For developers and contributors¶

Setting up a dedicated code editor¶

Using a code editor or IDE is useful when contributing to a codebase. Many products are available; use what is most familiar. For new developers, we recommend VS Code since it is lightweight, free, and has a breadth of community extensions.

Make your copy of mrsimulator on GitHub¶

Making a copy of someone’s code on GitHub is the same as making a fork. A fork is a complete copy of the code and its revision history.

Log in to a GitHub account.
Go to the mrsimulator Github home page.
Click on the fork button.

You will see a short animation of Octocat scanning a book on a flatbed scanner. After that, you should find yourself on the home page for your forked copy of mrsimulator.

Create a development environment¶

It is good practice to create separate virtual environments when developing packages. There are many environment managers available; however, we recommend using Anaconda or Miniconda.

Note

For Mac users with Apple Silicon, Anaconda and Miniconda are natively supported on M1 as of release 2022.05. See the downloads page for compatible versions.

If your Python is built for Apple Silicon, the following command should display a similar output.

$ file `which python`
/some/path/to/python: Mach-O 64-bit executable arm64

The following is an example of creating a Conda environment.

$ conda create -n mrsimulator-dev python=3.12

The above command will create a new environment named mrsimulator-dev using Python 3.12. To activate the environment, use

$ conda activate mrsimulator-dev

Make sure git is installed on your computer¶

Git is a source code management system. It keeps track of the changes made to the code and manages contributions from several individuals. You may notice that much of its terminology comes from river and tree metaphors, i.e., source, fork, branch, upstream, etc. You may read about git at the Git Basics.

If you are using anaconda/miniconda, you probably have git pre-installed. To check, type in terminal

$ git --version
# if git is installed, you will get something like git version 2.30.2

If git is not installed, install it before continuing.

Basic git configuration:

Follow the instructions at Set Up Git at GitHub to configure:

your user name and email in your copy of git.
authentication, so you don’t have to type your GitHub password every time you

You’ll need to access GitHub from the command line.

Copy your fork of mrsimulator from GitHub to your computer¶

Unless you plan on always editing the code using the online Github editor, you may need to copy the fork of MRSimulator from your GitHub account to your computer. Make a complete copy of the fork with

$ git clone --recursive https://github.com/your-user-name/mrsimulator.git

Insert your-user-name with your GitHub account username. If there is an error in this stage, it is probably an error in setting up authentication.

You now have a copy of the MRSimulator fork from your GitHub account to your local computer into a MRSimulator folder.

Understanding Remotes¶

In git, the name for another location of the same repository is remote. The repository that contains the latest “official” development version is traditionally called the upstream remote. You can read more about remotes on Git Basics.

At this point, your local copy of MRSimulator doesn’t know where the upstream development version of MRSimulator is. To let git know, change into the MRSimulator folder you created in the previous step and add a remote:

cd mrsimulator
git remote add mrsimulator git://github.com/deepanshs/mrsimulator.git

You can check that everything is set up correctly so far by asking git to show you all of the remotes it knows about for your local repository of MRSimulator with git remote -v, which should display

upstream git://github.com/deepanshs/mrsimulator.git (fetch)
upstream git://github.com/deepanshs/mrsimulator.git (push)
origin git@github.com:your-user-name/mrsimulator.git (fetch)
origin git@github.com:your-user-name/mrsimulator.git (push)

Build the development version of mrsimulator¶

OS-dependent prerequisites¶

Note

Installing OS-dependent prerequisites is a one-time process. If you are upgrading to a newer version of mrsimulator, skip to the next section.

OpenBLAS and FFTW libraries

On Linux, the package manager for your distribution is usually the easiest route to ensure you have the prerequisites to building the MRSimulator library. To build from source, you will need the OpenBLAS and FFTW development headers for your Linux distribution. Type the following command in the terminal based on your Linux distribution.

For (Debian/Ubuntu):

$ sudo apt-get install libopenblas-dev libfftw3-dev

For (Fedora/RHEL):

$ sudo yum install openblas-devel fftw-devel

Install a C/C++ compiler

The C-compiler comes with your Linux distribution. No further action is required.

