answer here, so we start with a
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more specific one: *what code is suitable for putting into SciPy?*
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Almost all of the new code added to scipy has in common that it's potentially
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useful in multiple scientific domains and it fits in the scope of existing
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scipy submodules. In principle new submodules can be added too, but this is
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far less common. For code that is specific to a single application, there may
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be an existing project that can use the code. Some scikits (`scikit-learn`_,
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`scikit-image`_, `statsmodels`_, etc.) are good examples here; they have a
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narrower focus and because of that more domain-specific code than SciPy.
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Now if you have code that you would like to see included in SciPy, how do you
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go about it? After checking that your code can be distributed in SciPy under a
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compatible license (see FAQ for details), the first step is to discuss on the
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scipy-dev mailing list. All new features, as well as changes to existing code,
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are discussed and decided on there. You can, and probably should, already
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start this discussion before your code is finished.
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Assuming the outcome of the discussion on the mailing list is positive and you
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have a function or piece of code that does what you need it to do, what next?
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Before code is added to SciPy, it at least has to have good documentation, unit
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tests and correct code style.
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1. Unit tests
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In principle you should aim to create unit tests that exercise all the code
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that you are adding. This gives some degree of confidence that your code
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runs correctly, also on Python versions and hardware or OSes that you don't
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have available yourself. An extensive description of how to write unit
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tests is given in the NumPy `testing guidelines`_.
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2. Documentation
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Clear and complete documentation is essential in order for users to be able
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to find and understand the code. Documentation for individual functions
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and classes -- which includes at least a basic description, type and
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meaning of all parameters and returns values, and usage examples in
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`doctest`_ format -- is put in docstrings. Those docstrings can be read
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within the interpreter, and are compiled into a reference guide in html and
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pdf format. Higher-level documentation for key (areas of) functionality is
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provided in tutorial format and/or in module docstrings. A guide on how to
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write documentation is given in `how to document`_.
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3. Code style
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Uniformity of style in which code is written is important to others trying
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to understand the code. SciPy follows the standard Python guidelines for
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code style, `PEP8`_. In order to check that your code conforms to PEP8,
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you can use the `pep8 package`_ style checker. Most IDEs and text editors
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have settings that can help you follow PEP8, for example by translating
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tabs by four spaces. Using `pyflakes`_ to check your code is also a good
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idea.
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At the end of this document a checklist is given that may help to check if your
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code fulfills all requirements for inclusion in SciPy.
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Another question you may have is: *where exactly do I put my code*? To answer
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this, it is useful to understand how the SciPy public API (application
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programming interface) is defined. For most modules the API is two levels
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deep, which means your new function should appear as
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``scipy.submodule.my_new_func``. ``my_new_func`` can be put in an existing or
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new file under ``/scipy/<submodule>/``, its name is added to the ``__all__``
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list in that file (which lists all public functions in the file), and those
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public functions are then imported in ``/scipy/<submodule>/__init__.py``. Any
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private functions/classes should have a leading underscore (``_``) in their
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name. A more detailed description of what the public API of SciPy is, is given
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in `SciPy API`_.
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Once you think your code is ready for inclusion in SciPy, you can send a pull
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request (PR) on Github. We won't go into the details of how to work with git
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here, this is described well in the `git workflow`_ section of the NumPy
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documentation and on the `Github help pages`_. When you send the PR for a new
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feature, be sure to also mention this on the scipy-dev mailing list. This can
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prompt interested people to help review your PR. Assuming that you already got
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positive feedback before on the general idea of your code/feature, the purpose
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of the code review is to ensure that the code is correct, efficient and meets
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the requirements outlined above. In many cases the code review happens
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relatively quickly, but it's possible that it stalls. If you have addressed
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all feedback already given, it's perfectly fine to ask on the mailing list
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again for review (after a reasonable amount of time, say a couple of weeks, has
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passed). Once the review is completed, the PR is merged into the "master"
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branch of SciPy.
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The above describes the requirements and process for adding code to SciPy. It
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doesn't yet answer the question though how decisions are made exactly. The
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basic answer is: decisions are made by consensus, by everyone who chooses to
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participate in the discussion on the mailing list. This includes developers,
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other users and yourself. Aiming for consensus in the discussion is important
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-- SciPy is a project by and for the scientific Python community. In those
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rare cases that agreement cannot be reached, the maintainers of the module
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in question can decide the issue.
