Only code reorganization (src/ directory) #100

thimotedupuch · 2025-08-14T18:53:23Z

@wheeheee This is the V2 of last PR.

This time I only reorganized the code inside the src/ directory, I did not change any code logic.

The code was previously using the mod subdirectory, that has been deleted and now follows the structure :

src/
	Wavelets.jl # Export the modules for the user and for the sourcecode
	Util/
		Util.jl  # export Util module
		util.jl
		dyadic.jl
		non_dyadic.jl

	Threshold/
		Threshold.jl # export Threshold module
		threshold.jl
		denoising.jl
		basis_functions.jl
		entropy.jl

	Transforms/
		Transforms.jl # export Transforms module
		transforms.jl
		transforms_filter.jl
		transforms_lifting.jl
		transforms_maximal_overlap.jl

	WT/
		WT.jl # export WL module
		wt.jl

	Plot/
		Plot.jl # export Plot module
		plot.jl

The reexport dependency is not needed anymore (I believe ?). Also the functions from the different submodules are all exported, as well as the submodules themselves (except for Util).

Here's an overview of the diff :

 ➜ jj diff --from master --to code_refactor --stat
src/Plot/Plot.jl                                      |   8 +
src/{mod/Plot.jl => Plot/plot.jl}                     |  55 +++---
src/Threshold/Threshold.jl                            |  27 +++
src/Threshold/basis_functions.jl                      |  56 ++++++
src/Threshold/denoising.jl                            | 122 ++++++++++++++
src/Threshold/entropy.jl                              | 129 ++++++++++++++
src/Threshold/threshold.jl                            | 129 ++++++++++++++
src/Transforms/Transforms.jl                          |  10 +
src/Transforms/transforms.jl                          | 226 ++++++++++++++++++++++++++
src/{mod => Transforms}/transforms_filter.jl          | 258 ++++++++++++++---------------
src/{mod => Transforms}/transforms_lifting.jl         | 208 +++++++++++-------------
src/{mod => Transforms}/transforms_maximal_overlap.jl |  12 +-
src/Util/Util.jl                                      |  44 +++++
src/Util/dyadic.jl                                    |  20 ++
src/Util/non_dyadic.jl                                |  27 +++
src/{mod/Util.jl => Util/util.jl}                     | 286 ++++++++++++---------------------
src/WT/WT.jl                                          |  13 +
src/WT/wt.jl                                          | 454 ++++++++++++++++++++++++++++++++++++++++++++++++++++
src/Wavelets.jl                                       |  75 ++++++--
src/mod/Threshold.jl                                  | 462 -----------------------------------------------------
src/mod/Transforms.jl                                 | 239 ---------------------------
src/mod/WT.jl                                         | 493 ---------------------------------------------------------
22 files changed, 1693 insertions(+), 1660 deletions(-)

 ➜ jj diff --from master --to code_refactor --summary
A src/Plot/Plot.jl
R src/{mod/Plot.jl => Plot/plot.jl}
A src/Threshold/Threshold.jl
A src/Threshold/basis_functions.jl
A src/Threshold/denoising.jl
A src/Threshold/entropy.jl
A src/Threshold/threshold.jl
A src/Transforms/Transforms.jl
A src/Transforms/transforms.jl
R src/{mod => Transforms}/transforms_filter.jl
R src/{mod => Transforms}/transforms_lifting.jl
R src/{mod => Transforms}/transforms_maximal_overlap.jl
A src/Util/Util.jl
A src/Util/dyadic.jl
A src/Util/non_dyadic.jl
R src/{mod/Util.jl => Util/util.jl}
A src/WT/WT.jl
A src/WT/wt.jl
M src/Wavelets.jl
D src/mod/Threshold.jl
D src/mod/Transforms.jl
D src/mod/WT.jl

If this gets merged I will be able to start actually working on the code.

@wheeheee for the logo we'll see later.

gummif · 2025-08-15T17:05:42Z

Thanks for taking time to clean up.

One thing I'm not sure is ok is having files with same name modulo case (e.g. wt.jl and WT.jl) on windows.

thimotedupuch · 2025-08-15T20:25:07Z

One thing I'm not sure is ok is having files with same name modulo case (e.g. wt.jl and WT.jl) on windows.

Okay, then what would be the ideal file structure ?

wheeheee · 2025-08-16T15:03:40Z

You could just rename the lowercase files to *_core.jl, *_main.jl, or even just _*.jl. That solves the problem with case-insensitivity on Windows.

thimotedupuch · 2025-08-17T09:27:34Z

Nice, thank you for fixing the tests!
It would be cool if the Julia programming language official docs could provide information about the recommended way of doing all of this : structuring the files, where to put the using statements, how to handle the namespace...

wheeheee · 2025-08-17T11:17:24Z

A lot of these are personal preferences, some communities like SciML have style guides, and there are recommendations on Julia's discourse if you search for them

wheeheee

not all comments are related to the reorganisation, but overall LGTM?

wheeheee · 2025-08-17T12:58:45Z

src/WT/_wt.jl

+        name(::$TYPE{N1,N2}) where {N1,N2} = string($NAMEBASE, N1, "/", N2)
+        vanishingmoments(::$TYPE{N1,N2}) where {N1,N2} = (N1, N2)
+    end
+    for i in length(RANGE1)


weird, probably 1:length(RANGE1)? but it somehow works because it's one element long, and 1[1] is ok in julia...

wheeheee · 2025-08-17T13:03:02Z

src/Threshold/denoising.jl

+function nspin2circ(nspin::Tuple, i::Int)
+    c1 = CartesianIndices(nspin)[i].I
+    c = Vector{Int}(undef, length(c1))
+    for k in 1:length(c1)
+        c[k] = c1[k] - 1
+    end
+    return c
+end


isn't this just collect(c1 .- 1)

wheeheee · 2025-08-17T13:04:05Z

src/Transforms/_transforms.jl

+        function ($Xwt!)(y::WPTArray{T}, scheme::GLS, L::Integer) where {T<:ValueType}
+            return ($Xwt!)(y, scheme, maketree(length(x), L, :full))
+        end


x looks like it is undefined in the function?

wheeheee · 2025-08-17T13:07:17Z

src/Transforms/transforms_filter.jl

-    nx = nout<<1
+    out::AbstractVector{<:Number}, iout::Integer, nout::Integer,
+    x::AbstractVector{<:Number}, ix::Integer,
+    shift::Integer=0, ss::Bool=false) where {T<:Number}


this may be the autoformatter's work on copy and paste, but I think it's fine without curlies. also, a bit noisy.

wheeheee · 2025-08-17T13:13:58Z

src/mod/WT.jl

seems like jujutsu is not so good at tracking renamed files? (Transforms.jl also.) git mv would have cut down the diffs

wheeheee · 2025-08-17T13:16:28Z

src/Util/non_dyadic.jl

+using ..Util
+


Suggested change

using ..Util

using Util while in Util seems redundant, although it doesn't error.

wheeheee · 2025-08-17T13:17:04Z

src/WT/_wt.jl

@@ -0,0 +1,454 @@
+using ..WT


Suggested change

using ..WT

this too

thimotedupuch · 2025-08-17T13:30:59Z

Yeah, thanks for the review
as I mentioned I did not change any code but there are a lot of possible improvements

Only code reorganization (src/ directory)

9a4337f

Thimoté Dupuch and others added 2 commits August 16, 2025 17:32

added underscore to filenames

54f5281

fix tests

a6dd8f6

wheeheee reviewed Aug 17, 2025

View reviewed changes

Only code reorganization (src/ directory) #100

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Only code reorganization (src/ directory) #100

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