User Directions

Table of Contents

How to Install and Use

To install OceanRobots.jl in julia proceed as usual via the package manager (using Pkg; Pkg.add("OceanRobots")).

To run a notebook interactively (.jl files) you want to use Pluto.jl. For example, copy and paste one of the above code links in the Pluto.jl interface. This will let you spin up the notebook in a web browser from the copied URL.

All you need to do beforehand is to install julia and Pluto.jl. The installation of OceanRobots.jl and other Julia packages will then happen automatically when you run the notebook.

You can also download the notebooks folder and run them as normal Julia programs. We recommend runing each notebook in its own environment as shown below.

Note

To download OceanRobots.jl folder, which includes the notebooks folder, you can use Git.jl.

using Pkg; Pkg.add("Git"); using Git
url="https://github.com/JuliaOcean/OceanRobots.jl"
run(`$(git()) clone $(url)`)
using Pkg; Pkg.add("Pluto"); using Pluto

notebook="MITgcm.jl/examples/Float_Argo.jl"
Pluto.activate_notebook_environment(notebook)
Pkg.instantiate()
include(notebook)
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
  No Changes to `~/work/OceanRobots.jl/OceanRobots.jl/docs/Project.toml`
  No Changes to `~/work/OceanRobots.jl/OceanRobots.jl/docs/Manifest.toml`

