Merge pull request #124 from gaelforget/v0p4p8a

V0p4p8a

docs/make.jl

@@ -1,5 +1,5 @@
-using Documenter, Literate, PlutoSliderServer
-using IndividualDisplacements, OceanStateEstimation
+using Documenter, Literate, PlutoSliderServer, IndividualDisplacements
+using OceanStateEstimation
 
 #download data dependencies if needed
 IndividualDisplacements.flt_example_download()
@@ -32,8 +32,10 @@ end
 ismd(f) = splitext(f)[2] == ".md"
 pages(folder) = [joinpath(folder, f) for f in readdir(joinpath(src, folder)) if ismd(f)]
 
-makedocs(
-    sitename = "IndividualDisplacements",
+makedocs(;
+    sitename = "IndividualDisplacements.jl",
+    repo = Remotes.GitHub("JuliaClimate", "IndividualDisplacements.jl"),
+    authors="JuliaClimate <gforget@mit.edu>",
     format = Documenter.HTML(),
     pages = [
 	"Introduction" => "index.md",

docs/src/API.md

@@ -42,4 +42,4 @@ vortex_flow_field
 
 ## Read External Files
 
-Trajectory simulated by the [MITgcm](https://mitgcm.readthedocs.io/en/latest/?badge=latest) or observed by the [global drifter program](https://www.aoml.noaa.gov/phod/gdp/index.php) can be read from file using, respectively `MITgcmTools.read_flt` (from [MITgcmTools.jl](https://gaelforget.github.io/MITgcmTools.jl/dev/)) or  `OceanRobots.drifters_hourly_read` (from [OceanRobots.jl](https://gaelforget.github.io/OceanRobots.jl/dev/)).
+Trajectory simulated by the [MITgcm](https://mitgcm.readthedocs.io/en/latest/?badge=latest) or observed by the [global drifter program](https://www.aoml.noaa.gov/phod/gdp/index.php) can be read from file using, respectively `.read_flt` (from [.jl](https://gaelforget.github.io/.jl/dev/)) or  `OceanRobots.drifters_hourly_read` (from [OceanRobots.jl](https://gaelforget.github.io/OceanRobots.jl/dev/)).

docs/src/examples.md

@@ -48,7 +48,7 @@ The flow field is based on a data-constrained, realistic, ocean model. The probl
 ## Additional Examples
 
 - Interactivity : [notebook (html)](interactive_UI.html) ➭ [notebook (code)](https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/examples/worldwide/interactive_UI.jl)
-- Atmosphere : [notebook (html)](https://gaelforget.github.io/MITgcmTools.jl/dev/examples/HS94_particles.html) ➭ [notebook (code)](https://raw.githubusercontent.com/gaelforget/MITgcmTools.jl/master/examples/HS94_particles.jl)
+- Atmosphere : [notebook (html)](https://gaelforget.github.io/MITgcm.jl/dev/examples/HS94_particles.html) ➭ [notebook (code)](https://raw.githubusercontent.com/gaelforget/MITgcm.jl/master/examples/HS94_particles.jl)
 - MITgcm : [Particle cloud](../particle_cloud/index.html), [Detailed look](../detailed_look/index.html) 
 - Plotting : [Plots.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/examples/more/recipes_plots.jl), [Makie.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/examples/more/recipes_makie.jl), [PyPlot.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/examples/more/recipes_pyplot.jl)
 

docs/src/index.md

@@ -2,7 +2,7 @@
 
 [IndividualDisplacements.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl) computes elementary point displacements over gridded domains. Inter-operability with global climate model output (on [Arakawa](https://en.wikipedia.org/wiki/Arakawa_grids) `C-grids` in general) that can be represented via [MeshArrays.jl](https://github.com/JuliaClimate/MeshArrays.jl) (see [these docs](https://juliaclimate.github.io/MeshArrays.jl/dev/)) is a central goal of [IndividualDisplacements.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl). 
 
-The initial example suite relies on gridded ocean transports estimated in [OCCA](https://doi.org/10.7910/DVN/RNXA2A) ([Forget 2010](http://dx.doi.org/10.1175/2009JPO4043.1)), [ECCOv4](https://eccov4.readthedocs.io/en/latest/) ([Forget et al. 2015](https://doi.org/10.5194/gmd-8-3071-2015)), and [CBIOMES](https://cbiomes.readthedocs.io/en/latest/) ([Forget, 2018](http://doi.org/10.5281/zenodo.1343303)). For the Atmosphere, an additional example based on an idealized model simulation is provided in [MITgcmTools.jl](https://gaelforget.github.io/MITgcmTools.jl/dev/). 
+The initial example suite relies on gridded ocean transports estimated in [OCCA](https://doi.org/10.7910/DVN/RNXA2A) ([Forget 2010](http://dx.doi.org/10.1175/2009JPO4043.1)), [ECCOv4](https://eccov4.readthedocs.io/en/latest/) ([Forget et al. 2015](https://doi.org/10.5194/gmd-8-3071-2015)), and [CBIOMES](https://cbiomes.readthedocs.io/en/latest/) ([Forget, 2018](http://doi.org/10.5281/zenodo.1343303)). For the Atmosphere, an additional example based on an idealized model simulation is provided in [MITgcm.jl](https://gaelforget.github.io/MITgcm.jl/dev/). 
 
 Typical applications include the simulation and analysis of materials moving through atmospheric flows (e.g. dust or chemicals) or oceanic flows (e.g. plastics or planktons). An illustration of the type of observations that [IndividualDisplacements.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl) can simulate is provided below. These data collected by [Ocean Drifting Buoy](https://doi.org/10.1002/2016JC011716) can be accessed via [OceanRobots.jl](https://gaelforget.github.io/OceanRobots.jl/dev/).
 

docs/src/workflow.md

@@ -4,11 +4,11 @@ As shown in the [Examples](@ref) section, the typical worflow is:
 
 1. set up a `FlowFields` data structure (`𝐹`)
 1. set up `Individuals` (`𝐼`) with initial position `📌` and `𝐹`
-1. displace `𝐼.📌` by	`∫!(𝐼,𝑇)` following `𝐼.𝐹` over `𝑇` 
+1. displace `𝐼` by	`solve!(𝐼,𝑇)` following `𝐼.𝐹` over `𝑇` 
 1. post-process by `𝐼.🔧` and record information in `𝐼.🔴`
 1. go back to `step 2` and continue if needed
 
-The data structures for steps `1` and `2` are documented below. Steps `3` and `4` normally take place as part of `∫!` which post-processes results, using 🔧, records them in 🔴, and finally updates the positions of individuals in 📌. Since 🔴 is a [DataFrame](https://juliadata.github.io/DataFrames.jl/latest/), it is easily manipulated, plotted, or saved in step `4` or after the fact.
+The data structures for steps `1` and `2` are documented below. Steps `3` and `4` normally take place as part of `solve!` (i.e. `∫!`) which post-processes results, using 🔧, records them in 🔴, and finally updates the positions of individuals in 📌. Since 🔴 is a [DataFrame](https://juliadata.github.io/DataFrames.jl/latest/), it is easily manipulated, plotted, or saved in step `4` or after the fact.
 
 ## Overview