Merge remote-tracking branch 'geo/master' into stringvar

.travis.yml

@@ -1,13 +1,13 @@
-language: cpp
-compiler:
- - clang
+# Documentation: http:https://docs.travis-ci.com/user/languages/julia/
+language: julia
+os:
+ - linux
+ - osx
+julia:
+ - 0.4
 notifications:
  email: false
-before_install:
- - sudo add-apt-repository ppa:staticfloat/julia-deps -y
- - sudo add-apt-repository ppa:staticfloat/julianightlies -y
- - sudo apt-get update -qq -y
- - sudo apt-get install libpcre3-dev julia -y
+# uncomment the following lines to override the default test script
 script:
- - julia -e 'Pkg.init(); run(`ln -s $(pwd()) $(Pkg.dir())/NetCDF`); Pkg.resolve(); Pkg.build("NetCDF")'
- - julia -e 'using NetCDF; @assert isdefined(:NetCDF); @assert typeof(NetCDF) === Module; include("$(Pkg.dir())/NetCDF/test/runtests.jl")'
+ - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+ - julia -e 'Pkg.clone("https://github.com/JuliaGeo/NetCDF.jl.git"); Pkg.test("NetCDF"; coverage=true)'

README.md

@@ -1,7 +1,7 @@
 NetCDF.jl
 ============
 
-[![Build Status](https://travis-ci.org/meggart/NetCDF.jl.png)](https://travis-ci.org/meggart/NetCDF.jl)
+[![Build Status](https://travis-ci.org/JuliaGeo/NetCDF.jl.png)](https://travis-ci.org/JuliaGeo/NetCDF.jl)
 
 NetCDF support for the julia programming language, there is a high-level and a medium-level interface for writing and reading netcdf files. 
 
@@ -44,4 +44,4 @@ To learn more, have a look at https://github.com/meggart/NetCDF.jl/blob/master/d
 Contact info:
 Fabian Gans ([email protected])
 Max-Planck-Institute for Biogeochemistry
-Jena, Germany
+Jena, Germany

REQUIRE

@@ -1,4 +1,5 @@
 julia 0.4-
 BinDeps
-@osx Homebrew
-Compat
+Conda
+Compat
+Formatting

deps/build.jl

@@ -1,27 +1,17 @@
 using BinDeps
 
 @BinDeps.setup
+netcdf = library_dependency("libnetcdf", aliases = ["libnetcdf4","libnetcdf-7"])
 
+using Conda
+provides(Conda.Manager, "libnetcdf", netcdf)
 
 @osx_only begin
  using Homebrew
- netcdf = library_dependency("libnetcdf", aliases = ["libnetcdf.7"])
- provides( Homebrew.HB, "netcdf", netcdf, os = :Darwin )
+ provides(Homebrew.HB, "netcdf", netcdf, os = :Darwin )
 end
 
-@linux_only begin
- netcdf = library_dependency("libnetcdf", aliases = ["libnetcdf-7"])
- provides(AptGet, Dict("libnetcdf-dev"=>netcdf))
- provides(Yum, Dict("netcdf-devel"=>netcdf))
-end
-
-@windows_only begin
- netcdf = library_dependency("netcdf")
- provides (Binaries,URI("http:https://www.paratools.com/Azure/NetCDF/paratools-netcdf-4.1.3.tar.gz"),netcdf,os=:Windows)
- push!(DL_LOAD_PATH, joinpath(Pkg.dir(),"NetCDF","deps","netcdf-4.1.3","bin"))
-end
-
-provides(Sources, URI("ftp:https://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.0.tar.gz"),netcdf)
-
+provides(AptGet, Dict("libnetcdf-dev"=>netcdf), os = :Linux)
+provides(Yum, Dict("netcdf-devel"=>netcdf), os = :Linux)
 
