Merge fae7edb into 22fc0bf

.travis.yml

@@ -3,7 +3,7 @@ os:
     - linux
     - osx
 julia:
-    - 0.6
+    - 0.7
     - nightly
 notifications:
     email: false

REQUIRE

@@ -1,3 +1,3 @@
-julia 0.6
+julia 0.7.0-beta
 BinaryProvider 0.3.0
 Compat 0.41.0

deps/.gitignore

@@ -0,0 +1 @@
+build.log

src/FITSIO.jl

@@ -1,8 +1,9 @@
-isdefined(Base, :__precompile__) && __precompile__()
+__precompile__()
+
 
 module FITSIO
 
-using Compat.Printf
+using Printf
 
 export FITS,
        HDU,
@@ -26,7 +27,6 @@ import Base: getindex,
              close,
              ndims,
              size,
-             endof,
              haskey,
              keys,
              values,

src/fits.jl

@@ -39,7 +39,7 @@ function length(f::FITS)
     Int(fits_get_num_hdus(f.fitsfile))
 end
 
-endof(f::FITS) = length(f)
+Base.lastindex(f::FITS) = length(f)
 
 # Iteration
 start(f::FITS) = 1
@@ -60,19 +60,19 @@ function show(io::IO, f::FITS)
     else
         print(io, "HDUs: ")
 
-        names = Vector{String}(nhdu)
-        vers = Vector{String}(nhdu)
-        types = Vector{String}(nhdu)
+        names = Vector{String}(undef, nhdu)
+        vers  = Vector{String}(undef, nhdu)
+        types = Vector{String}(undef, nhdu)
         for i = 1:nhdu
             t = fits_movabs_hdu(f.fitsfile, i)
             types[i] = (t == :image_hdu ? "Image" :
                         t == :binary_table ? "Table" :
                         t == :ascii_table ? "ASCIITable" :
                         error("unknown HDU type"))
             nname = fits_try_read_extname(f.fitsfile)
-            names[i] = get(nname, "")
+            names[i] = something(nname, "")
             nver = fits_try_read_extver(f.fitsfile)
-            vers[i] = isnull(nver) ? "" : string(get(nver))
+            vers[i] = nver === nothing ? "" : string(nver)
         end
 
         nums = [string(i) for i=1:nhdu]

src/header.jl

@@ -9,12 +9,12 @@
 function try_parse_hdrval(::Type{Bool}, s::String)
     if length(s) == 1
         if s[1] == 'T'
-            return Nullable(true)
+            return true
         elseif s[1] == 'F'
-            return Nullable(false)
+            return false
         end
     end
-    return Nullable{Bool}()
+    return nothing
 end
 
 # Note that trailing whitespace is not significant in FITS header
@@ -24,39 +24,39 @@ end
 # TODO: parse '' within the string as a single '.
 function try_parse_hdrval(::Type{String}, s::String)
     if length(s) < 2 || s[1] != '\'' || s[end] != '\''
-        return Nullable{String}()
+        return nothing
     end
 
-    i = endof(s) - 1
+    i = lastindex(s) - 1
     while i > 2
         if s[i] != ' '
-            return Nullable(s[2:i])
+            return s[2:i]
         end
         i -= 1
     end
-    return Nullable(s[2:i])
+    return s[2:i]
 end
 
 try_parse_hdrval(::Type{Float64}, s::String) = tryparse(Float64, s)
 try_parse_hdrval(::Type{Int}, s::String) = tryparse(Int, s)
 
 # Try to parse the header value as any type
 function try_parse_hdrval(s::String)
-    length(s) == 0 && return Nullable(nothing)
+    length(s) == 0 && return Some(nothing)
 
     nb = try_parse_hdrval(Bool, s)
-    isnull(nb) || return nb
+    nb === nothing || return nb
 
     ns = try_parse_hdrval(String, s)
-    isnull(ns) || return ns
+    ns === nothing || return ns
 
     ni = try_parse_hdrval(Int, s)
-    isnull(ni) || return ni
+    ni === nothing || return ni
 
     nf = try_parse_hdrval(Float64, s)
-    isnull(nf) || return nf
+    nf === nothing || return nf
 
