Development and contribution

Overview

Teaching: 10 min
Exercises: 20 min
Compatibility: ESMValTool v2.9.0

Questions

• What is a development installation?

• How can I test new or improved code?

• How can I incorporate my contributions into ESMValTool?

Objectives

• Execute a successful ESMValTool installation from the source code.

• Contribute to ESMValTool development.

We now know how ESMValTool works, but how do we develop it? ESMValTool is an open-source project in ESMValGroup. We can contribute to its development by:

• a new or updated recipe script, see lesson on Writing your own recipe
• a new or updated diagnostics script, see lesson on Writing your own diagnostic script
• a new or updated cmorizer script, see lesson on CMORization: Using observational datasets
• helping with reviewing process of pull requests, see ESMValTool documentation on Review of pull requests

In this lesson, we first show how to set up a development installation of ESMValTool so you can make changes or additions. We then explain how you can contribute these changes to the community.

Git knowledge

For this episode, you need some knowledge of Git. You can refresh your knowledge in the corresponding Git carpentries course.

Development installation

We’ll explore how ESMValTool can be installed it in a develop mode. Even if you aren’t collaborating with the community, this installation is needed to run your new codes with ESMValTool. Let’s get started.

1 Source code

The ESMValTool source code is available on a public GitHub repository: https://github.com/ESMValGroup/ESMValTool. To obtain the code, there are two options:

1. Download the code from the repository. A ZIP file called ESMValTool-main.zip is downloaded. To continue the installation, unzip the file, move to the ESMValTool-main directory and then follow the sequence of steps starting from the section on ESMValTool dependencies below.
2. Clone the repository if you want to contribute to the ESMValTool development:

git clone https://github.com/ESMValGroup/ESMValTool.git

This command will ask your GitHub username and a personal token as password. Please follow instructions on GitHub token authentication requirements to create a personal access token. Alternatively, you could generate a new SSH key and add it to your GitHub account. After the authentication, the output might look like:

Cloning into 'ESMValTool'...
remote: Enumerating objects: 163, done.
remote: Counting objects: 100% (163/163), done.
remote: Compressing objects: 100% (125/125), done.
remote: Total 95049 (delta 84), reused 76 (delta 30), pack-reused 94886
Receiving objects: 100% (95049/95049), 175.16 MiB | 5.48 MiB/s, done.
Resolving deltas: 100% (68808/68808), done.

Now, a folder called ESMValTool has been created in your working directory. This folder contains the source code of the tool. To continue the installation, we move into the ESMValTool directory:

cd ESMValTool

Note that the main branch is checked out by default. We can see this if we run:

git status

On branch main
Your branch is up to date with 'origin/main'.

nothing to commit, working tree clean

2 ESMValTool dependencies

Please don’t forget if an esmvaltool environment is already created following the lesson Installation, we should choose another name for the new environment in this lesson.

ESMValTool now uses mamba instead of conda for the recommended installation. For a minimal mamba installation, see section Install Mamba in lesson Installation.

It is good practice to update the version of mamba and conda on your machine before setting up ESMValTool. This can be done as follows:

mamba update --name base mamba conda

To simplify the installation process, an environment file environment.yml is provided in the ESMValTool directory. We create an environment by running:

mamba env create --name esmvaltool --file environment.yml

The environment is called esmvaltool by default. If an esmvaltool environment is already created following the lesson Installation, we should choose another name for the new environment in this lesson by:

mamba env create --name a_new_name --file environment.yml

This will create a new conda environment and install ESMValTool (with all dependencies that are needed for development purposes) into it with a single command.

For more information see conda managing environments.

Now, we should activate the environment:

conda activate esmvaltool

where esmvaltool is the name of the environment (replace by a_new_name in case another environment name was used).

3 ESMValTool installation

ESMValTool can be installed in a develop mode by running:

pip install --editable '.[develop]'

This will add the esmvaltool directory to the Python path in editable mode and install the development dependencies. We should check if the installation works properly. To do this, run the tool with:

esmvaltool --help

If the installation is successful, ESMValTool prints a help message to the console.

Checking the development installation

We can use the command mamba list to list installed packages in the esmvaltool environment. Use this command to check that ESMValTool is installed in a develop mode.

