update release and dev

1.8.0/_sources/devel/benchmarking.rst.txt

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+.. _benchmarking:
+
+.. include:: ../../benchmarks/README.rst

1.8.0/_sources/devel/installation_from_source.rst.txt

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+.. _installation-from-source:
+
+**********************
+Installing from source
+**********************
+
+Getting the source
+==================
+
+More likely you will want to get the source repository to be able to follow the
+latest changes.  In that case, you can use::
+
+    git clone https://github.com/dipy/dipy.git
+
+For more information about this see :ref:`following-latest`.
+
+After you've cloned the repository, you will have a new directory, containing
+the DIPY ``pyproject.toml`` file, among others.  We'll call this directory - that
+contains the ``pyproject.toml`` file - the *DIPY source root directory*.  Sometimes
+we'll also call it the ``<dipy root>`` directory.
+
+Building and installing
+=======================
+
+Install from source (all operating systems - recommended)
+---------------------------------------------------------
+
+Change directory into the *DIPY source root directory*.
+
+To clean your directory from temporary file, use::
+
+    git clean -fxd
+
+This command will delete all files not present in your github repository.
+
+Then, complete your installation by using this command::
+
+    pip install -r requirements/build.txt
+    pip install --no-build-isolation --user -e .
+
+This command will do the following :
+    - install the requirements for building dipy
+    - remove the old dipy installation if present
+    - build dipy
+    - install dipy locally on your user environment
+
+.. _install-source-nix:
+
+Install from source for Unix (e.g Linux, macOS)
+-----------------------------------------------
+
+Change directory into the *DIPY source root directory*.
+
+First, install some python build packages::
+
+    pip install -r requirements/build.txt
+
+Then, to install for the system::
+
+    pip install dipy
+
+Or, to build DIPY in the source tree (locally) so you can run the code in the source tree (recommended for following the latest source) run::
+
+    pip install --no-build-isolation --user -e .
+
+add the *DIPY source root directory* into your ``PYTHONPATH`` environment variable. Search google for ``PYTHONPATH`` for details or see `python module path`_ for an introduction.
+
+When adding dipy_ to the ``PYTHONPATH``, we usually add the ``PYTHONPATH`` at
+the end of ``~/.bashrc`` or (macOS) ``~/.bash_profile`` so we don't need to
+retype it every time. This should look something like::
+
+  export PYTHONPATH="/home/user_dir/Devel/dipy:\$PYTHONPATH"
+
+After changing the ``~/.bashrc`` or (macOS) ``~/.bash_profile`` try::
+
+  source ~/.bashrc
+
+or::
+
+  source ~/.bash_profile
+
+so that you can have immediate access to DIPY_ without needing to
+restart your terminal.
+
+
+Ubuntu/Debian
+-------------
+
+::
+
+    sudo apt-get install python-dev python-setuptools
+    sudo apt-get install python-numpy python-scipy
+    sudo apt-get install cython
+
+then::
+
+    sudo pip install nibabel
+
+(we need the latest version of this one - hence ``pip`` rather than
+``apt-get``).
+
+You might want the optional packages too (highly recommended)::
+
+    sudo apt-get install ipython python-h5py python-vtk python-matplotlib
+
+
+Now follow :ref:`install-source-nix`.
+
+Fedora / Mandriva maybe Redhat
+------------------------------
+
+Same as above but use yum rather than apt-get when necessary.
+
+Now follow :ref:`install-source-nix`.
+
+
+Windows
+-------
+
+Anaconda_ is probably the easiest way to install the dependencies that you need.
+To build from source, you will also need to install the exact compiler which is
+used with your specific version of python.
+
+For getting this information, type this command in shell like ``cmd`` or Powershell_::
+
+    python -c "import platform;print(platform.python_compiler())"
+
+This command should print information of this form::
+
+    MSC v.1900 64 bit (AMD64)
+
+Now that you find the relevant compiler, you have to install the VisualStudioBuildTools_
+by respecting the following table::
+
+    Visual C++ 2008  (9.0)          MSC_VER=1500
+    Visual C++ 2010 (10.0)          MSC_VER=1600
+    Visual C++ 2012 (11.0)          MSC_VER=1700
+    Visual C++ 2013 (12.0)          MSC_VER=1800
+    Visual C++ 2015 (14.0)          MSC_VER=1900