-    return Nullable{Any}()
+    return nothing
 end
 
 # functions for displaying header values in show(io, header)
@@ -68,17 +68,17 @@ hdrval_repr(v::Union{AbstractFloat, Integer}) = string(v)
 # (never error)
 function parse_header_val(s::String)
     nval = try_parse_hdrval(s)
-    return isnull(nval) ? s : get(nval)
+    return something(nval, s)
 end
 
-# Try to read the raw keys in order given; returns Nullable.
-# (null if no key exists or if parsing an existing key is unsuccessful.)
-function fits_try_read_keys{T}(f::FITSFile, ::Type{T}, keys)
+# Try to read the raw keys in order given
+# (`nothing` if no key exists or if parsing an existing key is unsuccessful.)
+function fits_try_read_keys(f::FITSFile, ::Type{T}, keys) where T
     status = Cint[0]
-    value = Vector{UInt8}(71)
+    value = Vector{UInt8}(undef, 71)
     for key in keys
         ccall((:ffgkey, libcfitsio), Cint,
-              (Ptr{Void},Ptr{UInt8},Ptr{UInt8},Ptr{UInt8},Ptr{Cint}),
+              (Ptr{Cvoid},Ptr{UInt8},Ptr{UInt8},Ptr{UInt8},Ptr{Cint}),
               f.ptr, key, value, C_NULL, status)
 
         # If the key is found, return it. If there was some other error
@@ -89,7 +89,7 @@ function fits_try_read_keys{T}(f::FITSFile, ::Type{T}, keys)
             error(fits_get_errstatus(status[1]))
         end
     end
-    return Nullable{T}()
+    return nothing
 end
 
 # Build a string with extension keywords, if present.
@@ -103,9 +103,9 @@ fits_try_read_extver(f::FITSFile) = fits_try_read_keys(f, Int, EXTVER_KEYS)
 function fits_get_ext_info_string(f::FITSFile)
     extname = fits_try_read_extname(f)
     extver = fits_try_read_extver(f)
-    if !isnull(extname) && !isnull(extver)
+    if extname !== nothing && extver !== nothing
         return " (name=$(repr(get(extname))), ver=$(get(extver)))"
-    elseif !isnull(extname)
+    elseif extname !== nothing
         return " (name=$(repr(get(extname))))"
     end
     return ""
@@ -133,18 +133,18 @@ function reserved_key_indices(hdr::FITSHeader)
     # Note that this removes anything matching NAXIS\d regardless of # of axes.
     if in("NAXIS", hdr.keys)
         for i=1:nhdr
-            if ismatch(r"^NAXIS\d*$", hdr.keys[i])
+            if occursin(r"^NAXIS\d*$", hdr.keys[i])
                 push!(indices, i)
             end
         end
     end
 
     if in("ZNAXIS", hdr.keys)
         for i=1:nhdr
-            if (ismatch(r"^ZNAXIS\d*$", hdr.keys[i]) ||
-                ismatch(r"^ZTILE\d*$", hdr.keys[i]) ||
-                ismatch(r"^ZNAME\d*$", hdr.keys[i]) ||
-                ismatch(r"^ZVAL\d*$", hdr.keys[i]))
+            if (occursin(r"^ZNAXIS\d*$", hdr.keys[i]) ||
+                occursin(r"^ZTILE\d*$", hdr.keys[i]) ||
+                occursin(r"^ZNAME\d*$", hdr.keys[i]) ||
+                occursin(r"^ZVAL\d*$", hdr.keys[i]))
                 push!(indices, i)
             end
         end
@@ -158,7 +158,7 @@ function reserved_key_indices(hdr::FITSHeader)
                        r"^TDMAX\d*$", r"^TDESC\d*$", r"^TROTA\d*$",
                        r"^TRPIX\d*$", r"^TRVAL\d*$", r"^TDELT\d*$",
                        r"^TCUNI\d*$", r"^TFIELDS$"]
-                if ismatch(re, hdr.keys[i])
+                if occursin(re, hdr.keys[i])
                     push!(indices, i)
                 end
             end
@@ -226,8 +226,8 @@ keyword does not already exist, a new record will be appended at the
 end of the header.
 """
 function write_key(hdu::HDU, key::String,
-                   value::Union{String, Bool, Integer, AbstractFloat, Void},
-                   comment::Union{String, Ptr{Void}}=C_NULL)
+                   value::Union{String, Bool, Integer, AbstractFloat, Nothing},
+                   comment::Union{String, Ptr{Cvoid}}=C_NULL)
     fits_assert_open(hdu.fitsfile)
     fits_movabs_hdu(hdu.fitsfile, hdu.ext)
     fits_update_key(hdu.fitsfile, key, value, comment)
@@ -250,20 +250,20 @@ function read_header(hdu::HDU)
 