Tip: see the documentation on conda list.

Solution

Run:

mamba list esmvaltool

# Name                    Version                   Build  Channel
esmvaltool                2.10.0.dev3+g2dbc2cfcc    pypi_0   pypi

4 Updating ESMValTool

The main branch has the latest features of ESMValTool. Please make sure that the source code on your machine is up-to-date. If you obtain the source code using git clone as explained in step 1 Source code, you can run git pull to update the source code. Then ESMValTool installation will be updated with changes from the main branch.

Contribution

We have seen how to install ESMValTool in a develop mode. Now, we try to contribute to its development. Let’s see how this can be achieved. We first discuss our ideas in an issue in ESMValTool repository. This can avoid disappointment at a later stage, for example, if more people are doing the same thing. It also gives other people an early opportunity to provide input and suggestions, which results in more valuable contributions.

Then, we create a new branch locally and start developing new codes. To create a new branch:

git checkout -b your_branch_name

If needed, a link to a git tutorial can be found in Setup.

Once our development is finished, we can initiate a pull request. To this end, we encourage you to join the ESMValTool development team.

For more extensive documentation on contributing code, including a section on the GitHubWorkflow, please see the Contributing code and documentation section in the ESMValtool documentation.

Review process

The pull request will be tested, discussed and merged as part of the “review process”. The process will take some effort and time to learn. However, a few (command line) tools can get you a long way, and we’ll cover those essentials in the next sections.

Tip: we encourage you to keep the pull requests small. Reviewing small incremental changes is more efficient.

Working example

We saw the ‘warming stripes’ diagnostic in lesson Writing your own recipe. Imagine the following task: you want to contribute warming stripes recipe and diagnostics to ESMValTool. You have to add the diagnostics warming_stripes.py and the recipe recipe_warming_stripes.yml to their locations in ESMValTool directory. After these changes, you should also check if everything works fine. This is where we take advantage of the tools that are introduced later.

Let’s get started. Note that since this is an exercise to get familiar with the development and contribution process, we will not create a GitHub issue at this time but proceed as though it has been done.

Check code quality

We aim to adhere to best practices and coding standards. There are several tools that check our code against those standards like:

• flake8 for checking against the PEP8 style guide
• yapf to ensure consistent formatting for the whole project
• isort to consistently sort the import statements
• yamllint to ensure there are no syntax errors in our recipes and config files
• lintr for diagnostic scripts written in R
• codespell to check grammar

The good news is that pre-commit has been already installed when we chose development installation. pre-commit is a command line and runs all of those tools. It also fixes some of those errors. To explore other tools, have a look at ESMValTool documentation on Code style.

Using pre-commit

Let’s checkout our local branch and add the script warming_stripes.py to the esmvaltool/diag_scripts directory.

cd ESMValTool
git checkout your_branch_name
cp path_of_warming_stripes.py esmvaltool/diag_scripts/

By default, pre-commit only runs on the files that have been staged in git:

git status
git add esmvaltool/diag_scripts/warming_stripes.py
pre-commit run --files esmvaltool/diag_scripts/warming_stripes.py

Inspect the output of pre-commit and fix the remaining errors.

Solution

The tail of the output of pre-commit:

Check for added large files..............................................Passed
Check python ast.........................................................Passed
Check for case conflicts.................................................Passed
Check for merge conflicts................................................Passed
Debug Statements (Python)................................................Passed
Fix End of Files.........................................................Passed
Trim Trailing Whitespace.................................................Passed
yamllint.............................................(no files to check)Skipped
nclcodestyle.........................................(no files to check)Skipped
style-files..........................................(no files to check)Skipped
lintr................................................(no files to check)Skipped
codespell................................................................Passed
isort....................................................................Passed
yapf.....................................................................Passed
docformatter.............................................................Failed
- hook id: docformatter
- files were modified by this hook
flake8...................................................................Failed
- hook id: flake8
- exit code: 1

esmvaltool/diag_scripts/warming_stripes.py:20:5:
F841 local variable 'nx' is assigned to but never used

As can be seen above, there are two Failed check:

1. docformatter: it is mentioned that “files were modified by this hook”. We run git diff to see the modifications. The output includes the following:

   +in the form of the popular warming stripes figure by Ed Hawkins."""
   