 @BinDeps.install

src/netcdf_helpers.jl

@@ -35,13 +35,13 @@ const error_description=
 const funext = [ (Float64, "double","float64a"),
  (Float32, "float","float32a"),
  (Int32 , "int","int32a"),
- (Uint8 , "text","uint8a"),
+ (UInt8 , "text","uint8a"),
  (Int8 , "schar","int8a"),
  (Int16 , "short","int16a"),
  (Int64 , "longlong","int64a")]
 
 const ida = zeros(Int32,1)
-const namea = zeros(Uint8,NC_MAX_NAME+1)
+const namea = zeros(UInt8,NC_MAX_NAME+1)
 const lengtha = zeros(Csize_t,1)
 const dimida = zeros(Int32,NC_MAX_VAR_DIMS)
 const ndima = zeros(Int32,1)
@@ -55,14 +55,14 @@ const dima = zeros(Int32,1)
 const varida = zeros(Int32,1)
 const vara = zeros(Int32,1);
 const dumids = zeros(Int32,NC_MAX_DIMS)
-const gstart = zeros(Uint,NC_MAX_DIMS)
-const gcount = zeros(Uint,NC_MAX_DIMS)
+const gstart = zeros(UInt,NC_MAX_DIMS)
+const gcount = zeros(UInt,NC_MAX_DIMS)
 
 for (t,ending,aname) in funext 
  @eval const $(symbol(aname)) = zeros($t,1)
 end
 
-function nc_open(fname::String,omode::Uint16)
+function nc_open(fname::AbstractString,omode::UInt16)
  # Function to open file fname, returns a NetCDF file ID
  nc_open(fname,omode,ida)
  return ida[1]
@@ -80,7 +80,7 @@ function nc_inq_dim(id::Integer,idim::Integer)
  return (name,lengtha[1])
 end
 
-function nc_inq_dimid(id::Integer,name::String)
+function nc_inq_dimid(id::Integer,name::AbstractString)
  # Function to read dimension id for a given function name
  NetCDF.nc_inq_dimid(id,name,dimida)
  return dimida[1]
@@ -124,38 +124,38 @@ function nc_get_att(ncid::Integer,varid::Integer,attnum::Integer)
 end
 
 #Define methods for writing attributes
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Int8}) = nc_put_att_schar(ncid,varid,name,NC_BYTE,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Int16}) = nc_put_att_short(ncid,varid,name,NC_SHORT,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Int32}) = nc_put_att_int(ncid,varid,name,NC_INT,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Int64}) = nc_put_att_long(ncid,varid,name,NC_LONG,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Float32}) = nc_put_att_float(ncid,varid,name,NC_FLOAT,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Float64}) = nc_put_att_double(ncid,varid,name,NC_DOUBLE,length(val),val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::String) = nc_put_att_text(ncid,varid,name,length(val)+1,val)
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Array{Any}) = error("Writing attribute array of type Any is not possible") 
-
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Int8) = begin int8a[1] = val; nc_put_att(ncid,varid,name,int8a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Int16) = begin int16a[1] = val; nc_put_att(ncid,varid,name,int16a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Int32) = begin int32a[1] = val; nc_put_att(ncid,varid,name,int32a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Int64) = begin int64a[1] = val; nc_put_att(ncid,varid,name,int64a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Float32) = begin float32a[1] = val; nc_put_att(ncid,varid,name,float32a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val::Float64) = begin float64a[1] = val; nc_put_att(ncid,varid,name,float64a) end
-nc_put_att(ncid::Integer,varid::Integer,name::String,val) = error("Writing attribute of type $(typeof(val)) is currently not possible.") 
-
-
-
-function nc_get_att(ncid::Integer,varid::Integer,name::String,attype::Integer,attlen::Integer)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Int8}) = nc_put_att_schar(ncid,varid,name,NC_BYTE,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Int16}) = nc_put_att_short(ncid,varid,name,NC_SHORT,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Int32}) = nc_put_att_int(ncid,varid,name,NC_INT,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Int64}) = nc_put_att_long(ncid,varid,name,NC_LONG,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Float32}) = nc_put_att_float(ncid,varid,name,NC_FLOAT,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Float64}) = nc_put_att_double(ncid,varid,name,NC_DOUBLE,length(val),val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::AbstractString) = nc_put_att_text(ncid,varid,name,length(val)+1,val)
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Array{Any}) = error("Writing attribute array of type Any is not possible") 
+
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Int8) = begin int8a[1] = val; nc_put_att(ncid,varid,name,int8a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Int16) = begin int16a[1] = val; nc_put_att(ncid,varid,name,int16a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Int32) = begin int32a[1] = val; nc_put_att(ncid,varid,name,int32a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Int64) = begin int64a[1] = val; nc_put_att(ncid,varid,name,int64a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Float32) = begin float32a[1] = val; nc_put_att(ncid,varid,name,float32a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val::Float64) = begin float64a[1] = val; nc_put_att(ncid,varid,name,float64a) end
+nc_put_att(ncid::Integer,varid::Integer,name::AbstractString,val) = error("Writing attribute of type $(typeof(val)) is currently not possible.") 
+
+
+
+function nc_get_att(ncid::Integer,varid::Integer,name::AbstractString,attype::Integer,attlen::Integer)
  valsa=Array(nctype2jltype[attype],attlen)
  nc_get_att!(ncid,varid,name,valsa)
 end
 
