Update dependencies.

tanaylab · Mar 24, 2024 · 7eef137 · 7eef137
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diff --git a/Manifest.toml b/Manifest.toml
@@ -15,10 +15,22 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[deps.CategoricalArrays]]
-deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"]
-git-tree-sha1 = "18d7f3e82c1a80dd38c16453b8fd3f0a7db92f23"
+deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"]
+git-tree-sha1 = "1568b28f91293458345dabba6a5ea3f183250a61"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "0.9.7"
+version = "0.10.8"
+
+    [deps.CategoricalArrays.extensions]
+    CategoricalArraysJSONExt = "JSON"
+    CategoricalArraysRecipesBaseExt = "RecipesBase"
+    CategoricalArraysSentinelArraysExt = "SentinelArrays"
+    CategoricalArraysStructTypesExt = "StructTypes"
+
+    [deps.CategoricalArrays.weakdeps]
+    JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+    RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+    SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
+    StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
 
 [[deps.Combinatorics]]
 git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
@@ -54,9 +66,9 @@ version = "0.1.0"
 
 [[deps.ConstructionBase]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9"
+git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2"
 uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.5.4"
+version = "1.5.5"
 
     [deps.ConstructionBase.extensions]
     ConstructionBaseIntervalSetsExt = "IntervalSets"
@@ -135,9 +147,9 @@ version = "0.1.1"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc"
+git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.2"
+version = "1.16.3"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -292,8 +304,8 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2023.1.10"
 
 [[deps.Muon]]
-deps = ["CategoricalArrays", "CompressHashDisplace", "DataFrames", "FileIO", "HDF5", "LinearAlgebra", "OrderedCollections", "Pkg", "Random", "SparseArrays", "StructArrays"]
-git-tree-sha1 = "ecd6b99bc847c48362c7a2de3b1ca58164e16713"
+deps = ["CategoricalArrays", "CompressHashDisplace", "DataFrames", "FileIO", "HDF5", "LinearAlgebra", "OrderedCollections", "Pkg", "PooledArrays", "Random", "SparseArrays", "StructArrays"]
+git-tree-sha1 = "4dc16783ceefb335cce04c4ef2052d90db9f95e0"
 repo-rev = "main"
 repo-url = "https://github.com/scverse/Muon.jl"
 uuid = "446846d7-b4ce-489d-bf74-72da18fe3629"
@@ -306,9 +318,9 @@ version = "1.2.0"
 
 [[deps.NamedArrays]]
 deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"]
-git-tree-sha1 = "6d42eca6c3a27dc79172d6d947ead136d88751bb"
+git-tree-sha1 = "0ae91efac93c3859f5c812a24c9468bb9e50b028"
 uuid = "86f7a689-2022-50b4-a561-43c23ac3c673"
-version = "0.10.0"
+version = "0.10.1"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -455,12 +467,6 @@ version = "0.6.18"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
-[[deps.StructTypes]]
-deps = ["Dates", "UUIDs"]
-git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70"
-uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-version = "1.10.0"
-
 [[deps.SuiteSparse_jll]]
 deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"

diff --git a/deps/document.jl b/deps/document.jl
@@ -32,6 +32,7 @@ REPO = "https://github.com/tanaylab/$(NAME).jl"
 makedocs(;
     authors = join(" ", AUTHORS),
     build = "../docs/v$(VERSION)",
+    remotes = nothing,
     source = "../src",
     clean = true,
     doctest = true,

diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-23T14:49:21","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-24T16:44:01","documenter_version":"1.3.0"}}
diff --git a/docs/v0.1.0/adapters.html b/docs/v0.1.0/adapters.html
@@ -198,10 +198,6 @@
 <span class="docs-label is-hidden-touch">GitHub
 </span>
 </a>
-<a class="docs-navbar-link" href="https://github.com/tanaylab/Daf.jl/blob/main/src/adapters.md" title="Edit source on GitHub">
-<span class="docs-icon fa-solid">
-</span>
-</a>
 <a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings">
 </a>
 <a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings">
@@ -239,8 +235,6 @@ <h1 id="Adapters">
 </a>.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/adapters.jl#L1-L3">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -427,8 +421,6 @@ <h1 id="Adapters">
 </a> functions to use clear generic names for their inputs and outputs, and still apply them to arbitrary data sets using more specific names. One can even invoke the same computation with different parameter values, and store the different results in the same data set under different names.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/adapters.jl#L21-L91">source
-</a>
 </section>
 </article>
 <h2 id="Index">

diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html
@@ -198,10 +198,6 @@
 <span class="docs-label is-hidden-touch">GitHub
 </span>
 </a>
-<a class="docs-navbar-link" href="https://github.com/tanaylab/Daf.jl/blob/main/src/anndata_format.md" title="Edit source on GitHub">
-<span class="docs-icon fa-solid">
-</span>
-</a>
 <a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings">
 </a>
 <a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings">
@@ -411,8 +407,6 @@ <h1 id="AnnData-Format">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/anndata_format.jl#L1-L73">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -490,8 +484,6 @@ <h1 id="AnnData-Format">
 </code> property, if it exists, otherwise, it will be &quot;X&quot;.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/anndata_format.jl#L94-L124">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -556,8 +548,6 @@ <h1 id="AnnData-Format">
 </code> object.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/anndata_format.jl#L359-L388">source
-</a>
 </section>
 </article>
 <h2 id="Index">

diff --git a/docs/v0.1.0/chains.html b/docs/v0.1.0/chains.html
@@ -198,10 +198,6 @@
 <span class="docs-label is-hidden-touch">GitHub
 </span>
 </a>
-<a class="docs-navbar-link" href="https://github.com/tanaylab/Daf.jl/blob/main/src/chains.md" title="Edit source on GitHub">
-<span class="docs-icon fa-solid">
-</span>
-</a>
 <a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings">
 </a>
 <a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings">
@@ -237,8 +233,6 @@ <h1 id="Chains">
 </code> data set that contains extra (or overriding) data on top of a larger read-only data set. In particular this allows creating several such incompatible extra data sets (e.g., different groupings of cells to metacells), without having to duplicate the common (read only) data.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/chains.jl#L1-L6">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -281,8 +275,6 @@ <h1 id="Chains">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/chains.jl#L57-L69">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -327,8 +319,6 @@ <h1 id="Chains">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/chains.jl#L91-L102">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -361,8 +351,6 @@ <h1 id="Chains">
 </a>.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/chains.jl#L25-L32">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -399,8 +387,6 @@ <h1 id="Chains">
 <p>Any modifications or additions to the chain are directed at the final writer. Deletions are only allowed for data that exists only in this writer. That is, it is impossible to delete from a chain something that exists in any of the readers; it is only possible to override it.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/chains.jl#L38-L50">source
-</a>
 </section>
 </article>
 <h2 id="Index">

diff --git a/docs/v0.1.0/computations.html b/docs/v0.1.0/computations.html
@@ -198,10 +198,6 @@
 <span class="docs-label is-hidden-touch">GitHub
 </span>
 </a>
-<a class="docs-navbar-link" href="https://github.com/tanaylab/Daf.jl/blob/main/src/computations.md" title="Edit source on GitHub">
-<span class="docs-icon fa-solid">
-</span>
-</a>
 <a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings">
 </a>
 <a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings">
@@ -237,8 +233,6 @@ <h1 id="Computations">
 </a> describing their inputs and outputs. This is enforced, so that the implementation need not worry about missing inputs, and the caller can rely on the results. It is also self-documenting, so the generated documentation is always contains a clear up-to-date description of the contract.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L1-L6">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -349,8 +343,6 @@ <h1 id="Computations">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L67-L100">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -397,8 +389,6 @@ <h1 id="Computations">
 </code> ensures that the correct value is used in the documentation.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L322-L343">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -457,8 +447,6 @@ <h1 id="Computations">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L267-L288">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -487,8 +475,6 @@ <h1 id="Computations">
 </a> with two such arguments.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L291-L294">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -517,8 +503,6 @@ <h1 id="Computations">
 </a> with two such arguments.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/computations.jl#L297-L300">source
-</a>
 </section>
 </article>
 <h2 id="Index">

diff --git a/docs/v0.1.0/concat.html b/docs/v0.1.0/concat.html
@@ -198,10 +198,6 @@
 <span class="docs-label is-hidden-touch">GitHub
 </span>
 </a>
-<a class="docs-navbar-link" href="https://github.com/tanaylab/Daf.jl/blob/main/src/concat.md" title="Edit source on GitHub">
-<span class="docs-icon fa-solid">
-</span>
-</a>
 <a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings">
 </a>
 <a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings">
@@ -237,8 +233,6 @@ <h1 id="Concat">
 <p>The exact behavior of concatenation is surprisingly complex when accounting for sparse vs. dense matrices, different matrix layouts, and properties which are not along the concatenation axis. The implementation is further complicated by minimizing the allocation of intermediate memory buffers for the data; that is, in principle, concatenating from and into memory-mapped data sets should not allocate &quot;any&quot; memory buffers - the data should be copied directly from one memory-mapped region to another.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/concat.jl#L1-L10">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -362,8 +356,6 @@ <h1 id="Concat">
 </code> existing properties in the target.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/concat.jl#L70-L131">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -430,8 +422,6 @@ <h1 id="Concat">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/concat.jl#L34-L52">source
-</a>
 </section>
 </article>
 <article class="docstring">
@@ -466,8 +456,6 @@ <h1 id="Concat">
 </li>
 </ul>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/198796ac5eff2aa3b7bd99af0e97b0d598320361/src/concat.jl#L55-L67">source
-</a>
 </section>
 </article>
 <h2 id="Index">