Try to decouple transpose! from LinearAlgebra.

tanaylab · Jun 1, 2024 · 25579ec · 25579ec
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diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-06-01T18:28:22","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-06-01T20:18:31","documenter_version":"1.4.1"}}
diff --git a/docs/v0.1.0/index.html b/docs/v0.1.0/index.html
@@ -1766,6 +1766,12 @@ <h1 id="Index">
 </a>
 </li>
 <li>
+<a href="matrix_layouts.html#Daf.MatrixLayouts.transpose!">
+<code>Daf.MatrixLayouts.transpose!
+</code>
+</a>
+</li>
+<li>
 <a href="messages.html#Daf.Messages.depict_percent">
 <code>Daf.Messages.depict_percent
 </code>
@@ -2162,12 +2168,6 @@ <h1 id="Index">
 </a>
 </li>
 <li>
-<a href="matrix_layouts.html#LinearAlgebra.transpose!">
-<code>LinearAlgebra.transpose!
-</code>
-</a>
-</li>
-<li>
 <a href="computations.html#Daf.Computations.@computation">
 <code>Daf.Computations.@computation
 </code>

diff --git a/docs/v0.1.0/matrix_layouts.html b/docs/v0.1.0/matrix_layouts.html
@@ -576,7 +576,7 @@ <h2 id="Changing-layout">
 </strong>, summing the UMIs of a gene is fast, and summing the UMIs of a cell is slow.
 </p>
 <p>In contrast, 
-<a href="matrix_layouts.html#LinearAlgebra.transpose!">
+<a href="matrix_layouts.html#Daf.MatrixLayouts.transpose!">
 <code>transpose!
 </code>
 </a> (with a 
@@ -656,8 +656,8 @@ <h2 id="Changing-layout">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="LinearAlgebra.transpose!" href="#LinearAlgebra.transpose!">
-<code>LinearAlgebra.transpose!
+<a class="docstring-binding" id="Daf.MatrixLayouts.transpose!" href="#Daf.MatrixLayouts.transpose!">
+<code>Daf.MatrixLayouts.transpose!
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -922,8 +922,8 @@ <h2 id="Index">
 </a>
 </li>
 <li>
-<a href="matrix_layouts.html#LinearAlgebra.transpose!">
-<code>LinearAlgebra.transpose!
+<a href="matrix_layouts.html#Daf.MatrixLayouts.transpose!">
+<code>Daf.MatrixLayouts.transpose!
 </code>
 </a>
 </li>

diff --git a/docs/v0.1.0/objects.inv b/docs/v0.1.0/objects.inv
diff --git a/docs/v0.1.0/search_index.js b/docs/v0.1.0/search_index.js
diff --git a/src/matrix_layouts.jl b/src/matrix_layouts.jl
@@ -37,6 +37,7 @@ export relayout!
 export require_major_axis
 export require_minor_axis
 export Rows
+export transpose!
 
 using ..GenericFunctions
 using ..GenericTypes
@@ -267,7 +268,7 @@ basically what `relayout!` does for you. In addition, `relayout!` will work for
     `NamedMatrix` with the same axes. If `destination` is also a `NamedMatrix`, then its axes must match `source`.
 """
 function relayout!(matrix::AbstractMatrix)::AbstractMatrix
-    return transpose(LinearAlgebra.transpose!(matrix))
+    return transpose(transpose!(matrix))
 end
 
 function relayout!(destination::AbstractMatrix, source::NamedMatrix)::NamedArray  # untested
@@ -354,40 +355,40 @@ end
 This is a shorthand for `LinearAlgebra.transpose!(similar(transpose(m)), m)`. That is, this will return a transpose of a
 matrix, but instead of simply using a zero-copy wrapper, it actually rearranges the data. See [`relayout!`](@ref).
 """
-function LinearAlgebra.transpose!(matrix::AbstractMatrix)::AbstractMatrix
+function transpose!(matrix::AbstractMatrix)::AbstractMatrix
     @debug "transpose! $(depict(matrix)) {"  # NOLINT
     result = LinearAlgebra.transpose!(similar(transpose(matrix)), matrix)
     @debug "transpose! $(depict(result)) }"  # NOLINT
     return result
 end
 
-function LinearAlgebra.transpose!(matrix::AbstractSparseMatrix)::AbstractMatrix
+function transpose!(matrix::AbstractSparseMatrix)::AbstractMatrix
     @assert require_major_axis(matrix) == Columns
     @debug "transpose! $(depict(matrix)) {"  # NOLINT
     result = SparseMatrixCSC(transpose(matrix))
     @debug "transpose! $(depict(result)) }"  # NOLINT
     return result
 end
 
-function LinearAlgebra.transpose!(matrix::NamedMatrix)::NamedArray
-    return NamedArray(LinearAlgebra.transpose!(matrix.array), flip_tuple(matrix.dicts), flip_tuple(matrix.dimnames))
+function transpose!(matrix::NamedMatrix)::NamedArray
+    return NamedArray(transpose!(matrix.array), flip_tuple(matrix.dicts), flip_tuple(matrix.dimnames))
 end
 
 function flip_tuple(tuple::Tuple{T1, T2})::Tuple{T2, T1} where {T1, T2}
     value1, value2 = tuple
     return (value2, value1)
 end
 
-function LinearAlgebra.transpose!(matrix::SparseArrays.ReadOnly)::AbstractMatrix
-    return LinearAlgebra.transpose!(parent(matrix))
+function transpose!(matrix::SparseArrays.ReadOnly)::AbstractMatrix
+    return transpose!(parent(matrix))
 end
 
-function LinearAlgebra.transpose!(matrix::Transpose)::AbstractMatrix
-    return transpose(LinearAlgebra.transpose!(parent(matrix)))
+function transpose!(matrix::Transpose)::AbstractMatrix
+    return transpose(transpose!(parent(matrix)))
 end
 
-function LinearAlgebra.transpose!(matrix::Adjoint)::AbstractMatrix
-    return adjoint(LinearAlgebra.transpose!(parent(matrix)))
+function transpose!(matrix::Adjoint)::AbstractMatrix
+    return adjoint(transpose!(parent(matrix)))
 end
 
 """