OceanAnalysis.jl

OceanAnalysis.jl is a Julia package designed to facilitate the analysis of oceanographic data. It is at a very early stage of development by someone who is in the early steps of exploring Julia as a supplement to R.

Installation

Official version

Once (if) the package is accepted by the Julia archive system, you may install it by typing the following in a Julia console.

julia using Pkg ; Pkg.add("OceanAnalysis")

Development version

Somewhat stable (for early users)

Type the following in a Julia console to use the "main" branch from the development website. This is updated after significant changes to the "develop" branch (that have passed the built-in test suite).

julia using Pkg ; Pkg.add(url="https://github.com/dankelley/OceanAnalysis.jl")

Unstable (for developers)

Type the following in a Julia console to use the "develop" branch from the development website. This is updated very frequently, because the author tests changes using this method.

julia using Pkg ; Pkg.add(url="https://github.com/dankelley/OceanAnalysis.jl", rev="develop")

Brittle (for the core developer)

In the commandline, navigate to the local source for the library. Then start a Julia console and type the following.

julia ] develop .

This sets Julia to look for changes in the files in that directory. Thereafter, issuing using OceanAnalysis in a Julia session will rebuild from that local source. Note that using the Pkg.add(url=...) method after using the develop method will reset things so that Julia rebuilds from the github page instead of the local files.

Usage Examples

CTD file

```julia

Read a built-in CTD file, and plot some hydrographic diagrams

using OceanAnalysis, Plots, Measures filename = joinpath(dirname(dirname(pathof(OceanAnalysis))), "data", "ctd.cnv") ctd = readctdcnv(filename) p1 = plotprofile(ctd, "SA") p2 = plotprofile(ctd, "CT") p3 = plot_TS(ctd) plot(p1, p2, p3, layout=(1, 3), size=(800, 400), margin=0.25cm) ```

Argo file

```julia

Read a built-in Argo file, and plot some hydrographic diagrams

using OceanAnalysis, Plots, Measures filename = joinpath(dirname(dirname(pathof(OceanAnalysis))), "data", "D4902911095.nc") ctd = readargo(filename) p1 = plotprofile(ctd, "SA") p2 = plotprofile(ctd, "CT") p3 = plot_TS(ctd) plot(p1, p2, p3, layout=(1, 3), size=(800, 400), margin=0.25cm) ```

History of changes

0.1.0

This version is in use by the author, and may also be suitable for other users who are comfortable with the possibility of changes to function names and arguments.

Breaking changes

• Switch to snake-case for function names and argument names. For example, the name of plotTS() was changed to plot_TS(), and its argument drawFreezing was changed to draw_freezing. The point of this is to fit what seems to be the Julia convention, which has the benefit of reinforcing to the user that this is distinct from the oce R package, which uses the camel-case notation.

Non-breaking changes

• Add pretty(), for use in contouring (especially for plot_TS()).
• Add depth_from_pressure(), z_from_pressure(), pressure_from_depth(), and pressure_from_z().
• Change the second digit of version string to indicate that the package is becoming suitable for at least exploratory testing on real data.

0.0.3

Breaking changes

There are no breaking changes; all change are additions or bug fixes.

Non-breaking changes

• Add built-in data file ctd.cnv.nc, and use it in an example in the Ctd() documentation.
• Add built-in data file D4902911_095.nc, and use it in an example in the plot_profile() documentation.
• get_element() can now return "N2".
• plot_profile() can now plot N2".

0.0.2

Breaking changes

There are no breaking changes; all change are additions or bug fixes.

Non-breaking changes

• Add N2() to compute the square of the buoyancy frequency.

Developer notes

Adding a package dependency

For example, to add Downloads as a dependency to the present package, navigate to the present-package source directory, start a Julia session, and type the following.

julia ] activate . add Downloads

Running tests

There is a small test suite built into the package. To run it, type the following in a Julia console:

julia ] activate . test OceanAnalysis

Building and viewing documentation on development machine

To build, type the following in a shell terminal. (Change the /Users/kelley part, as appropriate.)

sh cd /Users/kelley/git/OceanAnalysis.jl julia --project=. docs/make.jl

To view, do the following in a Julia console. (Change the /Users/kelley part, as appropriate.)

julia cd("/Users/kelley/git/OceanAnalysis.jl/") using LiveServer serve(; dir="docs/build", launch_browser=true)