Revision 5b7f4c5bc98f101fd4b38f61e9cbcaf41dd46a6c authored by Sheehan Olver on 11 April 2021, 05:42:03 UTC, committed by GitHub on 11 April 2021, 05:42:03 UTC
* Fix eigvals(:::SymTridagonal) with longer off-diagonal vector * Update tridiag.jl * Update lapack.jl * Revert "Update lapack.jl" This reverts commit 5c4047689c42a6fb4292aa3e6ceff3506e770142. * Update lapack.jl
1 parent c87d85f
iostream.jl
# This file is a part of Julia. License is MIT: https://julialang.org/license
## IOStream
const sizeof_ios_t = Int(ccall(:jl_sizeof_ios_t, Cint, ()))
"""
IOStream
A buffered IO stream wrapping an OS file descriptor.
Mostly used to represent files returned by [`open`](@ref).
"""
mutable struct IOStream <: IO
handle::Ptr{Cvoid}
ios::Array{UInt8,1}
name::AbstractString
mark::Int64
lock::ReentrantLock
_dolock::Bool
IOStream(name::AbstractString, buf::Array{UInt8,1}) = new(pointer(buf), buf, name, -1, ReentrantLock(), true)
end
function IOStream(name::AbstractString, finalize::Bool)
buf = zeros(UInt8,sizeof_ios_t)
x = IOStream(name, buf)
if finalize
finalizer(close, x)
end
return x
end
IOStream(name::AbstractString) = IOStream(name, true)
unsafe_convert(T::Type{Ptr{Cvoid}}, s::IOStream) = convert(T, pointer(s.ios))
show(io::IO, s::IOStream) = print(io, "IOStream(", s.name, ")")
macro _lock_ios(s, expr)
s = esc(s)
quote
l = ($s)._dolock
temp = ($s).lock
l && lock(temp)
val = $(esc(expr))
l && unlock(temp)
val
end
end
"""
fd(stream)
Return the file descriptor backing the stream or file. Note that this function only applies
to synchronous `File`'s and `IOStream`'s not to any of the asynchronous streams.
"""
fd(s::IOStream) = Int(ccall(:jl_ios_fd, Clong, (Ptr{Cvoid},), s.ios))
stat(s::IOStream) = stat(fd(s))
isopen(s::IOStream) = ccall(:ios_isopen, Cint, (Ptr{Cvoid},), s.ios) != 0
function close(s::IOStream)
bad = @_lock_ios s ccall(:ios_close, Cint, (Ptr{Cvoid},), s.ios) != 0
systemerror("close", bad)
end
function flush(s::IOStream)
sigatomic_begin()
bad = @_lock_ios s ccall(:ios_flush, Cint, (Ptr{Cvoid},), s.ios) != 0
sigatomic_end()
systemerror("flush", bad)
end
iswritable(s::IOStream) = ccall(:ios_get_writable, Cint, (Ptr{Cvoid},), s.ios)!=0
isreadable(s::IOStream) = ccall(:ios_get_readable, Cint, (Ptr{Cvoid},), s.ios)!=0
"""
truncate(file, n)
Resize the file or buffer given by the first argument to exactly `n` bytes, filling
previously unallocated space with '\\0' if the file or buffer is grown.
# Examples
```jldoctest
julia> io = IOBuffer();
julia> write(io, "JuliaLang is a GitHub organization.")
35
julia> truncate(io, 15)
IOBuffer(data=UInt8[...], readable=true, writable=true, seekable=true, append=false, size=15, maxsize=Inf, ptr=16, mark=-1)
julia> String(take!(io))
"JuliaLang is a "
julia> io = IOBuffer();
julia> write(io, "JuliaLang is a GitHub organization.");
julia> truncate(io, 40);
julia> String(take!(io))
"JuliaLang is a GitHub organization.\\0\\0\\0\\0\\0"
```
"""
function truncate(s::IOStream, n::Integer)
err = @_lock_ios s ccall(:ios_trunc, Cint, (Ptr{Cvoid}, Csize_t), s.ios, n) != 0
systemerror("truncate", err)
return s
end
"""
seek(s, pos)
Seek a stream to the given position.
