tSet NetCDF as optional dependency - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit 05ebf4c41035547007acc8e019ed0f8cbf3d3723
(DIR) parent 2ab3e5cc94c45a4baff6d1e5ca769c3eeebe0309
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Tue, 27 Feb 2018 21:56:16 -0500
Set NetCDF as optional dependency
Diffstat:
M .travis.yml | 2 +-
M REQUIRE | 1 -
M src/io.jl | 3 ++-
M src/ocean.jl | 132 +++++++++++++++++++------------
4 files changed, 86 insertions(+), 52 deletions(-)
---
(DIR) diff --git a/.travis.yml b/.travis.yml
t@@ -27,7 +27,7 @@ matrix:
- julia: nightly
before_script:
- - julia -e 'info("Preparing Python"); ENV["PYTHON"]=""; Pkg.add("PyCall"); Pkg.build("PyCall")'
+ - julia -e 'info("Preparing Python"); ENV["PYTHON"]=""; Pkg.add("PyCall"); Pkg.build("PyCall"); Pkg.add("NetCDF")'
script:
- if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
(DIR) diff --git a/REQUIRE b/REQUIRE
t@@ -1,5 +1,4 @@
julia 0.6
WriteVTK
-NetCDF
Documenter
Compat 0.42.0
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -1,10 +1,11 @@
import WriteVTK
-import NetCDF
+
hasJLD = false
if typeof(Pkg.installed("JLD")) == VersionNumber
import JLD
hasJLD = true
end
+
import Compat
using Compat.DelimitedFiles
using Compat.Dates
(DIR) diff --git a/src/ocean.jl b/src/ocean.jl
t@@ -1,3 +1,16 @@
+hasNetCDF = false
+if typeof(Pkg.installed("NetCDF")) == VersionNumber
+ import NetCDF
+ hasNetCDF = true
+else
+ if !hasNetCDF
+ warn("Package NetCDF not found. " *
+ "Ocean/atmosphere grid read not supported. " *
+ "Please install NetCDF and its " *
+ "requirements with `Pkg.add(\"NetCDF\")`.")
+ end
+end
+
using Compat.Test
export createEmptyOcean
t@@ -41,39 +54,46 @@ structure.
function readOceanNetCDF(velocity_file::String, grid_file::String;
regular_grid::Bool=false)
- time, u, v, h, e, zl, zi = readOceanStateNetCDF(velocity_file)
- xh, yh, xq, yq = readOceanGridNetCDF(grid_file)
+ if !hasNetCDF
+ warn("Package NetCDF not found. Ocean/atmosphere grid read not supported. " *
+ "Please install NetCDF and its " *
+ "requirements with `Pkg.add(\"NetCDF\")`.")
+ else
- if size(u[:,:,1,1]) != size(xq) || size(v[:,:,1,1]) != size(xq) ||
- size(xq) != size(yq)
- error("size mismatch between velocities and grid
- (u: $(size(u[:,:,1,1])), v: $(size(v[:,:,1,1])),
- xq: $(size(xq)), yq: $(size(yq)))")
- end
+ time, u, v, h, e, zl, zi = readOceanStateNetCDF(velocity_file)
+ xh, yh, xq, yq = readOceanGridNetCDF(grid_file)
- ocean = Ocean([grid_file, velocity_file],
+ if size(u[:,:,1,1]) != size(xq) || size(v[:,:,1,1]) != size(xq) ||
+ size(xq) != size(yq)
+ error("size mismatch between velocities and grid
+ (u: $(size(u[:,:,1,1])), v: $(size(v[:,:,1,1])),
+ xq: $(size(xq)), yq: $(size(yq)))")
+ end
+
+ ocean = Ocean([grid_file, velocity_file],
- time,
+ time,
- xq,
- yq,
- xh,
- yh,
+ xq,
+ yq,
+ xh,
+ yh,
- zl,
- zi,
+ zl,
+ zi,
- u,
- v,
- h,
- e,
- Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- zeros(size(xh)),
- 1, 1, 1, 1,
+ u,
+ v,
+ h,
+ e,
+ Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
+ zeros(size(xh)),
+ 1, 1, 1, 1,
- false, [0.,0.,0.], [1.,1.,1.], [1,1,1], [1.,1.,1.]
