This is a basic guide to setting up a development environment on your computer, to get you up and running with the nmrsim code base. It also provides brief guidelines for how to make a pull request. If you would like more information or guidance, or if these instructions are not working for you, you can create an Issue on GitHub and this guide can be improved.
- Developers Guide
- Creating a Development Environment
- Making a contribution
- Submit a pull request
- Code Style and Conventions
If you are completely new to Github, you may have to set up an account and install git. See the GitHub Help on Git Setup for more information.
Navigate to the nmrsim GitHub page, and click the “Fork” icon in the upper right. This will create your own copy of the repository that you can feel free to alter.
See the related GitHub Help on Forking a Repo for more info.
Using a terminal (e.g. Command Prompt on Windows; // on Mac), navigate to the directory where you would like to create the nmrsim project folder, then enter:
git clone https://github.com/your_GitHub_name_here/nmrsim.git cd nmrsim
The URL can be obtained from your fork’s GitHub page by clicking the “Clone or Download” button and copying the URL.
See the GitHub Help on Forking a Repo for more information.
For any Python project, you don’t want to install into your operating system’s Python. Instead, you should create a custom Python environment and install nmrsim plus dependencies there.
This can be tricky, and especially for Windows users may pose a significant barrier to entry. The instructions below have been tested for Mac and for Windows 10 machines that had an Anaconda install (and thus Python 3.6+). Linux users should be able to follow the Mac instructions, but can give feedback if they have trouble developing on a Linux machine. The examples use Python 3.7, but nmrsim should be compatible for 3.6+ (i.e. since the introduction of f-string syntax).
If your system already has a python version of 3.6 or higher, you can create a virtual environment from the command line with:
python -m venv env
This creates an ‘env’ folder with the python environment. Note that on your system you may need to use ‘python3’, ‘python3.7’ etc. instead of ‘python’ if you have more than one version of python installed (e.g. ‘python3’ if ‘python’ refers to version 2.7).
You can activate the environment with:
source env/bin/activate (Mac) env\Scripts\activate.bat (Windows)
NOTE: If you have an Anaconda install, and try to run the tests, it may fail. If you see two indicators for the environment in parentheses in the terminal, e.g.:
(env) (base) ...$
to make sure the conda environment isn’t superseding the venv environment.
You should see the (base) indicator disappear.
If your system does not have a Python version 3.6+ already installed, or if you want to have more than one version of Python on your system, look into the pyenv (Mac/Linux) or pyenv-win (Windows) libraries. Note that Windows 10 users can now get Python 3.7+ via the Microsoft store.
If you wish to deactivate the venv at any point,
deactivate from the command line.
It’s common for scientists to use an Anaconda or miniconda installation to manage their Python (or other software) dependencies. However, you will be installing packages in development mode with pip, and sometimes there are conflicts with pip- and conda-installed packages. This may work on your system, but if there are problems with package conflicts it may be best to use the venv option.
For example, the instructions worked on a 2019 Macbook Pro, but failed on a Windows 10 machine (despite the conda 3.7 environment being activated, the system Python 3.5 installation was still used to run pytest, causing any code with an f-string to fail).
To create a new Python environment named “nmrsim” and activate it, use the command line:
conda create --name nmrsim python=3.7 conda activate nmrsim (Mac) activate nmrsim (Windows)
If you later want to exit this environment, you can activate another environment, or enter:
conda deactivate (Mac) deactivate (Windows)
If you were to just install nmrsim directly from PyPI (by “pip install”), or if you just ran setup.py, the current nmrsim would be installed into your python environment immutably. Any changes you made to the code would not be noticed by you or the tests. Instead, you will install the package in “developer mode”. This will install nmrsim, plus dependencies. It will also install the developer dependencies, which are not required by casual nmrsim users, but are required for developers to run tests, check formatting and so on. From the command line, in the top nmrsim directory that contains setup.py, enter:
pip install -e ".[dev]"
To check your installation, run the tests using pytest, then navigate to the docs directory and build the documentation:
pytest cd docs make html
There will be several pop-up plots that are visual tests for correct behavior; close these windows as they pop up to proceed through the tests.
As an extra test of a correct installation, you can deliberately break some of the code you’re working on and re-run the tests to see the tests fail (assuming the code was covered by the tests).
Create a git branch with a descriptive name for your contribution, e.g.
git checkout -b add_dnmr_tutorial
Make your changes, and then:
When these tests both pass, navigate to the docs directory, and build the html documentation:
Open the docs/build/html/index.html page in your browser. If you made changes to the documentation, including public docstrings, navigate to where the change should appear and check that it looks OK. After you’re done with the documentation, run:
to delete the contents of the build directory prior to publishing your work.
Commit and push to your fork of nmrsim:
git status # check that your work is staged to commit git commit -m "Brief description of the change you made" git push
Pull requests should be made to nmrsim’s ‘develop’ branch, and not directly to ‘master’.
From your GitHub page for your fork, select the name of your working branch from the ‘branch’ drop-down menu (e.g. “add_dnmr_tutorial” using the above example). Click ‘New pull request’.
You should check that ‘base repository’ is ‘sametz/nmrsim’, ‘base’ is ‘develop’, ‘head repository’ is ‘yourGitHubname/nmrsim’, and ‘compare’ is your branch name (e.g. ‘add_dnmr_tutorial’). Check that you have a commit message (a longer message in the “Leave a comment” text field is optional) and click “Create pull request” when ready.
The package maintainer will respond via GitHub notification. If there is no response after a week, feel free to email them (sametz at udel dot edu) with ‘nmrsim’ somewhere in the subject line… they may be busy, on vacation or just distracted :) but will eventually respond.
If your code is passing the flake8 test, and if the html documentation looks OK, then it should be acceptable. Here are some of the guidelines:
PEP 8 (the Python style guide) is followed, with the following exceptions:
- The max line length is 119, the width of a GitHub preview. This can be exceeded with good reason. The PEP 8 guideline of 79 characters is a good goal, but readability (e.g. splitting up long URLs) shouldn’t be sacrificed.
- Some naming conventions are violated for consistency with NMR terms and with pre-existing code. For example, many variables are upper-case single letters, including H for Hamiltonian, J for coupling constant(s), and (scandalously) I (upper-case ‘i’) for signal intensity.
The project’s .flake8 file makes accomodations for these and other exceptions.
imports should be sorted into three categories, with a blank line separating the categories:
- standard library
- third-party libraries
- nmrsim modules
Within each, they should be sorted alphabetically (ignoring “from”).
We currently don’t use type annotations, because this is difficult to implement with numpy and related packages.
Docstrings are only required for public classes and functions (i.e. not for those whose name begins in a single underscore, e.g. _normalize). However, you may document private classes and functions if you wish– it can make the code’s purpose clearer to others, and it’s possible that private code may at some point be ‘promoted’ to the public API.
Currently, “test docstrings” are not used. If you think they should, feel free to make a case for them.
The nmrsim project uses Sphinx for documentation, and restructuredtext (.rst) for content. Semantic line breaks are encouraged– they make editing and formatting easier.