[ Info: REPL environment updated from notebook ✓



   Installed LRUCache ──────────────── v1.6.1
   Installed Hyperscript ───────────── v0.0.5
   Installed Dataverse ─────────────── v0.2.5
   Installed PNGFiles ──────────────── v0.4.3
   Installed JpegTurbo ─────────────── v0.1.5
   Installed HypergeometricFunctions ─ v0.3.27
   Installed OffsetArrays ──────────── v1.15.0
   Installed Cairo_jll ─────────────── v1.18.2+1
   Installed EnumX ─────────────────── v1.0.4
   Installed ConcurrentUtilities ───── v2.4.3
   Installed InlineStrings ─────────── v1.4.2
   Installed PlutoUI ───────────────── v0.7.61
   Installed StaticArrays ──────────── v1.9.11
   Installed FileIO ────────────────── v1.16.6
   Installed Pango_jll ─────────────── v1.55.5+0
   Installed Hwloc_jll ─────────────── v2.11.2+3
   Installed FreeType2_jll ─────────── v2.13.3+1
   Installed NetCDF_jll ────────────── v400.902.209+0
   Installed DataStructures ────────── v0.18.20
   Installed OceanRobots ───────────── v0.2.15
   Installed JLD2 ──────────────────── v0.5.11
   Installed HDF5_jll ──────────────── v1.14.2+1
   Installed CodecZlib ─────────────── v0.7.6
   Installed libpng_jll ────────────── v1.6.46+0
   Installed ColorSchemes ──────────── v3.28.0
   Installed MPICH_jll ─────────────── v4.2.3+0
   Installed oneTBB_jll ────────────── v2021.12.0+0
   Installed ColorTypes ────────────── v0.11.5
   Installed Zstd_jll ──────────────── v1.5.7+0
   Installed libzip_jll ────────────── v1.11.2+2
   Installed JSON3 ─────────────────── v1.14.1
   Installed OpenMPI_jll ───────────── v5.0.6+0
   Installed ColorVectorSpace ──────── v0.10.0
   Installed MIMEs ─────────────────── v1.0.0
   Installed CommonDataModel ───────── v0.3.7
   Installed Blosc_jll ─────────────── v1.21.6+2
   Installed NCDatasets ────────────── v0.14.6
   Installed MeshArrays ────────────── v0.3.19
   Installed YAML ──────────────────── v0.4.12
   Installed DocStringExtensions ───── v0.9.3
   Installed IntervalArithmetic ────── v0.22.22
   Installed Pixman_jll ────────────── v0.43.4+0
   Installed Adapt ─────────────────── v4.1.1
   Installed OpenSSL_jll ───────────── v3.0.15+3
   Installed XML2_jll ──────────────── v2.13.5+0
   Installed MakieCore ─────────────── v0.9.0
   Installed CairoMakie ────────────── v0.13.1
   Installed GeometryBasics ────────── v0.5.2
   Installed MPItrampoline_jll ─────── v5.5.1+2
   Installed FilePathsBase ─────────── v0.9.22
   Installed URIs ──────────────────── v1.5.1
   Installed QuadGK ────────────────── v2.11.1
   Installed Requires ──────────────── v1.3.0
   Installed StringManipulation ────── v0.4.0
   Installed DiskArrays ────────────── v0.4.8
   Installed Distributions ─────────── v0.25.117
   Installed Makie ─────────────────── v0.22.1
Precompiling project...
    528.5 ms  ✓ EnumX
    660.1 ms  ✓ Requires
    835.4 ms  ✓ URIs
    939.5 ms  ✓ InlineStrings
    522.3 ms  ✓ CodecZlib
    766.4 ms  ✓ LRUCache
   2372.0 ms  ✓ OffsetArrays
   1279.3 ms  ✓ ConcurrentUtilities
    822.4 ms  ✓ DocStringExtensions
   1142.1 ms  ✓ Hyperscript
   2373.0 ms  ✓ MIMEs
    768.5 ms  ✓ OpenSSL_jll
    742.1 ms  ✓ libpng_jll
    793.1 ms  ✓ oneTBB_jll
    917.6 ms  ✓ Hwloc_jll
    908.3 ms  ✓ Pixman_jll
    917.8 ms  ✓ Zstd_jll
   4045.2 ms  ✓ ColorTypes
   1722.2 ms  ✓ FilePathsBase
    914.9 ms  ✓ FreeType2_jll
   2799.4 ms  ✓ DataStructures
   1017.1 ms  ✓ XML2_jll
   3415.6 ms  ✓ StringManipulation
   1502.5 ms  ✓ MPItrampoline_jll
    650.2 ms  ✓ Adapt
   2085.8 ms  ✓ YAML
   4588.1 ms  ✓ IntervalArithmetic
   1544.4 ms  ✓ InlineStrings → ParsersExt
    559.0 ms  ✓ LRUCache → SerializationExt
   1803.5 ms  ✓ DiskArrays
   1933.7 ms  ✓ MKL_jll
   7884.9 ms  ✓ FileIO
   2648.3 ms  ✓ OpenMPI_jll
  14018.3 ms  ✓ StaticArrays
   1058.8 ms  ✓ Blosc_jll
    924.9 ms  ✓ libzip_jll
   1919.7 ms  ✓ MPICH_jll
   8411.6 ms  ✓ HypergeometricFunctions
    990.5 ms  ✓ FilePathsBase → FilePathsBaseMmapExt
   2516.5 ms  ✓ FilePathsBase → FilePathsBaseTestExt
   2075.3 ms  ✓ QuadGK
   4148.2 ms  ✓ ColorVectorSpace
    795.8 ms  ✓ OffsetArrays → OffsetArraysAdaptExt
    986.8 ms  ✓ IntervalArithmetic → IntervalArithmeticIntervalSetsExt
   2601.6 ms  ✓ CommonDataModel
   1459.2 ms  ✓ IntervalArithmetic → IntervalArithmeticRecipesBaseExt
   7118.4 ms  ✓ PlutoUI
  19527.3 ms  ✓ JSON3
   1125.6 ms  ✓ StaticArrays → StaticArraysChainRulesCoreExt
    911.0 ms  ✓ StaticArrays → StaticArraysStatisticsExt
   4980.0 ms  ✓ Cairo_jll
   1050.7 ms  ✓ Adapt → AdaptStaticArraysExt
   1995.7 ms  ✓ HDF5_jll
  13393.0 ms  ✓ Distributions
    974.9 ms  ✓ ColorVectorSpace → SpecialFunctionsExt
  18205.7 ms  ✓ GeometryBasics
  12357.9 ms  ✓ ColorSchemes
  33955.6 ms  ✓ FileIO → HTTPExt
   8428.8 ms  ✓ MeshArrays
   2406.5 ms  ✓ Pango_jll
   1851.9 ms  ✓ NetCDF_jll
   1727.9 ms  ✓ Distributions → DistributionsTestExt
   1757.1 ms  ✓ Distributions → DistributionsChainRulesCoreExt
  56601.3 ms  ✓ JLD2
   9231.2 ms  ✓ MakieCore
   8201.6 ms  ✓ NCDatasets
  11353.2 ms  ✓ MeshArrays → MeshArraysDataDepsExt
  37780.0 ms  ✓ JpegTurbo
  49471.4 ms  ✓ PNGFiles
   4136.8 ms  ✓ MeshArrays → MeshArraysJLD2Ext
   5667.4 ms  ✓ MeshArrays → MeshArraysShapefileExt
 118562.3 ms  ✓ Dataverse
  34038.2 ms  ✓ OceanRobots
 192051.1 ms  ✓ Makie
   9635.1 ms  ✓ MeshArrays → MeshArraysMakieExt
  11572.1 ms  ✓ OceanRobots → OceanRobotsMakieExt
  43465.3 ms  ✓ CairoMakie
  77 dependencies successfully precompiled in 331 seconds. 284 already precompiled.
  70 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions. Otherwise, loading dependents of these packages may trigger further precompilation to work with the unexpected versions.
Precompiling PlutoUI...
   3016.1 ms  ✓ PlutoUI
  1 dependency successfully precompiled in 3 seconds. 42 already precompiled.
19603×2 DataFrame
   Row │ folder  wmo
       │ Any     Any
───────┼─────────────────
     1 │ aoml    13857
     2 │ aoml    13858
     3 │ aoml    13859
     4 │ aoml    15819
     5 │ aoml    15820
     6 │ aoml    15851
     7 │ aoml    15852
     8 │ aoml    15853
   ⋮   │   ⋮        ⋮
 19597 │ nmdis   2901627
 19598 │ nmdis   2901628
 19599 │ nmdis   2901629
 19600 │ nmdis   2901630
 19601 │ nmdis   2901631
 19602 │ nmdis   2901632
 19603 │ nmdis   2901633
       19588 rows omitted┌──────────┬─────────┐
│   folder │     wmo │
├──────────┼─────────┤
│     aoml │   13857 │
│     aoml │ 3900417 │
│     aoml │ 4902897 │
│     aoml │ 5902439 │
│     aoml │ 5906066 │
│     bodc │ 6901119 │
│ coriolis │ 6900953 │
│ coriolis │ 7900553 │
│   incois │ 2900554 │
│      jma │ 5900647 │
└──────────┴─────────┘
┌ Warning: specifycing files_list here is deprecated
└ @ ArgoData ~/.julia/packages/ArgoData/2B48R/src/data_structures.jl:178
downloading floats list via ArgoData.jl
  Activating project at `~/work/OceanRobots.jl/OceanRobots.jl/docs`