- )
- return ocean
+ false, [0.,0.,0.], [1.,1.,1.], [1,1,1], [1.,1.,1.]
+ )
+ return ocean
+ end
end
export readOceanStateNetCDF
t@@ -97,23 +117,30 @@ layer thicknesses, interface heights, and vertical coordinates.
"""
function readOceanStateNetCDF(filename::String)
- if !isfile(filename)
- error("$(filename) could not be opened")
- end
+ if !hasNetCDF
+ warn("Package NetCDF not found. Ocean/atmosphere grid read not supported. " *
+ "Please install NetCDF and its " *
+ "requirements with `Pkg.add(\"NetCDF\")`.")
+ else
- u_staggered = convert(Array{Float64, 4}, NetCDF.ncread(filename, "u"))
- v_staggered = convert(Array{Float64, 4}, NetCDF.ncread(filename, "v"))
- u, v = interpolateOceanVelocitiesToCorners(u_staggered, v_staggered)
+ if !isfile(filename)
+ error("$(filename) could not be opened")
+ end
+
+ u_staggered = convert(Array{Float64, 4}, NetCDF.ncread(filename, "u"))
+ v_staggered = convert(Array{Float64, 4}, NetCDF.ncread(filename, "v"))
+ u, v = interpolateOceanVelocitiesToCorners(u_staggered, v_staggered)
- time = convert(Vector{Float64},
- NetCDF.ncread(filename, "time") .* 24. * 60. * 60.)
- h = convert(Array{Float64, 4}, NetCDF.ncread(filename, "h"))
- e = convert(Array{Float64, 4}, NetCDF.ncread(filename, "e"))
+ time = convert(Vector{Float64},
+ NetCDF.ncread(filename, "time") .* 24. * 60. * 60.)
+ h = convert(Array{Float64, 4}, NetCDF.ncread(filename, "h"))
+ e = convert(Array{Float64, 4}, NetCDF.ncread(filename, "e"))
- zl = convert(Vector{Float64}, NetCDF.ncread(filename, "zl"))
- zi = convert(Vector{Float64}, NetCDF.ncread(filename, "zi"))
+ zl = convert(Vector{Float64}, NetCDF.ncread(filename, "zl"))
+ zi = convert(Vector{Float64}, NetCDF.ncread(filename, "zi"))
- return time, u, v, h, e, zl, zi
+ return time, u, v, h, e, zl, zi
+ end
end
export readOceanGridNetCDF
t@@ -130,19 +157,26 @@ located in the simulation `INPUT/` subdirectory.
"""
function readOceanGridNetCDF(filename::String)
- if !isfile(filename)
- error("$(filename) could not be opened")
- end
- x = convert(Array{Float64, 2}, NetCDF.ncread(filename, "x"))
- y = convert(Array{Float64, 2}, NetCDF.ncread(filename, "y"))
+ if !hasNetCDF
+ warn("Package NetCDF not found. Ocean/atmosphere grid read not supported. " *
+ "Please install NetCDF and its " *
+ "requirements with `Pkg.add(\"NetCDF\")`.")
+ else
- xh = x[2:2:end, 2:2:end]
- yh = y[2:2:end, 2:2:end]
+ if !isfile(filename)
+ error("$(filename) could not be opened")
+ end
+ x = convert(Array{Float64, 2}, NetCDF.ncread(filename, "x"))
+ y = convert(Array{Float64, 2}, NetCDF.ncread(filename, "y"))
+
+ xh = x[2:2:end, 2:2:end]
+ yh = y[2:2:end, 2:2:end]
- xq = x[1:2:end, 1:2:end]
- yq = y[1:2:end, 1:2:end]
+ xq = x[1:2:end, 1:2:end]
+ yq = y[1:2:end, 1:2:end]
- return xh, yh, xq, yq
+ return xh, yh, xq, yq
+ end
end
export interpolateOceanVelocitiesToCorners