Practices

  • Purpose: In the development of SimPEG, we strive to follow best practices. Here, we provide an overview of those practices and some tools we use to support them.

Here we cover

Testing

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On each update, SimPEG is tested using the continuous integration service Travis CI. We use Codecov to check and provide stats on how much of the code base is covered by tests. This tells which lines of code have been run in the test suite. It does not tell you about the quality of the tests run! In order to assess that, have a look at the tests we are running - they tell you the assumptions that we do not want to break within the code base.

Within the repository, the tests are located in the top-level tests directory. Tests are organized similar to the structure of the repository. There are several types of tests we employ, this is not an exhaustive list, but meant to provide a few places to look when you are developing and would like to check that the code you wrote satisfies the assumptions you think it should.

All tests inherit from unittest which is a part of core python. Checkout the docs on unittest.

Compare with known values

In a simple case, you might now the exact value of what the output should be and you can assert that this is in fact the case. For example, in test_basemesh.py, we setup a 3D BaseRectangularMesh and assert that it has 3 dimensions.

import unittest
import sys
from SimPEG.Mesh.BaseMesh import BaseRectangularMesh
import numpy as np

class TestBaseMesh(unittest.TestCase):

    def setUp(self):
        self.mesh = BaseRectangularMesh([6, 2, 3])

    def test_meshDimensions(self):
        self.assertTrue(self.mesh.dim, 3)

The class inherits from unittest.TestCase. When running the tests, the setUp is run first, in this case we attach a mesh to the instance of this class, and then all functions with the naming convention test_XXX are run. Here we check that the dimensions are correct for the 3D mesh.

If the value is not an integer, you can be subject to floating point errors, so assertTrue might be too harsh. In this case, you will want to use a tolerance. For instance in test_maps.py

class MapTests(unittest.TestCase):

    # method setUp is used to create meshes

    def test_mapMultiplication(self):
        M = Mesh.TensorMesh([2,3])
        expMap = Maps.ExpMap(M)
        vertMap = Maps.SurjectVertical1D(M)
        combo = expMap*vertMap
        m = np.arange(3.0)
        t_true = np.exp(np.r_[0,0,1,1,2,2.])
        self.assertLess(np.linalg.norm((combo * m)-t_true,np.inf),TOL)

These are rather simple examples, more advanced tests might include solving an electromagnetic problem numerically and comparing it to an analytical solution , or performing an adjoint test to test Jvec and Jtvec.

Order and Derivative Tests

Order tests can be used when you are testing differential operators (we are using a second-order, staggered grid discretization for our operators). For example, testing a 2D curl operator in test_operators.py

import numpy as np
import unittest
from SimPEG.Tests import OrderTest

class TestCurl2D(OrderTest):
    name = "Cell Grad 2D - Dirichlet"
    meshTypes = ['uniformTensorMesh']
    meshDimension = 2
    meshSizes = [8, 16, 32, 64]

    def getError(self):
        # Test function
        ex = lambda x, y: np.cos(y)
        ey = lambda x, y: np.cos(x)
        sol = lambda x, y: -np.sin(x)+np.sin(y)

        sol_curl2d = call2(sol, self.M.gridCC)
        Ec = cartE2(self.M, ex, ey)
        sol_ana = self.M.edgeCurl*self.M.projectFaceVector(Ec)
        err = np.linalg.norm((sol_curl2d-sol_ana), np.inf)

        return err

    def test_order(self):
        self.orderTest()

Derivative tests are a particular type or Order and Derivative Tests, and since they are used so extensively, SimPEG includes a checkDerivative method.

In the case of testing a derivative, we consider a Taylor expansion of a function about \(x\). For a small perturbation \(\Delta x\),

\[f(x + \Delta x) \simeq f(x) + J(x) \Delta x + \mathcal{O}(h^2)\]

As \(\Delta x\) decreases, we expect \(\|f(x) - f(x + \Delta x)\|\) to have first order convergence (e.g. the improvement in the approximation is directly related to how small \(\Delta x\) is, while if we include the first derivative in our approximation, we expect that \(\|f(x) + J(x)\Delta x - f(x + \Delta x)\|\) to converge at a second-order rate. For example, all maps have an associated derivative test . An example from test_FDEM_derivs.py

def derivTest(fdemType, comp):

    # setup problem, survey

    def fun(x):
        return survey.dpred(x), lambda x: prb.Jvec(x0, x)
    return Tests.checkDerivative(fun, x0, num=2, plotIt=False, eps=FLR)

Style

Code issues

Consistency make code more readable and easier for collaborators to jump in. PEP 8 provides conventions for coding in Python. SimPEG is currently not PEP 8 compliant, but we are working towards it and would appreciate contributions that do too!

There are a few resources we use to promote these practices: the service Quantified Code to check for consistency (... we have some work to do. Pull requests are welcome!)

Sublime has PEP 8 linter packages that you can use. I use SublimeLinter-pep8. You can install it by going to your package manager (cmd + shift + p), install package and search for SublimeLinter-pep8. Installation instructions are available at https://github.com/SublimeLinter/SublimeLinter-pep8.

This highlights and gives you tips on how to correct the code.

../../_images/pep8sublime.png

Below is a sample user-settings configuration for the SublimeLinter (Sublime Text > Preferences > Package Settings > SublimeLinter > Settings-User)

{
    "user": {
        "debug": false,
        "delay": 0.25,
        "error_color": "D02000",
        "gutter_theme": "Packages/SublimeLinter/gutter-themes/Default/Default.gutter-theme",
        "gutter_theme_excludes": [],
        "lint_mode": "background",
        "linters": {
            "pep8": {
                "@disable": false,
                "args": [],
                "excludes": [],
                "ignore": "",
                "max-line-length": null,
                "select": ""
            },
            "proselint": {
                "@disable": false,
                "args": [],
                "excludes": []
            }
        },
        "mark_style": "solid underline",
        "no_column_highlights_line": false,
        "passive_warnings": false,
        "paths": {
            "linux": [],
            "osx": [
                "/anaconda/bin"
            ],
            "windows": []
        },
        "python_paths": {
            "linux": [],
            "osx": [],
            "windows": []
        },
        "rc_search_limit": 3,
        "shell_timeout": 10,
        "show_errors_on_save": false,
        "show_marks_in_minimap": true,
        "syntax_map": {
            "html (django)": "html",
            "html (rails)": "html",
            "html 5": "html",
            "javascript (babel)": "javascript",
            "magicpython": "python",
            "php": "html",
            "python django": "python",
            "pythonimproved": "python"
        },
        "warning_color": "DDB700",
        "wrap_find": true
    }
}

Pull Requests

Pull requests are a chance to get peer review on your code. For the git flow, we do all pull requests onto dev before merging to master. If you are working on a specific geophysical application, e.g. electromagnetics, pull requests should first go through that method’s dev branch, in this case, em/dev. This way, we make sure that new changes are up-to date with the given method, and there is a chance to catch bugs before putting changes onto master. We do code reviews on pull requests, with the aim of promoting best practices and ensuring that new contributions can be built upon by the SimPEG community. For more info on best practices for version control and git flow, check out the article A successful git branching model

Licensing

MIT license

We want SimPEG to be a useful resource for the geoscience community and believe that following open development practices is the best way to do that. SimPEG is licensed under the MIT license which is allows open and commercial use and extension of SimPEG. It does not force packages that use SimPEG to be open source nor does it restrict commercial use.