# Examples
```jldoctest
julia> io = IOBuffer("JuliaLang is a GitHub organization.");
julia> seek(io, 5);
julia> read(io, Char)
'L': ASCII/Unicode U+004C (category Lu: Letter, uppercase)
```
"""
function seek(s::IOStream, n::Integer)
ret = @_lock_ios s ccall(:ios_seek, Int64, (Ptr{Cvoid}, Int64), s.ios, n)
systemerror("seek", ret == -1)
ret < -1 && error("seek failed")
return s
end
"""
seekstart(s)
Seek a stream to its beginning.
# Examples
```jldoctest
julia> io = IOBuffer("JuliaLang is a GitHub organization.");
julia> seek(io, 5);
julia> read(io, Char)
'L': ASCII/Unicode U+004C (category Lu: Letter, uppercase)
julia> seekstart(io);
julia> read(io, Char)
'J': ASCII/Unicode U+004A (category Lu: Letter, uppercase)
```
"""
seekstart(s::IO) = seek(s,0)
"""
seekend(s)
Seek a stream to its end.
"""
function seekend(s::IOStream)
err = @_lock_ios s ccall(:ios_seek_end, Int64, (Ptr{Cvoid},), s.ios) != 0
systemerror("seekend", err)
return s
end
"""
skip(s, offset)
Seek a stream relative to the current position.
# Examples
```jldoctest
julia> io = IOBuffer("JuliaLang is a GitHub organization.");
julia> seek(io, 5);
julia> skip(io, 10);
julia> read(io, Char)
'G': ASCII/Unicode U+0047 (category Lu: Letter, uppercase)
```
"""
function skip(s::IOStream, delta::Integer)
ret = @_lock_ios s ccall(:ios_skip, Int64, (Ptr{Cvoid}, Int64), s.ios, delta)
systemerror("skip", ret == -1)
ret < -1 && error("skip failed")
return s
end
"""
position(s)
Get the current position of a stream.
# Examples
```jldoctest
julia> io = IOBuffer("JuliaLang is a GitHub organization.");
julia> seek(io, 5);
julia> position(io)
5
julia> skip(io, 10);
julia> position(io)
15
julia> seekend(io);
julia> position(io)
35
```
"""
function position(s::IOStream)
pos = @_lock_ios s ccall(:ios_pos, Int64, (Ptr{Cvoid},), s.ios)
systemerror("position", pos == -1)
return pos
end
function filesize(s::IOStream)
sz = @_lock_ios s ccall(:ios_filesize, Int64, (Ptr{Cvoid},), s.ios)
if sz == -1
err = Libc.errno()
throw(IOError(string("filesize: ", Libc.strerror(err), " for ", s.name), err))
end
return sz
end
_eof_nolock(s::IOStream) = ccall(:ios_eof_blocking, Cint, (Ptr{Cvoid},), s.ios) != 0
eof(s::IOStream) = @_lock_ios s _eof_nolock(s)
## constructing and opening streams ##
# "own" means the descriptor will be closed with the IOStream
"""
fdio([name::AbstractString, ]fd::Integer[, own::Bool=false]) -> IOStream
Create an [`IOStream`](@ref) object from an integer file descriptor. If `own` is `true`, closing
this object will close the underlying descriptor. By default, an `IOStream` is closed when
it is garbage collected. `name` allows you to associate the descriptor with a named file.
