Remove daf_ prefix for functions.

tanaylab · Mar 22, 2024 · 198796a · 198796a
1 parent 34d603e
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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":"1.10.2","generation_timestamp":"2024-03-22T11:48:45","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-22T16:39:14","documenter_version":"1.3.0"}}
diff --git a/docs/v0.1.0/adapters.html b/docs/v0.1.0/adapters.html
@@ -239,16 +239,16 @@ <h1 id="Adapters">
 </a>.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/adapters.jl#L1-L3">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/adapters.jl#L1-L3">source
 </a>
 </section>
 </article>
 <article class="docstring">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="Daf.Adapters.daf_adapter" href="#Daf.Adapters.daf_adapter">
-<code>Daf.Adapters.daf_adapter
+<a class="docstring-binding" id="Daf.Adapters.adapter" href="#Daf.Adapters.adapter">
+<code>Daf.Adapters.adapter
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -257,7 +257,7 @@ <h1 id="Adapters">
 <section>
 <div>
 <pre>
-<code class="language-julia hljs">daf_adapter(
+<code class="language-julia hljs">adapter(
     computation::Function,
     view::Union{DafWriter, DafReadOnly},
     [name::Maybe{AbstractString} = nothing,
@@ -275,8 +275,8 @@ <h1 id="Adapters">
 </code> on a 
 <code>view
 </code> data set and return the result; copy a 
-<a href="views.html#Daf.Views.daf_view">
-<code>daf_view
+<a href="views.html#Daf.Views.viewer">
+<code>viewer
 </code>
 </a> of the updated data set into the base 
 <code>Daf
@@ -297,7 +297,7 @@ <h1 id="Adapters">
 <p>To address these issues, the common idiom for applying computations to 
 <code>Daf
 </code> data is to use the 
-<code>daf_adapter
+<code>adapter
 </code> as follows:
 </p>
 <ul>
@@ -306,8 +306,8 @@ <h1 id="Adapters">
 </code> of your data which presents the data properties under the names expected by the 
 <code>computation
 </code>, using 
-<a href="views.html#Daf.Views.daf_view">
-<code>daf_view
+<a href="views.html#Daf.Views.viewer">
+<code>viewer
 </code>
 </a>. If the 
 <code>computation
@@ -322,7 +322,7 @@ <h1 id="Adapters">
 <li>Pass this 
 <code>view
 </code> to 
-<code>daf_adapter
+<code>adapter
 </code>, which will invoke the 
 <code>computation
 </code> with a (writable) 
@@ -387,11 +387,11 @@ <h1 id="Adapters">
 </code>, you can pass the data set directly as the 
 <span>$view$
 </span>. The call to 
-<code>daf_adapter
+<code>adapter
 </code> may still be needed to filter or rename the 
 <code>computation
 </code>&#39;s output. If the outputs can also be used as-is, then there&#39;s no need to invoke 
-<code>daf_adapter
+<code>adapter
 </code>; directly apply the 
 <code>computation
 </code> to the data and be done.
@@ -406,17 +406,17 @@ <h1 id="Adapters">
 # Here `daf` contains the inputs for the computation, but possibly
 # under a different name.
 
-result = daf_adapter(
+result = adapter(
     &quot;example&quot;,                 # A name to use to generate the temporary `Daf` data names.
-    daf_view(daf; ...),        # How to view the input in the way expected by the computation.
+    viewer(daf; ...),        # How to view the input in the way expected by the computation.
     axes = ..., data = ...,    # How and what to view from the output for copying back into `daf`.
     empty = ...,               # If the input view specifies a subset of some axes.
 ) do adapted                   # The writable adapted data we can pass to the computation.
     computation(adapted, ...)  # Actually do the computation.
     return ...                 # An additional result outside `daf`.
 end
 
-# Here `daf` will contain the specific renamed outputs specified in `daf_adapter`,
+# Here `daf` will contain the specific renamed outputs specified in `adapter`,
 # and you can also access the additional non-`daf` data `result`.
 </code>
 </pre>
@@ -427,7 +427,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/adapters.jl#L21-L91">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/adapters.jl#L21-L91">source
 </a>
 </section>
 </article>

diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html
@@ -411,7 +411,7 @@ <h1 id="AnnData-Format">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/anndata_format.jl#L1-L73">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/anndata_format.jl#L1-L73">source
 </a>
 </section>
 </article>
@@ -490,7 +490,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/anndata_format.jl#L94-L124">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/anndata_format.jl#L94-L124">source
 </a>
 </section>
 </article>
@@ -556,7 +556,7 @@ <h1 id="AnnData-Format">
 </code> object.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/anndata_format.jl#L359-L388">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/anndata_format.jl#L359-L388">source
 </a>
 </section>
 </article>

