move fld_read fld_write to FileIO (deprecating) #94

JeffFessler · 2021-05-21T17:52:26Z

This (not-quite) breaking change moves fld_read and fld_write to the newly improved FileIO package that in turn uses AVSfldIO under its hood. For now these are still supported via @deprecated.

Now one can simply use load and save from FileIO to read/write AVS .fld files.

johnnychen94 · 2021-05-21T17:58:41Z

src/io/fld-read.jl

+    fld_header()

+Deprecated: use `AVSfldIO.fld_header` instead.
 """
-`header = string_to_array(header_lines)`
-
-convert long string with embedded newlines into string array
-"""
-function string_to_array(header_lines::String)
-	newline = '\n'
-
-	# ensure there is a newline at end, since dumb editors can forget...
-	if header_lines[end] != newline
-		header_lines *= newline
-	end
-
-	ends = findall(isequal(newline), header_lines)
-	(length(ends) <= 0) && throw("no newlines?")
-
-	header = split(header_lines, newline, keepempty=false)
-
-	# strip comments (lines that begin with #)
-	header = filter(line -> line[1] != '#', header)
-
-	return header
+function fld_header()
+    throw("fld_header is deprecated: use AVSfldIO.fld_header instead.")
 end


There's a @deprecate macro that you can use to handle such code movement without breaking people's codes. Similar suggestions to others.

Suggested change

fld_header()

Deprecated: use `AVSfldIO.fld_header` instead.

"""

`header = string_to_array(header_lines)`

convert long string with embedded newlines into string array

"""

function string_to_array(header_lines::String)

newline = '\n'

# ensure there is a newline at end, since dumb editors can forget...

if header_lines[end] != newline

header_lines *= newline

end

ends = findall(isequal(newline), header_lines)

(length(ends) <= 0) && throw("no newlines?")

header = split(header_lines, newline, keepempty=false)

# strip comments (lines that begin with #)

header = filter(line -> line[1] != '#', header)

return header

function fld_header()

throw("fld_header is deprecated: use AVSfldIO.fld_header instead.")

end

@deprecate fld_header AVSfldIO.fld_header

Thanks very much for this suggestion. I didn't know about this command!
I will use it in the next commit (before merging this PR).

It's a bit sad though that by default there is no warning given to users:
https://docs.julialang.org/en/v1/base/base/#Base.@deprecate
So it seems like most users will not know about this change until we really remove it anyway.

So it seems like most users will not know about this change until we really remove it anyway.

Correct... This is because Julia is designed for high performance, and warnings will hurt the performance. This is another reason that people need to be careful about the semantics versioning 😄

codecov · 2021-05-21T18:00:55Z

Codecov Report

Merging #94 (f4413fc) into master (5daacda) will decrease coverage by 0.05%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master      #94      +/-   ##
==========================================
- Coverage   99.79%   99.73%   -0.06%     
==========================================
  Files          49       46       -3     
  Lines        2406     2251     -155     
==========================================
- Hits         2401     2245     -156     
- Misses          5        6       +1

Impacted Files	Coverage Δ
src/fbp/sino_geom.jl	`97.82% <0.00%> (-0.73%)`	⬇️
src/MIRT.jl

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5daacda...f4413fc. Read the comment docs.