How to Seek Support

If something is unclear or proves difficult to use, please seek support by opening an issue on the repository.

How to Contribute

Thank you for considering contributing to OceanRobots.jl! If you're interested in contributing we want your help no matter how big or small a contribution you make!

Reporting Bugs

If you encounter a bug, please help us fix it by following these steps:

  1. Ensure the bug is not already reported by checking the issue tracker.
  2. If the bug isn't reported, open a new issue. Clearly describe the issue, including steps to reproduce it.

Suggesting Enhancements

If you have ideas for enhancements, new features, or improvements, we'd love to hear them! Follow these steps:

  1. Check the issue tracker to see if your suggestion has been discussed.
  2. If not, open a new issue, providing a detailed description of your suggestion and the use case it addresses.

Code Contribution

If you'd like to contribute code to the project:

  1. Fork the repository.
  2. Clone your fork: git clone https://github.com/juliaocean/OceanRobots.jl
  3. Create a new branch for your changes: git checkout -b feature-branch
  4. Make your changes and commit them with a clear message.
  5. Push your changes to your fork: git push origin feature-branch
  6. Open a pull request against the master branch of the main repository.

Pull Request Process

Please ensure your pull request follows these guidelines:

  1. Adheres to the coding standards.
  2. Includes relevant tests for new functionality.
  3. Has a clear commit history and messages.
  4. References the relevant issue if applicable.

Please don't hesistate to get in touch to discuss, or with any questions!

License

By contributing to this project, you agree that your contributions will be licensed under the LICENSE file of this repository.