     # Below, we use a direct call to ffgkyn so that we can keep reusing the
     # same buffers.
-    key = Vector{UInt8}(81)
-    value = Vector{UInt8}(81)
-    comment = Vector{UInt8}(81)
+    key = Vector{UInt8}(undef, 81)
+    value = Vector{UInt8}(undef, 81)
+    comment = Vector{UInt8}(undef, 81)
     status = Cint[0]
 
     nkeys, morekeys = fits_get_hdrspace(hdu.fitsfile)
 
     # Initialize output arrays
-    keys = Vector{String}(nkeys)
-    values = Vector{Any}(nkeys)
-    comments = Vector{String}(nkeys)
+    keys = Vector{String}(undef, nkeys)
+    values = Vector{Any}(undef, nkeys)
+    comments = Vector{String}(undef, nkeys)
     for i=1:nkeys
         ccall((:ffgkyn,libcfitsio), Cint,
-              (Ptr{Void},Cint,Ptr{UInt8},Ptr{UInt8},Ptr{UInt8},Ptr{Cint}),
+              (Ptr{Cvoid},Cint,Ptr{UInt8},Ptr{UInt8},Ptr{UInt8},Ptr{Cint}),
               hdu.fitsfile.ptr, i, key, value, comment, status)
         keys[i] = unsafe_string(pointer(key))
         values[i] = parse_header_val(unsafe_string(pointer(value)))

src/image.jl

@@ -64,9 +64,9 @@ Get total number of pixels in image (product of ``size(hdu)``).
 """
 length(hdu::ImageHDU) = prod(size(hdu))
 
-# `endof` is needed so that hdu[:] can throw DimensionMismatch
+# `lastindex` is needed so that hdu[:] can throw DimensionMismatch
 # when ndim != 1, rather than no method.
-endof(hdu::ImageHDU) = length(hdu::ImageHDU)
+Base.lastindex(hdu::ImageHDU) = length(hdu::ImageHDU)
 
 # Read a full image from an HDU
 """
@@ -82,23 +82,23 @@ function read(hdu::ImageHDU)
     fits_movabs_hdu(hdu.fitsfile, hdu.ext)
     sz = fits_get_img_size(hdu.fitsfile)
     bitpix = fits_get_img_equivtype(hdu.fitsfile)
-    data = Array{TYPE_FROM_BITPIX[bitpix]}(sz...)
+    data = Array{TYPE_FROM_BITPIX[bitpix]}(undef, sz...)
     fits_read_pix(hdu.fitsfile, data)
     data
 end
 
 # _checkbounds methods copied from Julia v0.4 Base.
 _checkbounds(sz, i::Integer) = 1 <= i <= sz
 _checkbounds(sz, i::Colon) = true
-_checkbounds(sz, r::Range{Int}) =
+_checkbounds(sz, r::AbstractRange{Int}) =
     (isempty(r) || (minimum(r) >= 1 && maximum(r) <= sz))
 
 # helper functions for constructing cfitsio indexing vectors in read(hdu, ...)
-_first(i::Union{Integer, Range}) = first(i)
+_first(i::Union{Integer, AbstractRange}) = first(i)
 _first(::Colon) = 1
-_last(sz, i::Union{Integer, Range}) = last(i)
+_last(sz, i::Union{Integer, AbstractRange}) = last(i)
 _last(sz, ::Colon) = sz
-_step(r::Range) = step(r)
+_step(r::AbstractRange) = step(r)
 _step(::Union{Integer, Colon}) = 1
 