"""
function fdio(name::AbstractString, fd::Integer, own::Bool=false)
s = IOStream(name)
ccall(:ios_fd, Ptr{Cvoid}, (Ptr{Cvoid}, Clong, Cint, Cint),
s.ios, fd, 0, own)
return s
end
fdio(fd::Integer, own::Bool=false) = fdio(string("<fd ",fd,">"), fd, own)
"""
open(filename::AbstractString; lock = true, keywords...) -> IOStream
Open a file in a mode specified by five boolean keyword arguments:
| Keyword | Description | Default |
|:-----------|:-----------------------|:----------------------------------------|
| `read` | open for reading | `!write` |
| `write` | open for writing | `truncate \\| append` |
| `create` | create if non-existent | `!read & write \\| truncate \\| append` |
| `truncate` | truncate to zero size | `!read & write` |
| `append` | seek to end | `false` |
The default when no keywords are passed is to open files for reading only.
Returns a stream for accessing the opened file.
The `lock` keyword argument controls whether operations will be locked for
safe multi-threaded access.
!!! compat "Julia 1.5"
The `lock` argument is available as of Julia 1.5.
"""
function open(fname::AbstractString; lock = true,
read :: Union{Bool,Nothing} = nothing,
write :: Union{Bool,Nothing} = nothing,
create :: Union{Bool,Nothing} = nothing,
truncate :: Union{Bool,Nothing} = nothing,
append :: Union{Bool,Nothing} = nothing,
)
flags = open_flags(
read = read,
write = write,
create = create,
truncate = truncate,
append = append,
)
s = IOStream(string("<file ",fname,">"))
if !lock
s._dolock = false
end
systemerror("opening file $(repr(fname))",
ccall(:ios_file, Ptr{Cvoid},
(Ptr{UInt8}, Cstring, Cint, Cint, Cint, Cint),
s.ios, fname, flags.read, flags.write, flags.create, flags.truncate) == C_NULL)
if flags.append
systemerror("seeking to end of file $fname", ccall(:ios_seek_end, Int64, (Ptr{Cvoid},), s.ios) != 0)
end
return s
end
"""
open(filename::AbstractString, [mode::AbstractString]; lock = true) -> IOStream
Alternate syntax for open, where a string-based mode specifier is used instead of the five
booleans. The values of `mode` correspond to those from `fopen(3)` or Perl `open`, and are
equivalent to setting the following boolean groups:
| Mode | Description | Keywords |
|:-----|:------------------------------|:------------------------------------|
| `r` | read | none |
| `w` | write, create, truncate | `write = true` |
| `a` | write, create, append | `append = true` |
| `r+` | read, write | `read = true, write = true` |
| `w+` | read, write, create, truncate | `truncate = true, read = true` |
| `a+` | read, write, create, append | `append = true, read = true` |
The `lock` keyword argument controls whether operations will be locked for
safe multi-threaded access.
# Examples
```jldoctest
julia> io = open("myfile.txt", "w");
julia> write(io, "Hello world!");
julia> close(io);
julia> io = open("myfile.txt", "r");
julia> read(io, String)
"Hello world!"
julia> write(io, "This file is read only")
ERROR: ArgumentError: write failed, IOStream is not writeable
[...]
julia> close(io)
julia> io = open("myfile.txt", "a");
julia> write(io, "This stream is not read only")
28
julia> close(io)
julia> rm("myfile.txt")
```
!!! compat "Julia 1.5"
The `lock` argument is available as of Julia 1.5.