OpenBLAS/Accelerate and FFTW libraries

You will require the brew package manager to install the development headers for the OpenBLAS (if applicable) and FFTW libraries. Read more on installing brew from homebrew.

Step-1 Install the FFTW library using the homebrew formulae.

$ brew install fftw

Step-2 By default, the MRSimulator package links to the openblas library for BLAS operations. Mac users may opt to choose the in-build Apple’s Accelerate library. If you opt for Apple’s Accelerate library, skip to Step-3. If you wish to link the mrsimulator package to the OpenBLAS library, type the following in the terminal,

$ brew install openblas

Step-3 If you choose to link the MRSimulator package to the OpenBLAS library, skip to the next section.

(a) You will need to install the BLAS development header for Apple’s Accelerate library. The easiest way is to install the Xcode Command Line Tools. Note this is a one-time installation. If you have previously installed the Xcode Command Line Tools, you may skip this sub-step. Type the following in the terminal,

$ xcode-select --install

(b) The next step is to let the MRSimulator setup know your preference. Open the settings.py file, located at the root level of the MRSimulator source code folder, in a text editor. You should see

# -*- coding: utf-8 -*-
# BLAS library
use_openblas = True
# mac-os only
use_accelerate = False

To link the MRSimulator package to Apple’s Accelerate library, change the fields to

# -*- coding: utf-8 -*-
# BLAS library
use_openblas = False
# mac-os only
use_accelerate = True

Install a C/C++ compiler

The C-compiler installs with the Xcode Command Line Tools. No further action is required.

Install conda

Skip this step if you already have miniconda or Anaconda for python >= 3.10 installed on your system. Download the latest version of conda on your operating system from either miniconda or Anaconda websites. Make sure you download conda for Python 3. Double-click the downloaded .exe file and follow the installation steps.

OpenBLAS and FFTW libraries

Launch the Anaconda prompt (it should be located under the start menu). Within the anaconda prompt, type the following to install the package dependencies.

$ conda install -c conda-forge openblas fftw

Install a C/C++ compiler

Because the core of the MRSimulator package is written in C, you will require a C-compiler to build and install the package. Download and install the Microsoft Visual C++ compiler from Build Tools for Visual Studio.

Build and install¶

Before building the development version of mrsimulator, install the development requirement packages with pip. In the directory where your copy of MRSimulator is, type:

$ pip install -r requirements-dev.txt
$ pip install -e .

As before, if you get an error that you don’t have the permission to install the package into the default site-packages directory, you may try installing by adding the --user option.

Note

If you are using a Mac with Apple Silicon and unable to install MRSimulator, open an issue on the GitHub page.

Note for the developers and contributors¶

Before commits: MRSimulator follows Python community standards for writing code and documentation. To help guide the developers and contributors toward these standards, we have created a .pre-commit-config.yaml file that, when used with pre-commit, will inspect the code and document for issues. To set up pre-commit, type the following one-time install statements in the terminals,

$ pre-commit install

Once set up, navigate to the root level of the MRSimulator folder and type

$ pre-commit run

The above statement auto-fixes some issues and lists others for you to fix. Review the changes and address the listed issues before a git commit.

Note

The pre-commit command ignores unstaged changes. Before running pre-commit run, make sure to stage files for a commit.

Running tests: We use the pytest module for unit tests. At the root level of the MRSimulator folder, type

$ pytest

which will run a series of tests alerting you to any unit tests that fail.

Checking test coverage: To check which lines in the codebase are covered when running a test, use the following command.

$ pytest --cov-report=html

To view the unit test coverage report, open the mrsimulator/htmlcov/index.html file in a web browser.

Building docs: We use the sphinx Python documentation generator for building docs. Navigate to the docs directory within the MRSimulator folder, and type,

$ make html

The above command will build the documentation and store the build at mrsimulator/docs/_build/html. Open the index.html file in a web browser within this folder to view the locally-built documentation.