 # Shape of array to create for read(hdu, ...), dropping trailing
@@ -107,16 +107,16 @@ _step(::Union{Integer, Colon}) = 1
 @inline _index_shape(sz, I...) = _index_shape_dim(sz, 1, I...)
 _index_shape_dim(sz, dim, I::Integer...) = ()
 _index_shape_dim(sz, dim, ::Colon) = (sz[dim],)
-_index_shape_dim(sz, dim, r::Range) = (length(r),)
+_index_shape_dim(sz, dim, r::AbstractRange) = (length(r),)
 @inline _index_shape_dim(sz, dim, ::Colon, I...) =
     tuple(sz[dim], _index_shape_dim(sz, dim+1, I...)...)
 @inline _index_shape_dim(sz, dim, ::Integer, I...) =
     _index_shape_dim(sz, dim+1, I...)
-@inline _index_shape_dim(sz, dim, r::Range, I...) =
+@inline _index_shape_dim(sz, dim, r::AbstractRange, I...) =
     tuple(length(r), _index_shape_dim(sz, dim+1, I...)...)
 
 # Read a subset of an ImageHDU
-function read_internal(hdu::ImageHDU, I::Union{Range{Int}, Integer, Colon}...)
+function read_internal(hdu::ImageHDU, I::Union{AbstractRange{Int}, Integer, Colon}...)
     fits_assert_open(hdu.fitsfile)
     fits_movabs_hdu(hdu.fitsfile, hdu.ext)
     sz = fits_get_img_size(hdu.fitsfile)
@@ -138,14 +138,14 @@ function read_internal(hdu::ImageHDU, I::Union{Range{Int}, Integer, Colon}...)
 
     # construct output array
     bitpix = fits_get_img_equivtype(hdu.fitsfile)
-    data = Array{TYPE_FROM_BITPIX[bitpix]}(_index_shape(sz, I...))
+    data = Array{TYPE_FROM_BITPIX[bitpix]}(undef, _index_shape(sz, I...))
 
     fits_read_subset(hdu.fitsfile, firsts, lasts, steps, data)
     data
 end
 
 # general method and version that returns a single value rather than 0-d array
-read(hdu::ImageHDU, I::Union{Range{Int}, Int, Colon}...) =
+read(hdu::ImageHDU, I::Union{AbstractRange{Int}, Int, Colon}...) =
     read_internal(hdu, I...)
 read(hdu::ImageHDU, I::Int...) = read_internal(hdu, I...)[1]
 
@@ -159,10 +159,10 @@ following array element types are supported: `UInt8`, `Int8`,
 `Float64`. If a `FITSHeader` object is passed as the `header` keyword
 argument, the header will also be added to the new HDU.
 """
-function write{T}(f::FITS, data::Array{T};
-                  header::Union{Void, FITSHeader}=nothing,
-                  name::Union{Void, String}=nothing,
-                  ver::Union{Void, Integer}=nothing)
+function write(f::FITS, data::Array{T};
+               header::Union{Nothing, FITSHeader}=nothing,
+               name::Union{Nothing, String}=nothing,
+               ver::Union{Nothing, Integer}=nothing) where T
     fits_assert_open(f.fitsfile)
     s = size(data)
     fits_create_img(f.fitsfile, T, [s...])
@@ -215,7 +215,7 @@ Same as above but only copy odd columns in y:
 copy_section(hdu, f, 1:200, 1:2:200)
 ```
 """
-function copy_section(hdu::ImageHDU, dest::FITS, r::Range{Int}...)
+function copy_section(hdu::ImageHDU, dest::FITS, r::AbstractRange{Int}...)
     fits_assert_open(hdu.fitsfile)
     fits_assert_open(dest.fitsfile)
     fits_movabs_hdu(hdu.fitsfile, hdu.ext)