johnnychen94 · 2021-05-21T18:01:25Z

test/io/fld-read.jl

+using Test: @testset, @test_throws

-
-dir = mktempdir()
-
-
-@testset "fld eof" begin
-	file = joinpath(dir, "fld-read-eof-test.fld")
-	open(file, "w") do fid
-	#	@show fid
-	    println(fid, "# AVS field file eof test")
-	end
-	@test_throws String fld_read(file)
-
-	open(file, "r") do fid
-		@test_throws String fld_read_single(
-			file, fid,
-			(99,), Float32, fieldtype,
-			false, # is_external_file,
-			"", # extfile,
-			Float32, "ieee-le", 0, 0,
-		)
-	end
-end
-
-
-@testset "fld misc" begin
-	@test_throws String arg_get(["1", "2"], "3")
-	@test string_to_array("0") isa AbstractArray{<:AbstractString}
-end
-
-
-@testset "fld ascii" begin
-	tdir = mktempdir()
-	file = joinpath(tdir, "fld-read-test.fld")
-	extfilename = "fld-read-test.txt"
-	chat = isinteractive()
-
-	data = Float32.(1:5)
-	head = [
-		"# AVS field file"
-		"ndim=1"
-		"dim1=5"
-		"nspace=1"
-		"veclen=1"
-		"data=float"
-		"field=uniform"
-		"variable 1 file=$extfilename filetype=ascii"
-	]
-	open(file, "w") do fid
-		for line in head
-			println(fid, line)
-		end
-	end
-
-	@test fld_header(file) isa Array{<:AbstractString}
-
-	# ensure that it throws if no extfile
-	@test_throws String tmp = fld_read(file)
-
-	# write ascii and test
-	extfile = joinpath(tdir, extfilename)
-	open(extfile, "w") do fid
-		for d in data
-			println(fid, d)
-		end
-	end
-
-#	run(`op range $file`)
-	tmp = fld_read(file ; chat=chat)
-	@test tmp == data
-	@test eltype(tmp) == Float32
-
-	rm(file)
-	rm(extfile)
+@testset "fld-read" begin
+	@test_throws String fld_header()
+	@test_throws String fld_read()


No need to delete these tests very quickly. Instead, you can move them to a separate file test/deprecated.jl so as to make sure old usages are still valid. And then in the future appropriately remove them when the symbols are removed.

Good idea. I'll put a simple and quick version of the test here.
I'd like CI to run faster here, so I'll leave the full tests to AVSfldIO.jl

johnnychen94 · 2021-05-21T18:03:11Z

As I've commented, with @deprecate, this code arrangement can be done safely without breaking people's codes, so only a patch version bump can be sufficient.

johnnychen94 · 2021-05-21T18:05:58Z

Although one of my labmates does MRI-related things and once tried this package, I haven't actually had a chance to use this package. But by all means, just feel free to reach for help if there are any similar code maintenance issues and I'd be very much happy to help and review. I wish we could have more good quality image processing toolboxes in Julia and so that more people come using it.

JeffFessler · 2021-05-21T22:46:26Z

I have other changes to make soon, so no version bump yet.

JeffFessler · 2021-05-23T04:02:23Z

@johnnychen94
It seems to me that @deprecate is working less generally than I first thought.
I thought it would cover all possible method signatures, but apparently it only does one at a time:
https://github.com/JuliaLang/julia/blob/a08a3ff1f957f6bd570ff5756dff4290eb6f43da/base/deprecated.jl#L174
Some of my methods, especially jim have a lot of signatures so it may be a pain to @deprecate them all, even when using kwargs. I wish there were a one-stop way like fun(args... ; kwargs...) to cover them all.
Any tricks I should know about to simplify?

johnnychen94 · 2021-05-23T07:52:46Z

Can you provide an example of this or maybe submit a draft PR? Without any signature to the methods, it's just a plain symbol deprecation and would apply to all methods if I understand it correctly.

julia> f(x, y=1) = x + y
f (generic function with 2 methods)

julia> @deprecate g f
g (generic function with 1 method)

julia> g(1)
┌ Warning: `g` is deprecated, use `f` instead.
│   caller = top-level scope at REPL[4]:1
└ @ Core REPL[4]:1
2

julia> g(1, 2)
┌ Warning: `g` is deprecated, use `f` instead.
│   caller = top-level scope at REPL[5]:1
└ @ Core REPL[5]:1
3

If only a specific method/signature needs to be deprecated, then we need to be careful about the signature:

julia> f(x, y=1) = x + y
f (generic function with 2 methods)

julia> @deprecate g(x) f(x)
g (generic function with 1 method)

julia> g(1)
┌ Warning: `g(x)` is deprecated, use `f(x)` instead.
│   caller = top-level scope at REPL[3]:1
└ @ Core REPL[3]:1
2

julia> g(1, 2)
ERROR: MethodError: no method matching g(::Int64, ::Int64)
Closest candidates are:
  g(::Any) at deprecated.jl:70
Stacktrace:
 [1] top-level scope
   @ REPL[4]:1