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Contributing by helping maintain existing code
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==============================================
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The previous section talked specifically about adding new functionality to
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SciPy. A large part of that discussion also applies to maintenance of existing
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code. Maintenance means fixing bugs, improving code quality or style,
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documenting existing functionality better, adding missing unit tests, keeping
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build scripts up-to-date, etc. The SciPy `issue list`_ contains all
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reported bugs, build/documentation issues, etc. Fixing issues
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helps improve the overall quality of SciPy, and is also a good way
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of getting familiar with the project. You may also want to fix a bug because
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you ran into it and need the function in question to work correctly.
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The discussion on code style and unit testing above applies equally to bug
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fixes. It is usually best to start by writing a unit test that shows the
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problem, i.e. it should pass but doesn't. Once you have that, you can fix the
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code so that the test does pass. That should be enough to send a PR for this
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issue. Unlike when adding new code, discussing this on the mailing list may
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not be necessary - if the old behavior of the code is clearly incorrect, no one
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will object to having it fixed. It may be necessary to add some warning or
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deprecation message for the changed behavior. This should be part of the
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review process.
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Reviewing pull requests
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=======================
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Reviewing open pull requests (PRs) is very welcome, and a valuable way to help
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increase the speed at which the project moves forward. If you have specific
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knowledge/experience in a particular area (say "optimization algorithms" or
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"special functions") then reviewing PRs in that area is especially valuable -
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sometimes PRs with technical code have to wait for a long time to get merged
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due to a shortage of appropriate reviewers.
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We encourage everyone to get involved in the review process; it's also a
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great way to get familiar with the code base. Reviewers should ask
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themselves some or all of the following questions:
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- Was this change adequately discussed (relevant for new features and changes
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in existing behavior)?
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- Is the feature scientifically sound? Algorithms may be known to work based on
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literature; otherwise, closer look at correctness is valuable.
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- Is the intended behavior clear under all conditions (e.g. unexpected inputs
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like empty arrays or nan/inf values)?
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- Does the code meet the quality, test and documentation expectation outline
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under `Contributing new code`_?
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If we do not know you yet, consider introducing yourself.
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Other ways to contribute
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========================
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There are many ways to contribute other than contributing code.
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Triaging issues (investigating bug reports for validity and possible actions to
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take) is also a useful activity. SciPy has many hundreds of open issues;
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closing invalid ones and correctly labeling valid ones (ideally with some first
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thoughts in a comment) allows prioritizing maintenance work and finding related
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issues easily when working on an existing function or submodule.
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Participating in discussions on the scipy-user and scipy-dev `mailing lists`_ is
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a contribution in itself. Everyone who writes to those lists with a problem or
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an idea would like to get responses, and writing such responses makes the
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project and community function better and appear more welcoming.
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The `scipy.org`_ website contains a lot of information on both SciPy the
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project and SciPy the community, and it can always use a new pair of hands.
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The sources for the website live in their own separate repo:
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https://github.com/scipy/scipy.org
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Recommended development setup
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=============================
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Since Scipy contains parts written in C, C++, and Fortran that need to be
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compiled before use, make sure you have the necessary compilers and Python
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development headers installed. Having compiled code also means that importing
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Scipy from the development sources needs some additional steps, which are
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explained below.
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First fork a copy of the main Scipy repository in Github onto your own
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account and then create your local repository via::
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$ git clone git@github.com:YOURUSERNAME/scipy.git scipy
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$ cd scipy
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$ git remote add upstream git://github.com/scipy/scipy.git
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To build the development version of Scipy and run tests, spawn
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interactive shells with the Python import paths properly set up etc.,
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do one of::
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$ python runtests.py -v
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$ python runtests.py -v -s optimize
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$ python runtests.py -v -t scipy.special.tests.test_basic::test_xlogy
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$ python runtests.py --ipython
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$ python runtests.py --python somescript.py
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$ python runtests.py --bench
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This builds Scipy first, so the first time it may take some time. If
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you specify ``-n``, the tests are run against the version of Scipy (if
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any) found on current PYTHONPATH. *Note: if you run into a build issue,
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more detailed build documentation can be found in :doc:`building/index` and at
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https://github.com/scipy/scipy/tree/master/doc/source/building*
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Using ``runtests.py`` is the recommended approach to running tests.