"""
function open(fname::AbstractString, mode::AbstractString; lock = true)
mode == "r" ? open(fname, lock = lock, read = true) :
mode == "r+" ? open(fname, lock = lock, read = true, write = true) :
mode == "w" ? open(fname, lock = lock, truncate = true) :
mode == "w+" ? open(fname, lock = lock, truncate = true, read = true) :
mode == "a" ? open(fname, lock = lock, append = true) :
mode == "a+" ? open(fname, lock = lock, append = true, read = true) :
throw(ArgumentError("invalid open mode: $mode"))
end
## low-level calls ##
function write(s::IOStream, b::UInt8)
iswritable(s) || throw(ArgumentError("write failed, IOStream is not writeable"))
Int(@_lock_ios s ccall(:ios_putc, Cint, (Cint, Ptr{Cvoid}), b, s.ios))
end
function unsafe_write(s::IOStream, p::Ptr{UInt8}, nb::UInt)
iswritable(s) || throw(ArgumentError("write failed, IOStream is not writeable"))
return Int(@_lock_ios s ccall(:ios_write, Csize_t, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), s.ios, p, nb))
end
# num bytes available without blocking
bytesavailable(s::IOStream) = @_lock_ios s ccall(:jl_nb_available, Int32, (Ptr{Cvoid},), s.ios)
function readavailable(s::IOStream)
lock(s.lock)
nb = ccall(:jl_nb_available, Int32, (Ptr{Cvoid},), s.ios)
if nb == 0
ccall(:ios_fillbuf, Cssize_t, (Ptr{Cvoid},), s.ios)
nb = ccall(:jl_nb_available, Int32, (Ptr{Cvoid},), s.ios)
end
a = Vector{UInt8}(undef, nb)
nr = ccall(:ios_readall, Csize_t, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), s, a, nb)
if nr != nb
unlock(s.lock)
throw(EOFError())
end
unlock(s.lock)
return a
end
function read(s::IOStream, ::Type{UInt8})
b = @_lock_ios s ccall(:ios_getc, Cint, (Ptr{Cvoid},), s.ios)
if b == -1
throw(EOFError())
end
return b % UInt8
end
if ENDIAN_BOM == 0x04030201
function read(s::IOStream, T::Union{Type{Int16},Type{UInt16},Type{Int32},Type{UInt32},Type{Int64},Type{UInt64}})
n = sizeof(T)
lock(s.lock)
if ccall(:jl_ios_buffer_n, Cint, (Ptr{Cvoid}, Csize_t), s.ios, n) != 0
unlock(s.lock)
throw(EOFError())
end
x = ccall(:jl_ios_get_nbyte_int, UInt64, (Ptr{Cvoid}, Csize_t), s.ios, n) % T
unlock(s.lock)
return x
end
read(s::IOStream, ::Type{Float16}) = reinterpret(Float16, read(s, Int16))
read(s::IOStream, ::Type{Float32}) = reinterpret(Float32, read(s, Int32))
read(s::IOStream, ::Type{Float64}) = reinterpret(Float64, read(s, Int64))
end
function unsafe_read(s::IOStream, p::Ptr{UInt8}, nb::UInt)
nr = @_lock_ios s ccall(:ios_readall, Csize_t, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t), s, p, nb)
if nr != nb
throw(EOFError())
end
nothing
end
## text I/O ##
take!(s::IOStream) =
@_lock_ios s ccall(:jl_take_buffer, Vector{UInt8}, (Ptr{Cvoid},), s.ios)
function readuntil(s::IOStream, delim::UInt8; keep::Bool=false)
@_lock_ios s ccall(:jl_readuntil, Array{UInt8,1}, (Ptr{Cvoid}, UInt8, UInt8, UInt8), s.ios, delim, 0, !keep)
end
# like readuntil, above, but returns a String without requiring a copy
function readuntil_string(s::IOStream, delim::UInt8, keep::Bool)
@_lock_ios s ccall(:jl_readuntil, Ref{String}, (Ptr{Cvoid}, UInt8, UInt8, UInt8), s.ios, delim, 1, !keep)
end
function readline(s::IOStream; keep::Bool=false)
@_lock_ios s ccall(:jl_readuntil, Ref{String}, (Ptr{Cvoid}, UInt8, UInt8, UInt8), s.ios, '\n', 1, keep ? 0 : 2)
end
function readbytes_all!(s::IOStream,
b::Union{Array{UInt8}, FastContiguousSubArray{UInt8,<:Any,<:Array{UInt8}}},
nb::Integer)
olb = lb = length(b)
nr = 0
let l = s._dolock, slock = s.lock
l && lock(slock)