JeffFessler · 2021-05-23T11:34:53Z

Thanks. The issue that was unexpected to me is that @deprecate doesn't handle kwargs automatically:

f(x ; y=5) = x + y
@deprecate g f
@show g(1) # works
@show g(2 ; y=3) # fails

Oh well. I've addressed it in #96 hopefully.

johnnychen94 · 2021-05-23T11:37:47Z

The issue that was unexpected to me is that @deprecate doesn't handle kwargs automatically:

Oops! I didn't know that. Looks like this works:

@deprecate g(args...; kwargs...) f(args...; kwargs...)

JeffFessler · 2021-05-23T11:45:52Z

Perfect! That is the elegant solution I was hoping to use!

JeffFessler added 7 commits May 21, 2021 12:47

fld deprecate

5723ce8

FileIO

78b630f

brain test

dddff1c

brainweb

911b614

xtick

5811f77

AVSfldIO !?

653397e

log

e2cd2f8

johnnychen94 reviewed May 21, 2021

View reviewed changes

JeffFessler added 3 commits May 21, 2021 15:54

deprecate

ad34d4a

deprecated tests

3054c5f

test deprecated fld io

f4413fc

JeffFessler changed the title ~~move fld_read fld_write to FileIO (breaking)~~ move fld_read fld_write to FileIO (deprecating) May 21, 2021

JeffFessler merged commit 5bb5b9e into master May 22, 2021

JeffFessler deleted the fld-break branch May 22, 2021 17:32

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

move fld_read fld_write to FileIO (deprecating) #94

move fld_read fld_write to FileIO (deprecating) #94

JeffFessler commented May 21, 2021 •

edited

Loading

johnnychen94 May 21, 2021 •

edited

Loading

JeffFessler May 21, 2021

johnnychen94 May 22, 2021 •

edited

Loading

codecov bot commented May 21, 2021 •

edited

Loading

johnnychen94 May 21, 2021 •

edited

Loading

JeffFessler May 21, 2021

johnnychen94 commented May 21, 2021

johnnychen94 commented May 21, 2021 •

edited

Loading

JeffFessler commented May 21, 2021

JeffFessler commented May 23, 2021

johnnychen94 commented May 23, 2021 •

edited

Loading

JeffFessler commented May 23, 2021

johnnychen94 commented May 23, 2021

JeffFessler commented May 23, 2021

move fld_read fld_write to FileIO (deprecating) #94

move fld_read fld_write to FileIO (deprecating) #94

Conversation

JeffFessler commented May 21, 2021 • edited Loading

johnnychen94 May 21, 2021 • edited Loading

Choose a reason for hiding this comment

JeffFessler May 21, 2021

Choose a reason for hiding this comment

johnnychen94 May 22, 2021 • edited Loading

Choose a reason for hiding this comment

codecov bot commented May 21, 2021 • edited Loading

Codecov Report

johnnychen94 May 21, 2021 • edited Loading

Choose a reason for hiding this comment

JeffFessler May 21, 2021

Choose a reason for hiding this comment

johnnychen94 commented May 21, 2021

johnnychen94 commented May 21, 2021 • edited Loading

JeffFessler commented May 21, 2021

JeffFessler commented May 23, 2021

johnnychen94 commented May 23, 2021 • edited Loading

JeffFessler commented May 23, 2021

johnnychen94 commented May 23, 2021

JeffFessler commented May 23, 2021

JeffFessler commented May 21, 2021 •

edited

Loading

johnnychen94 May 21, 2021 •

edited

Loading

johnnychen94 May 22, 2021 •

edited

Loading

codecov bot commented May 21, 2021 •

edited

Loading

johnnychen94 May 21, 2021 •

edited

Loading

johnnychen94 commented May 21, 2021 •

edited

Loading

johnnychen94 commented May 23, 2021 •

edited

Loading