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There are also a number of alternatives to it, for example in-place
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build or installing to a virtualenv. See the FAQ below for details.
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Some of the tests in Scipy are very slow and need to be separately
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enabled. See the FAQ below for details.
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SciPy structure
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===============
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All SciPy modules should follow the following conventions. In the
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following, a *SciPy module* is defined as a Python package, say
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``yyy``, that is located in the scipy/ directory.
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* Ideally, each SciPy module should be as self-contained as possible.
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That is, it should have minimal dependencies on other packages or
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modules. Even dependencies on other SciPy modules should be kept to
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a minimum. A dependency on NumPy is of course assumed.
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* Directory ``yyy/`` contains:
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- A file ``setup.py`` that defines
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``configuration(parent_package='',top_path=None)`` function
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for `numpy.distutils`.
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- A directory ``tests/`` that contains files ``test_<name>.py``
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corresponding to modules ``yyy/<name>{.py,.so,/}``.
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* Private modules should be prefixed with an underscore ``_``,
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for instance ``yyy/_somemodule.py``.
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* User-visible functions should have good documentation following
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the Numpy documentation style, see `how to document`_
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* The ``__init__.py`` of the module should contain the main reference
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documentation in its docstring. This is connected to the Sphinx
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documentation under ``doc/`` via Sphinx's automodule directive.
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The reference documentation should first give a categorized list of
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the contents of the module using ``autosummary::`` directives, and
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after that explain points essential for understanding the use of the
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module.
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Tutorial-style documentation with extensive examples should be
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separate, and put under ``doc/source/tutorial/``
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See the existing Scipy submodules for guidance.
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For further details on Numpy distutils, see:
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https://github.com/numpy/numpy/blob/master/doc/DISTUTILS.rst.txt
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Useful links, FAQ, checklist
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============================
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Checklist before submitting a PR
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--------------------------------
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- Are there unit tests with good code coverage?
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- Do all public function have docstrings including examples?
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- Is the code style correct (PEP8, pyflakes)
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- Is the commit message `formatted correctly`_?
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- Is the new functionality tagged with ``.. versionadded:: X.Y.Z`` (with
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X.Y.Z the version number of the next release - can be found in setup.py)?
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- Is the new functionality mentioned in the release notes of the next
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release?
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- Is the new functionality added to the reference guide?
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- In case of larger additions, is there a tutorial or more extensive
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module-level description?
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- In case compiled code is added, is it integrated correctly via setup.py
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(and preferably also Bento configuration files - bento.info and bscript)?
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- If you are a first-time contributor, did you add yourself to THANKS.txt?
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Please note that this is perfectly normal and desirable - the aim is to
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give every single contributor credit, and if you don't add yourself it's
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simply extra work for the reviewer (or worse, the reviewer may forget).
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- Did you check that the code can be distributed under a BSD license?
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Useful SciPy documents
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----------------------
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- The `how to document`_ guidelines
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- NumPy/SciPy `testing guidelines`_
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- `SciPy API`_
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- The `SciPy Roadmap`_
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- NumPy/SciPy `git workflow`_
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- How to submit a good `bug report`_
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FAQ
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---
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*I based my code on existing Matlab/R/... code I found online, is this OK?*
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It depends. SciPy is distributed under a BSD license, so if the code that you
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based your code on is also BSD licensed or has a BSD-compatible license (e.g.
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MIT, PSF) then it's OK. Code which is GPL or Apache licensed, has no
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clear license, requires citation or is free for academic use only can't be
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included in SciPy. Therefore if you copied existing code with such a license
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or made a direct translation to Python of it, your code can't be included.
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If you're unsure, please ask on the scipy-dev mailing list.
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*Why is SciPy under the BSD license and not, say, the GPL?*
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Like Python, SciPy uses a "permissive" open source license, which allows
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proprietary re-use. While this allows companies to use and modify the software
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without giving anything back, it is felt that the larger user base results in
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more contributions overall, and companies often publish their modifications
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anyway, without being required to. See John Hunter's `BSD pitch`_.