+    Visual C++ 2017 (15.0)          MSC_VER=1910
+    Visual C++ 2019 (16.0)          MSC_VER=1920
+    Visual C++ 2022 (17.0)          MSC_VER=1930
+
+After the VisualStudioBuildTools_ installation,  restart a command shell and
+change directory into the *DIPY source root directory*.
+
+Start to install the build tools::
+
+    pip install -r requirements/build.txt
+
+Then to install into your system::
+
+    pip install dipy
+
+To install inplace - so that DIPY is running out of the source code directory::
+
+    pip install --no-build-isolation --user -e .
+
+(this is the mode we recommend for following the latest source code).
+
+If you get an error saying  "unable to find vcvarsall.bat" then you need to
+check your environment variable ``PATH`` or reinstall VisualStudioBuildTools_.
+Setuptools should automatically detect the compiler and use it.
+
+macOS
+-----
+
+Make sure you have Xcode_ and Anaconda_ installed.
+
+From here follow the :ref:`install-source-nix` instructions.
+
+OpenMP with macOS
+-----------------
+OpenMP_ is a standard library for efficient multithreaded applications. This
+is used in DIPY for speeding up many different parts of the library (e.g., denoising
+and bundle registration). If you do not have an OpenMP-enabled compiler, you can
+still compile DIPY from source using the above instructions, but it might not take
+advantage of the multithreaded parts of the code. To be able to compile
+DIPY from source with OpenMP on macOS, you will have to do a few more things. First
+of all, you will need to install the Homebrew_ package manager. Next, you will need
+to install and configure the compiler. You have two options: using the GCC compiler
+or the CLANG compiler. This depends on your python installation:
+
+Under Anaconda
+~~~~~~~~~~~~~~~~
+
+We recommend to install llvm via Anaconda_. Run the following::
+
+    conda install -c conda-forge llvm-openmp
+
+In case the compiler is not detected automatically, you can specify the compiler
+by using the environment variable ``CC``.
+
+Under Homebrew Python or python.org Python
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you are already using the Homebrew Python, or the standard python.org Python,
+you will need to use the llvm compiler with OMP. Run::
+
+    brew install llvm
+    export CC=/usr/local/bin/clang-omp
+
+Building and installing
+~~~~~~~~~~~~~~~~~~~~~~~
+Whether you are using Anaconda_ or Hombrew/python.org Python, you will need to then
+run ``pip install dipy``. When you do that, it should now
+compile the code with this OpenMP-enabled compiler, and things should go faster!
+
+Testing
+========
+
+If you want to run the tests::
+
+    sudo pip install pytest
+
+Then, in the terminal from ``<dipy root>``::
+
+    pytest -svv dipy
+
+You can also run the examples in ``<dipy root>/doc``.
+
+Documentation
+=============
+
+To build the documentation in HTML in your computer you will need to do::
+
+    sudo pip install sphinx
+
+Then change directory to ``<dipy root>`` and::
+
+    cd doc
+    make clean
+    make -C . html
+
+Tip
+---
+
+Building the entire ``DIPY`` documentation takes a few hours. You may want to
+skip building the documentation for the examples, which will reduce the
+documentation build time to a few minutes. You can do so by executing::
+
+    make -C . html-no-examples
+
+Troubleshooting
+---------------
+
+If you encounter the following error when trying to build the documentation::
+
+    tools/build_modref_templates.py dipy reference
+    *WARNING* API documentation not generated: Can not import dipy
+    tools/docgen_cmd.py dipy reference_cmd
+    *WARNING* Command line API documentation not generated: Cannot import dipy
+    Build API docs...done.
+    cd examples_built && ../../tools/make_examples.py
+    Traceback (most recent call last):
+      File "../../tools/make_examples.py", line 33, in <module>
+        import dipy
+    ModuleNotFoundError: No module named 'dipy'
+
+it is probably due to a conflict between the picked ``Sphinx`` version: this
+happens when the system's ``Sphinx`` package is used instead of the virtual
+environment's ``Sphinx`` package, and the former trying to import a ``DIPY``
+version in the system: the ``Sphinx`` package used should correspond to that of
+the virtual environment where ``DIPY`` lives. This can be solved by specifying
+the path to the ``Sphinx`` package in the virtual environment::
+
+    make html SPHINXBUILD='python <path_to_sphinx>/sphinx-build'
+
+
+.. include:: ../links_names.inc