GC.@preserve b while nr < nb
if lb < nr+1
try
lb = max(65536, (nr+1) * 2)
resize!(b, lb)
catch
l && unlock(slock)
rethrow()
end
end
thisr = Int(ccall(:ios_readall, Csize_t, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t),
s.ios, pointer(b, nr+1), min(lb-nr, nb-nr)))
nr += thisr
(nr == nb || thisr == 0 || _eof_nolock(s)) && break
end
l && unlock(slock)
end
if lb > olb && lb > nr
resize!(b, max(olb, nr)) # shrink to just contain input data if was resized
end
return nr
end
function readbytes_some!(s::IOStream,
b::Union{Array{UInt8}, FastContiguousSubArray{UInt8,<:Any,<:Array{UInt8}}},
nb::Integer)
olb = length(b)
if nb > olb
resize!(b, nb)
end
local nr
@_lock_ios s begin
nr = GC.@preserve b Int(ccall(:ios_read, Csize_t, (Ptr{Cvoid}, Ptr{Cvoid}, Csize_t),
s.ios, pointer(b), nb))
end
lb = length(b)
if lb > olb && lb > nr
resize!(b, max(olb, nr)) # shrink to just contain input data if was resized
end
return nr
end
"""
readbytes!(stream::IOStream, b::AbstractVector{UInt8}, nb=length(b); all::Bool=true)
Read at most `nb` bytes from `stream` into `b`, returning the number of bytes read.
The size of `b` will be increased if needed (i.e. if `nb` is greater than `length(b)`
and enough bytes could be read), but it will never be decreased.
If `all` is `true` (the default), this function will block repeatedly trying to read all
requested bytes, until an error or end-of-file occurs. If `all` is `false`, at most one
`read` call is performed, and the amount of data returned is device-dependent. Note that not
all stream types support the `all` option.
"""
function readbytes!(s::IOStream,
b::Union{Array{UInt8}, FastContiguousSubArray{UInt8,<:Any,<:Array{UInt8}}},
nb=length(b);
all::Bool=true)
return all ? readbytes_all!(s, b, nb) : readbytes_some!(s, b, nb)
end
function read(s::IOStream)
# First we try to fill the buffer. If that gives us the whole file,
# copy it out and return. Otherwise look at the file size and use it
# to prealloate space. Determining the size requires extra syscalls,
# which we want to avoid for small files.
@_lock_ios s begin
nb = ccall(:ios_fillbuf, Cssize_t, (Ptr{Cvoid},), s.ios)
if nb != -1
b = StringVector(nb)
readbytes_all!(s, b, nb)
else
sz = try # filesize is just a hint, so ignore if it fails
filesize(s)
catch ex
ex isa IOError || rethrow()
Int64(-1)
end
if sz > 0
pos = position(s)
if pos > 0
sz -= pos
end
end
b = StringVector(sz < 0 ? 1024 : sz)
nr = readbytes_all!(s, b, sz < 0 ? typemax(Int) : sz)
resize!(b, nr)
end
end
return b
end
"""
read(s::IOStream, nb::Integer; all=true)
Read at most `nb` bytes from `s`, returning a `Vector{UInt8}` of the bytes read.
If `all` is `true` (the default), this function will block repeatedly trying to read all
requested bytes, until an error or end-of-file occurs. If `all` is `false`, at most one
`read` call is performed, and the amount of data returned is device-dependent. Note that not
all stream types support the `all` option.
"""
function read(s::IOStream, nb::Integer; all::Bool=true)
# When all=false we have to allocate a buffer of the requested size upfront
# since a single call will be made
b = Vector{UInt8}(undef, all && nb == typemax(Int) ? 1024 : nb)
nr = readbytes!(s, b, nb, all=all)
resize!(b, nr)
return b
end
## peek ##
function peek(s::IOStream, ::Type{UInt8})
b = @_lock_ios s ccall(:ios_peekc, Cint, (Ptr{Cvoid},), s.ios)
if b == -1
throw(EOFError())
end
return b % UInt8
end
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