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*How do I set up a development version of SciPy in parallel to a released
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version that I use to do my job/research?*
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One simple way to achieve this is to install the released version in
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site-packages, by using a binary installer or pip for example, and set
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up the development version in a virtualenv. First install
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`virtualenv`_ (optionally use `virtualenvwrapper`_), then create your
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virtualenv (named scipy-dev here) with::
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$ virtualenv scipy-dev
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Now, whenever you want to switch to the virtual environment, you can use the
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command ``source scipy-dev/bin/activate``, and ``deactivate`` to exit from the
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virtual environment and back to your previous shell. With scipy-dev
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activated, install first Scipy's dependencies::
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$ pip install Numpy pytest Cython
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After that, you can install a development version of Scipy, for example via::
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$ python setup.py install
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The installation goes to the virtual environment.
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*How do I set up an in-place build for development*
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For development, you can set up an in-place build so that changes made to
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``.py`` files have effect without rebuild. First, run::
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$ python setup.py build_ext -i
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Then you need to point your PYTHONPATH environment variable to this directory.
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Some IDEs (Spyder for example) have utilities to manage PYTHONPATH. On Linux
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and OSX, you can run the command::
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$ export PYTHONPATH=$PWD
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and on Windows
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$ set PYTHONPATH=/path/to/scipy
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Now editing a Python source file in SciPy allows you to immediately
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test and use your changes (in ``.py`` files), by simply restarting the
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interpreter.
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*Are there any video examples for installing from source, setting up a
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development environment, etc...?*
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Currently, there are two video demonstrations for Anaconda Python on macOS:
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`Anaconda SciPy Dev Part I (macOS)`_ is a four-minute
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overview of installing Anaconda, building SciPy from source, and testing
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changes made to SciPy from the Spyder IDE.
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`Anaconda SciPy Dev Part II (macOS)`_ shows how to use
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a virtual environment to easily switch between the "pre-built version" of SciPy
|
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|
installed with Anaconda and your "source-built version" of SciPy created
|
||
|
according to Part I.
|
||
|
|
||
|
|
||
|
*Are there any video examples of the basic development workflow?*
|
||
|
|
||
|
`SciPy Development Workflow`_ is a five-minute example of fixing a bug and
|
||
|
submitting a pull request. While it's intended as a followup to
|
||
|
`Anaconda SciPy Dev Part I (macOS)`_ and `Anaconda SciPy Dev Part II (macOS)`_,
|
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|
the process is similar for other development setups.
|
||
|
|
||
|
|
||
|
*Can I use a programming language other than Python to speed up my code?*
|
||
|
|
||
|
Yes. The languages used in SciPy are Python, Cython, C, C++ and Fortran. All
|
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|
of these have their pros and cons. If Python really doesn't offer enough
|
||
|
performance, one of those languages can be used. Important concerns when
|
||
|
using compiled languages are maintainability and portability. For
|
||
|
maintainability, Cython is clearly preferred over C/C++/Fortran. Cython and C
|
||
|
are more portable than C++/Fortran. A lot of the existing C and Fortran code
|
||
|
in SciPy is older, battle-tested code that was only wrapped in (but not
|
||
|
specifically written for) Python/SciPy. Therefore the basic advice is: use
|
||
|
Cython. If there's specific reasons why C/C++/Fortran should be preferred,
|
||
|
please discuss those reasons first.
|
||
|
|
||
|
|
||
|
*How do I debug code written in C/C++/Fortran inside Scipy?*
|
||
|
|
||
|
The easiest way to do this is to first write a Python script that
|
||
|
invokes the C code whose execution you want to debug. For instance
|
||
|
``mytest.py``::
|
||
|
|
||
|
from scipy.special import hyp2f1
|
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|
print(hyp2f1(5.0, 1.0, -1.8, 0.95))
|
||
|
|
||
|
Now, you can run::
|
||
|
|
||
|
gdb --args python runtests.py -g --python mytest.py
|
||
|
|
||
|
If you didn't compile with debug symbols enabled before, remove the
|
||
|
``build`` directory first. While in the debugger::
|
||
|
|
||
|
(gdb) break cephes_hyp2f1
|
||
|
(gdb) run
|
||
|
|
||
|
The execution will now stop at the corresponding C function and you
|
||
|
can step through it as usual. Instead of plain ``gdb`` you can of
|
||
|
course use your favourite alternative debugger; run it on the
|
||
|
``python`` binary with arguments ``runtests.py -g --python mytest.py``.
