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ClimaAnalysis.jl

Analyzing and visualizing ClimaAtmos simulations

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ClimaAnalysis.jl is a Julia library to post-process and visualize ClimaAtmos simulations (and, more generally, NetCDF files).

Check out the documentation for more information and tutorials.

Features

  • Read, organize, and process NetCDF files
  • Visualize heatmaps and 1D profiles with Makie
  • Visualize heatmaps on a globe with GeoMakie
  • Apply averages and other reductions to the output variables
  • Slice variables along a given value (e.g., take the slice with altitude of 500 meters)
  • Window variables within given ranges (e.g., select times between 10 and 100 days)
  • Perform mathematical operations between output variables
  • Extract dimensions from conventional names (e.g., times)
  • Interpolate output variables onto arbitrary points
  • Reinterpolate output variables onto pressure levels

ClimaAnalysis.jl Developer Guidelines

These guidelines aim to ensure consistent code quality, maintainability, and a smooth collaborative workflow for ClimaAnalysis.jl. Please, read these guidelines even if you are familiar with other CliMA packages as there may be some differences.

Tests and environments

We prioritize well-tested code to guarantee ClimaAnalysis.jl functions reliably. Here are some principles we follow:

Tests are collected in the test folder and are exclusively there

This means that all the tests can be run with Pkg.test().

There are no checked Manifest.toml files

While checking in Manifest.toml files ensures reproducibility, it also introduces some nuisance, including:

  • lot of git/repository noise just for "up deps";
  • multiple environments that have to be managed;
  • busywork to keep the manifests updated.

In this repository, we have two environments:

  • project,
  • documentation.

The project environment defines the test dependencies in its extras (to reduce the number of environments and to avoid the "cannot merge projects" problem).

:note: Please, open an issue if you find workflow problems/friction with this system.

Running tests

ClimaAnalysis.jl defines the test dependencies directly in the main Project.toml. This means that the package can be tested simply by running ] test in a Julia REPL, as shown below:

Start a Julia session in the ClimaAnalysis directory:

julia --project

Enter Pkg mode by typing ]. This will change the prompt. Run test.

When doing so, Julia will start a new temporary environment where the tests are run in isolation. Tests are running checking for in-bounds and for deprecations, and this can result in code invalidation and new precompilation.

Note, the project environment does not contain the test dependencies. Therefore, you will find that some dependencies are missing if you try "manually" run the test in a REPL. To solve this problem, use TestEnv. Install TestEnv in your base environment (julia -e 'using Pkg; Pkg.add("TestEnv")'). Then, when you want to use the test dependencies, activate it from your REPL with using TestEnv; TestEnv.activate(). This will bump you to an environment where the test dependencies are available.

:note: Please, open an issue if you find workflow problems/friction with this system.

Code Formatting with JuliaFormatter.jl

One of the tests consists in checking that the code is uniformly formatted. We use JuliaFormatter.jl to achieve consistent formatting. Here's how to use it:

You can either install in your base environment with

julia -e 'using Pkg; Pkg.add("JuliaFormatter")'

or use it from within the TestEnv (or base) environments (see previous section).

Then, you can format the package running:

using JuliaFormatter; format(".")

or just with format(".") if the package is already imported.

The rules for formatting are defined in the .JuliaFormatter.toml.

If you are used to formatting from the command line instead of the REPL, you can install JuliaFormatter in your base environment and call

julia -e 'using JuliaFormatter; format(".")'

You could also define a shell alias

alias julia_format_here="julia -e 'using JuliaFormatter; format(\".\")'"

:note: Please, open an issue if you find workflow problems/friction with this system.

Documentation

Documentation is generated with Documenter.jl. We strive to have complete and up-to-date information.

To generate documentation, run

julia --project=docs docs/make.jl

Please, update the documentation if you add new features or change the behavior of existing ones.

We encourage using jldoctest to add and test examples in docstrings.

Pull Request (PR) and commits

Here's how to structure your contributions effectively:

  • Descriptive Title: Briefly summarize the changes your PR introduces. Commit titles should preferably be under 50 characters, start with a capital latter, and use imperative verbs (e.g., "Remove superfluous function call").
  • Detailed Description: Explain the purpose of your changes. Focus on the intent.
  • Breaking Changes: If your PR introduces breaking changes, highlight them clearly in the description.

Your pull request can contain one or multiple commits. In either cases, it is important that each commit is atomic (meaning that each commit represents a single logical change).

Please, squash commits that represent a single logical change (e.g., do not have two commits when the second just fixes the first).

Pull requests are not merged, but rebased, ensuring a linear history (this is handled automatically by GitHub).