diff --git a/docs/v0.1.0/chains.html b/docs/v0.1.0/chains.html
@@ -237,7 +237,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/chains.jl#L1-L6">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/chains.jl#L1-L6">source
 </a>
 </section>
 </article>
@@ -281,7 +281,7 @@ <h1 id="Chains">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/chains.jl#L57-L69">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/chains.jl#L57-L69">source
 </a>
 </section>
 </article>
@@ -327,7 +327,7 @@ <h1 id="Chains">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/chains.jl#L91-L102">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/chains.jl#L91-L102">source
 </a>
 </section>
 </article>
@@ -361,7 +361,7 @@ <h1 id="Chains">
 </a>.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/chains.jl#L25-L32">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/chains.jl#L25-L32">source
 </a>
 </section>
 </article>
@@ -399,7 +399,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/chains.jl#L38-L50">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/chains.jl#L38-L50">source
 </a>
 </section>
 </article>

diff --git a/docs/v0.1.0/computations.html b/docs/v0.1.0/computations.html
@@ -237,7 +237,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L1-L6">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L1-L6">source
 </a>
 </section>
 </article>
@@ -349,7 +349,7 @@ <h1 id="Computations">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L67-L100">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L67-L100">source
 </a>
 </section>
 </article>
@@ -397,7 +397,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L322-L343">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L322-L343">source
 </a>
 </section>
 </article>
@@ -457,7 +457,7 @@ <h1 id="Computations">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L267-L288">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L267-L288">source
 </a>
 </section>
 </article>
@@ -487,7 +487,7 @@ <h1 id="Computations">
 </a> with two such arguments.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L291-L294">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L291-L294">source
 </a>
 </section>
 </article>
@@ -517,7 +517,7 @@ <h1 id="Computations">
 </a> with two such arguments.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/computations.jl#L297-L300">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/computations.jl#L297-L300">source
 </a>
 </section>
 </article>

diff --git a/docs/v0.1.0/concat.html b/docs/v0.1.0/concat.html
@@ -237,7 +237,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/concat.jl#L1-L10">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/concat.jl#L1-L10">source
 </a>
 </section>
 </article>
@@ -362,7 +362,7 @@ <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/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/concat.jl#L70-L131">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/concat.jl#L70-L131">source
 </a>
 </section>
 </article>
@@ -430,7 +430,7 @@ <h1 id="Concat">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/concat.jl#L34-L52">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/concat.jl#L34-L52">source
 </a>
 </section>
 </article>
@@ -466,7 +466,7 @@ <h1 id="Concat">
 </li>
 </ul>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/concat.jl#L55-L67">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/concat.jl#L55-L67">source
 </a>
 </section>
 </article>

diff --git a/docs/v0.1.0/contracts.html b/docs/v0.1.0/contracts.html
@@ -235,7 +235,7 @@ <h1 id="Contracts">
 </code> data.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L1-L3">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L1-L3">source
 </a>
 </section>
 </article>
@@ -270,7 +270,7 @@ <h1 id="Contracts">
 </a>.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L83-L90">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L83-L90">source
 </a>
 </section>
 </article>
@@ -318,7 +318,7 @@ <h1 id="Contracts">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L41-L60">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L41-L60">source
 </a>
 </section>
 </article>
@@ -370,7 +370,7 @@ <h1 id="Contracts">
 </div>
 </div>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L63-L80">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L63-L80">source
 </a>
 </section>
 </article>
@@ -412,7 +412,7 @@ <h1 id="Contracts">
 </code> - data that may exist when the computation is done, depending on some condition, which may include the existence of optional input and/or the value of parameters to the computation, and/or the content of the data.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L23-L38">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L23-L38">source
 </a>
 </section>
 </article>
@@ -438,7 +438,7 @@ <h1 id="Contracts">
 </code> data when a computation is invoked. This verifies that all the required data exists and is of the appropriate type, and that if any of the optional data exists, it has the appropriate type.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L100-L105">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L100-L105">source
 </a>
 </section>
 </article>
@@ -464,7 +464,7 @@ <h1 id="Contracts">
 </code> data when a computation is complete. This verifies that all the guaranteed output data exists and is of the appropriate type, and that if any of the optional output data exists, it has the appropriate type.
 </p>
 </div>
-<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/067da03aa5b8f2b096ddf3e0088f8712e4aa3426/src/contracts.jl#L110-L115">source
+<a class="docs-sourcelink" target="_blank" href="https://github.com/tanaylab/Daf.jl/blob/34d603e89c37b4bc935f0a66ea2585c12a5b7bb3/src/contracts.jl#L110-L115">source
 </a>
 </section>
 </article>