|
||
|
|
||
|
|
||
|
*How do I enable additional tests in Scipy?*
|
||
|
|
||
|
Some of the tests in Scipy's test suite are very slow and not enabled
|
||
|
by default. You can run the full suite via::
|
||
|
|
||
|
$ python runtests.py -g -m full
|
||
|
|
||
|
This invokes the test suite ``import scipy; scipy.test("full")``,
|
||
|
enabling also slow tests.
|
||
|
|
||
|
There is an additional level of very slow tests (several minutes),
|
||
|
which are disabled also in this case. They can be enabled by setting
|
||
|
the environment variable ``SCIPY_XSLOW=1`` before running the test
|
||
|
suite.
|
||
|
|
||
|
|
||
|
.. _scikit-learn: http://scikit-learn.org
|
||
|
|
||
|
.. _scikit-image: http://scikit-image.org/
|
||
|
|
||
|
.. _statsmodels: http://statsmodels.sourceforge.net/
|
||
|
|
||
|
.. _testing guidelines: https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
|
||
|
|
||
|
.. _formatted correctly: http://docs.scipy.org/doc/numpy/dev/gitwash/development_workflow.html#writing-the-commit-message
|
||
|
|
||
|
.. _how to document: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
|
||
|
|
||
|
.. _bug report: http://scipy.org/bug-report.html
|
||
|
|
||
|
.. _PEP8: http://www.python.org/dev/peps/pep-0008/
|
||
|
|
||
|
.. _pep8 package: http://pypi.python.org/pypi/pep8
|
||
|
|
||
|
.. _pyflakes: http://pypi.python.org/pypi/pyflakes
|
||
|
|
||
|
.. _SciPy API: https://docs.scipy.org/doc/scipy/reference/api.html
|
||
|
|
||
|
.. _SciPy Roadmap: https://scipy.github.io/devdocs/roadmap.html
|
||
|
|
||
|
.. _git workflow: http://docs.scipy.org/doc/numpy/dev/gitwash/index.html
|
||
|
|
||
|
.. _Github help pages: https://help.github.com/articles/set-up-git/
|
||
|
|
||
|
.. _issue list: https://github.com/scipy/scipy/issues
|
||
|
|
||
|
.. _Github: https://github.com/scipy/scipy
|
||
|
|
||
|
.. _scipy.org: https://scipy.org/
|
||
|
|
||
|
.. _scipy.github.com: http://scipy.github.com/
|
||
|
|
||
|
.. _scipy.org-new: https://github.com/scipy/scipy.org-new
|
||
|
|
||
|
.. _documentation wiki: https://docs.scipy.org/scipy/Front%20Page/
|
||
|
|
||
|
.. _SciPy Central: http://scipy-central.org/
|
||
|
|
||
|
.. _doctest: http://www.doughellmann.com/PyMOTW/doctest/
|
||
|
|
||
|
.. _virtualenv: http://www.virtualenv.org/
|
||
|
|
||
|
.. _virtualenvwrapper: http://www.doughellmann.com/projects/virtualenvwrapper/
|
||
|
|
||
|
.. _bsd pitch: http://nipy.sourceforge.net/nipy/stable/faq/johns_bsd_pitch.html
|
||
|
|
||
|
.. _Pytest: https://pytest.org/
|
||
|
|
||
|
.. _mailing lists: https://www.scipy.org/scipylib/mailing-lists.html
|
||
|
|
||
|
.. _Anaconda SciPy Dev Part I (macOS): https://youtu.be/1rPOSNd0ULI
|
||
|
|
||
|
.. _Anaconda SciPy Dev Part II (macOS): https://youtu.be/Faz29u5xIZc
|
||
|
|
||
|
.. _SciPy Development Workflow: https://youtu.be/HgU01gJbzMY
|