Add forward-links to documentation.

tanaylab · Apr 16, 2024 · 72d096c · 72d096c
1 parent 567f872
commit 72d096c
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diff --git a/Makefile b/Makefile
@@ -70,7 +70,7 @@ coverage: untested_lines line_coverage
 .PHONY: docs
 docs: docs/v0.1.0/index.html
 
-docs/v0.1.0/index.html: src/*.jl src/*.md deps/document.sh deps/document.jl
+docs/v0.1.0/index.html: src/*.jl src/*.md deps/document.sh deps/document.jl docs/make.jl
 	deps/document.sh
 
 .PHONY: clean

diff --git a/docs/make.jl b/docs/make.jl
@@ -9,6 +9,7 @@ push!(LOAD_PATH, "..")
 
 using NestedTests
 using Pkg
+using Daf
 
 for file in readdir("docs"; join = true)
     if !endswith(file, "make.jl")

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":"2024-04-16T09:01:55","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-04-16T14:56:58","documenter_version":"1.4.0"}}
diff --git a/docs/v0.1.0/adapters.html b/docs/v0.1.0/adapters.html
@@ -497,7 +497,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html
@@ -650,7 +650,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/chains.html b/docs/v0.1.0/chains.html
@@ -497,7 +497,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/computations.html b/docs/v0.1.0/computations.html
@@ -611,7 +611,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/concat.html b/docs/v0.1.0/concat.html
@@ -552,7 +552,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/contracts.html b/docs/v0.1.0/contracts.html
@@ -562,7 +562,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/copies.html b/docs/v0.1.0/copies.html
@@ -791,7 +791,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/example_data.html b/docs/v0.1.0/example_data.html
@@ -347,7 +347,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/files_format.html b/docs/v0.1.0/files_format.html
@@ -732,7 +732,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/formats.html b/docs/v0.1.0/formats.html
@@ -2291,7 +2291,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/generic_functions.html b/docs/v0.1.0/generic_functions.html
@@ -435,7 +435,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/generic_logging.html b/docs/v0.1.0/generic_logging.html
@@ -405,7 +405,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/generic_types.html b/docs/v0.1.0/generic_types.html
@@ -499,7 +499,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/groups.html b/docs/v0.1.0/groups.html
@@ -424,7 +424,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/h5df_format.html b/docs/v0.1.0/h5df_format.html
@@ -745,7 +745,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/index.html b/docs/v0.1.0/index.html
@@ -2146,7 +2146,7 @@ <h1 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/matrix_layouts.html b/docs/v0.1.0/matrix_layouts.html
@@ -871,7 +871,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/memory_format.html b/docs/v0.1.0/memory_format.html
@@ -345,7 +345,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/messages.html b/docs/v0.1.0/messages.html
@@ -427,7 +427,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/operations.html b/docs/v0.1.0/operations.html
@@ -1556,7 +1556,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/queries.html b/docs/v0.1.0/queries.html
@@ -4032,7 +4032,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/read_only.html b/docs/v0.1.0/read_only.html
@@ -419,7 +419,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/readers.html b/docs/v0.1.0/readers.html
@@ -732,8 +732,10 @@ <h2 id="Vector-properties">
 </code> is 
 <code>nothing
 </code>, it will be returned. If it is a 
+<a href="storage_types.html#Daf.StorageTypes.StorageVector">
 <code>StorageVector
-</code>, it has to be of the same size as the 
+</code>
+</a>, it has to be of the same size as the 
 <code>axis
 </code>, and is returned. If it is a 
 <a href="storage_types.html#Daf.StorageTypes.StorageScalar">
@@ -970,8 +972,10 @@ <h2 id="Utilities">
 </code>
 </pre>
 <p>Return the version number of the axis. This is incremented every time 
+<a href="writers.html#Daf.Writers.delete_axis!">
 <code>delete_axis!
-</code> is called. It is used by interfaces to other programming languages to minimize copying data.
+</code>
+</a> is called. It is used by interfaces to other programming languages to minimize copying data.
 </p>
 <div class="admonition is-info">
 <header class="admonition-header">Note
@@ -1006,12 +1010,18 @@ <h2 id="Utilities">
 </code>
 </pre>
 <p>Return the version number of the vector. This is incremented every time 
+<a href="writers.html#Daf.Writers.set_vector!">
 <code>set_vector!
-</code>, 
+</code>
+</a>, 
+<a href="writers.html#Daf.Writers.empty_dense_vector!">
 <code>empty_dense_vector!
-</code> or 
+</code>
+</a> or 
+<a href="writers.html#Daf.Writers.empty_sparse_vector!">
 <code>empty_sparse_vector!
-</code> are called. It is used by interfaces to other programming languages to minimize copying data.
+</code>
+</a> are called. It is used by interfaces to other programming languages to minimize copying data.
 </p>
 <div class="admonition is-info">
 <header class="admonition-header">Note
@@ -1042,16 +1052,27 @@ <h2 id="Utilities">
 <section>
 <div>
 <pre>
-<code class="language-julia hljs">matrix_version_counter(daf::DafReader, rows_axis::AbstractString, columns_axis::AbstractString, name::AbstractString)::UInt32
+<code class="language-julia hljs">matrix_version_counter(
+    daf::DafReader,
+    rows_axis::AbstractString,
+    columns_axis::AbstractString,
+    name::AbstractString
+)::UInt32
 </code>
 </pre>
 <p>Return the version number of the matrix. The order of the axes does not matter. This is incremented every time 
+<a href="writers.html#Daf.Writers.set_matrix!">
 <code>set_matrix!
-</code>, 
+</code>
+</a>, 
+<a href="writers.html#Daf.Writers.empty_dense_matrix!">
 <code>empty_dense_matrix!
-</code> or 
+</code>
+</a> or 
+<a href="writers.html#Daf.Writers.empty_sparse_matrix!">
 <code>empty_sparse_matrix!
-</code> are called. It is used by interfaces to other programming languages to minimize copying data.
+</code>
+</a> are called. It is used by interfaces to other programming languages to minimize copying data.
 </p>
 <div class="admonition is-info">
 <header class="admonition-header">Note
@@ -1224,7 +1245,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/reconstruction.html b/docs/v0.1.0/reconstruction.html
@@ -435,7 +435,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/registry.html b/docs/v0.1.0/registry.html
@@ -714,7 +714,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/search_index.js b/docs/v0.1.0/search_index.js
diff --git a/docs/v0.1.0/storage_types.html b/docs/v0.1.0/storage_types.html
@@ -691,7 +691,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/tokens.html b/docs/v0.1.0/tokens.html
@@ -896,7 +896,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/views.html b/docs/v0.1.0/views.html
@@ -970,7 +970,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">

diff --git a/docs/v0.1.0/writers.html b/docs/v0.1.0/writers.html
@@ -1320,7 +1320,7 @@ <h2 id="Index">
 <hr/>
 <p>This document was generated with 
 <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
-</a> version 1.3.0. Using Julia version 1.10.0.
+</a> version 1.4.0. Using Julia version 1.10.0.
 </p>
 </section>
 <footer class="modal-card-foot">