   The syntax """ at the end of docstring is moved by one line. Shifting it to the next line should fix this error.

2. flake8: the error message is about an unused local variable nx. We should check our codes regarding the usage of nx. For now, let’s assume that it is added by mistake and remove it. Note that you have to run git add again to re-stage the file. Then rerun pre-commit and check that it passes.

Run unit tests

Previous section introduced some tools to check code style and quality. There is lack of mechanism to determine whether or not our code is getting the right answer. To achieve that, we need to write and run tests for widely-used functions. ESMValTool comes with a lot of tests that are in the folder tests.

To run tests, first we make sure that the working directory is ESMValTool and our local branch is checked out. Then, we can run tests using pytest locally:

pytest

Tests will also be run automatically by CircleCI, when you submit a pull request.

Running tests

Make sure our local branch is checked out and add the recipe recipe_warming_stripes.yml to the esmvaltool/recipes directory:

cp path_of_recipe_warming_stripes.yml esmvaltool/recipes/

Run pytest and inspect the results, this might take a few minutes. If a test is failed, try to fix it.

Solution

Run:

pytest

When pytest run is complete, you can inspect the test reports that are printed in the console. Have a look at the second section of the report FAILURES:

================================ FAILURES ==========================================
______________ test_recipe_valid[recipe_warming_stripes.yml] ______________

The test message shows that the recipe recipe_warming_stripes.yml is not a valid recipe. Look for a line that starts with an E in the rest of the message:

E           esmvalcore._task.DiagnosticError: Cannot execute script
'~/esmvaltool_tutorial/warming_stripes.py' (~/esmvaltool_tutorial/warming_stripes.py):
file does not exist.

To fix the recipe, we need to edit the path of the diagnostic script as warming_stripes.py:

   scripts:
     warming_stripes_script:
       script: warming_stripes.py

For details, see lesson Writing your own diagnostic script.

Build documentation

When we add or update a code, we also update its corresponding documentation. The ESMValTool documentation is available on docs.esmvaltool.org. The source files are located in ESMValTool/doc/sphinx/source/.

To build documentation locally, first we make sure that the working directory is ESMValTool and our local branch is checked out. Then, we run:

sphinx-build -Ea doc/sphinx/source/ doc/sphinx/build/

Similar to code, documentation should be well written and adhere to standards. If the documentation is built properly, the previous command prints a message to the console:

build succeeded.

The HTML pages are in doc/sphinx/build.

The main page of the documentation has been built into index.html in doc/sphinx/build/ directory. To preview this page locally, we open the file in a web browser:

xdg-open doc/sphinx/build/index.html

Creating a documentation

In previous exercises, we added the recipe recipe_warming_stripes.yml to ESMValTool. Now, we create a documentation file recipe_warming_stripes.rst for this recipe:

nano doc/sphinx/source/recipes/recipe_warming_stripes.rst

Add a reference i.e. .. _recipe_warming_stripes:, a section title and some text about the recipe like:

.. _recipe_warming_stripes:

Reproducing Ed Hawkins' warming stripes visualization
======================================================

This recipe produces warming stripes plots.

Save and close the file. We can think of this file as one page of a book. Examples of documentation pages can be found in the folder ESMValTool/doc/sphinx/source/recipes. Then, we need to decide where this page should be located inside the book. The table of content is defined by index.rst. Let’s have a look at the content:

nano doc/sphinx/source/recipes/index.rst

Add the recipe name i.e. recipe_warming_stripes to the section Other in this file and preview the recipe documentation page locally.

Solution

First, we add the recipe name recipe_warming_stripes to the section Other:

Other
^^^^^
.. toctree::
  :maxdepth: 1
  ...
  ...
  recipe_warming_stripes

Then, we build and preview the documentation page:

sphinx-build -Ea doc/sphinx/source/ doc/sphinx/build/
xdg-open doc/sphinx/build/recipes/recipe_warming_stripes.html

Congratulations! You are now ready to make a pull request.

Key Points

• A development installation is needed if you want to incorporate your code into ESMValTool.

• Contributions include adding a new or improved script or helping with a review process.

• There are several tools to help improve the quality of your code.

• It is possible to run tests on your machine.

• You can preview documentation pages locally.