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Uint8}) = begin nc_get_att_text(ncid,varid,name,valsa); ascii(valsa) end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Ptr{Uint8}}) = begin nc_get_att_string(ncid,varid,name,valsa); [bytestring(pointer(valsa[i])) for i=1:length(valsa)] end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Int8}) = begin nc_get_att_schar(ncid,varid,name,valsa); valsa end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Int16}) = begin nc_get_att_short(ncid,varid,name,valsa); valsa end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Int32}) = begin nc_get_att_int(ncid,varid,name,valsa); valsa end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Int64}) = begin nc_get_att_long(ncid,varid,name,valsa); valsa end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Float32}) = begin nc_get_att_float(ncid,varid,name,valsa); valsa end
-nc_get_att!(ncid::Integer,varid::Integer,name::String,valsa::Array{Float64}) = begin nc_get_att_double(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{UInt8}) = begin nc_get_att_text(ncid,varid,name,valsa); ascii(valsa) end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Ptr{UInt8}}) = begin nc_get_att_string(ncid,varid,name,valsa); [bytestring(pointer(valsa[i])) for i=1:length(valsa)] end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Int8}) = begin nc_get_att_schar(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Int16}) = begin nc_get_att_short(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Int32}) = begin nc_get_att_int(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Int64}) = begin nc_get_att_long(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Float32}) = begin nc_get_att_float(ncid,varid,name,valsa); valsa end
+nc_get_att!(ncid::Integer,varid::Integer,name::AbstractString,valsa::Array{Float64}) = begin nc_get_att_double(ncid,varid,name,valsa); valsa end
 
 
 function nc_inq_var(nc::NcFile,varid::Integer)
@@ -192,7 +192,7 @@ function getatts_all(ncid::Integer,varid::Integer,natts::Integer)
  atts=Dict{Any,Any}()
  for attnum=0:natts-1
  attname,attval=nc_get_att(ncid,varid,attnum)
- if ((length(attval)==1) & !(typeof(attval)<:String))
+ if ((length(attval)==1) & !(typeof(attval)<:AbstractString))
  attval=attval[1]
  end
  atts[attname]=attval
@@ -242,7 +242,7 @@ function parsedimargs(dim)
  #Determine number of dimensions
  ndim=0
  for a in dim
- if (typeof(a)<:String)
+ if (typeof(a)<:AbstractString)
  ndim=ndim+1
  end
  NC_VERBOSE ? println(a) : nothing
@@ -251,7 +251,7 @@ function parsedimargs(dim)
  idim=1
  for a in dim
  NC_VERBOSE ? println(a,idim) : nothing
- if (typeof(a)<:String)
+ if (typeof(a)<:AbstractString)
  #Assume a name is given
  #first create an NcDim object from the last dim
  if (name!=nothing)