Rename to a name long enough to be acceptable to the Julia package re…

…pository.
tanaylab · Sep 20, 2024 · 4f5af0e · 4f5af0e
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "DafJL"
+name = "DataAxesFormats"
 uuid = "1375bf9c-a47d-45a1-aad5-626dd8629d98"
 authors = ["Oren Ben-Kiki <[email protected]>"]
 version = "0.1.0"

diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
 # DAF - Data in Axes in Formats
 
-The `DafJL` package provides a uniform generic interface for accessing 1D and 2D data arranged along some set of axes.
-This is a much-needed generalization of the [AnnData](https://github.com/scverse/anndata) functionality. Unlike other
-generalizations (e.g., [Muon](https://github.com/scverse/mudata)), `Daf` attempts to provide a simple generic unified 1D
-and 2D data storage, which can be used for "any" purpose, not necessarily scRNA and/or ATAC data, though such use cases
-were the driving force for the development of `Daf`.
+The `DataAxesFormats` package provides a uniform generic interface for accessing 1D and 2D data arranged along some set
+of axes. This is a much-needed generalization of the [AnnData](https://github.com/scverse/anndata) functionality. Unlike
+other generalizations (e.g., [Muon](https://github.com/scverse/mudata)), `Daf` attempts to provide a simple generic
+unified 1D and 2D data storage, which can be used for "any" purpose, not necessarily scRNA and/or ATAC data, though such
+use cases were the driving force for the development of `Daf`.
 
 The key features of `Daf` are:
 
@@ -26,13 +26,12 @@ The key features of `Daf` are:
   - There is explicit control over 2D data layout (row or column major), and support for both dense and sparse matrices,
     both of which are crucial for performance.
   - This is implemented in Julia, as a seed for efficient computation pipelines (which are hard to implement in Python
-    without resorting to using C/C++ code). WIP: a [DafPY](https://pypi.org/project/dafpy/) Python package, which
-    is a thin wrapper around `DafJL` allowing efficient (zero-copy) access to the data using `numpy`, `scipy` and
+    without resorting to using C/C++ code). WIP: a [DafPY](https://pypi.org/project/dafpy/) Python package, which is a
+    thin wrapper around `DataAxesFormats` allowing efficient (zero-copy) access to the data using `numpy`, `scipy` and
     `pandas` vector and matrix types. WIP: Implement a similar R package using
-    [JuliaCall](https://libraries.io/cran/JuliaCall) to allow direct access to `DafJL` from R
-    code.
+    [JuliaCall](https://libraries.io/cran/JuliaCall) to allow direct access to `DataAxesFormats` from R code.
 
-See the [v0.1.0 documentation](https://tanaylab.github.io/DafJL/v0.1.0) for details.
+See the [v0.1.0 documentation](https://tanaylab.github.io/DataAxesFormats.jl/v0.1.0) for details.
 
 ## Status
 

diff --git a/deps/aqua.jl b/deps/aqua.jl
@@ -1,6 +1,6 @@
 push!(LOAD_PATH, ".")
 
 using Aqua
-using DafJL
-Aqua.test_ambiguities([DafJL])
-Aqua.test_all(DafJL; ambiguities = false, unbound_args = false, deps_compat = false)
+using DataAxesFormats
+Aqua.test_ambiguities([DataAxesFormats])
+Aqua.test_all(DataAxesFormats; ambiguities = false, unbound_args = false, deps_compat = false)
diff --git a/deps/build.jl b/deps/build.jl
@@ -1 +1 @@
-println("Building DafJL...")
+println("Building DataAxesFormats...")
diff --git a/deps/document.jl b/deps/document.jl
@@ -20,7 +20,7 @@ global_logger(detect_problems)
 
 push!(LOAD_PATH, ".")
 
-using DafJL
+using DataAxesFormats
 using Pkg
 
 PROJECT_TOML = Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))
@@ -36,7 +36,7 @@ makedocs(;
     source = "../src",
     clean = true,
     doctest = true,
-    modules = [DafJL],
+    modules = [DataAxesFormats],
     highlightsig = true,
     sitename = "$(NAME).jl v$(VERSION)",
     draft = false,

diff --git a/deps/jet.jl b/deps/jet.jl
@@ -17,9 +17,9 @@ global_logger(detect_problems)
 push!(LOAD_PATH, ".")
 
 using JET
-using DafJL
+using DataAxesFormats
 
-println(report_package("DafJL"))
+println(report_package("DataAxesFormats"))
 
 if seen_problems
     exit(1)

diff --git a/deps/static_analysis.jl b/deps/static_analysis.jl
@@ -8,7 +8,7 @@ language_server.global_env.symbols = symbols
 language_server.global_env.extended_methods = SymbolServer.collect_extended_methods(language_server.global_env.symbols)
 language_server.global_env.project_deps = collect(keys(language_server.global_env.symbols))
 
-file = StaticLint.loadfile(language_server, abspath("src/DafJL.jl"))
+file = StaticLint.loadfile(language_server, abspath("src/DataAxesFormats.jl"))
 StaticLint.semantic_pass(LanguageServer.getroot(file))
 
 global errors = 0

diff --git a/docs/v0.1.0/.documenter-siteinfo.json b/docs/v0.1.0/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-20T15:05:46","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-20T15:50:16","documenter_version":"1.7.0"}}
diff --git a/docs/v0.1.0/adapters.html b/docs/v0.1.0/adapters.html
@@ -5,14 +5,14 @@
 <head>
 <meta charset="UTF-8"/>
 <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
-<title>Adapters · DafJL.jl v0.1.0
+<title>Adapters · DataAxesFormats.jl v0.1.0
 </title>
-<meta name="title" content="Adapters · DafJL.jl v0.1.0"/>
-<meta property="og:title" content="Adapters · DafJL.jl v0.1.0"/>
-<meta property="twitter:title" content="Adapters · DafJL.jl v0.1.0"/>
-<meta name="description" content="Documentation for DafJL.jl v0.1.0."/>
-<meta property="og:description" content="Documentation for DafJL.jl v0.1.0."/>
-<meta property="twitter:description" content="Documentation for DafJL.jl v0.1.0."/>
+<meta name="title" content="Adapters · DataAxesFormats.jl v0.1.0"/>
+<meta property="og:title" content="Adapters · DataAxesFormats.jl v0.1.0"/>
+<meta property="twitter:title" content="Adapters · DataAxesFormats.jl v0.1.0"/>
+<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.0."/>
+<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.0."/>
+<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.0."/>
 <script data-outdated-warner src="assets/warner.js">
 </script>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/>
@@ -44,11 +44,11 @@
 <div id="documenter">
 <nav class="docs-sidebar">
 <a class="docs-logo" href="index.html">
-<img src="assets/logo.svg" alt="DafJL.jl v0.1.0 logo"/>
+<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.0 logo"/>
 </a>
 <div class="docs-package-name">
 <span class="docs-autofit">
-<a href="index.html">DafJL.jl v0.1.0
+<a href="index.html">DataAxesFormats.jl v0.1.0
 </a>
 </span>
 </div>
@@ -220,7 +220,7 @@
 </ul>
 </nav>
 <div class="docs-right">
-<a class="docs-navbar-link" href="https://github.com/tanaylab/DafJL.jl/blob/main{path}?plain=1#L{line}" title="View the repository on GitHub">
+<a class="docs-navbar-link" href="https://github.com/tanaylab/DataAxesFormats.jl/blob/main{path}?plain=1#L{line}" title="View the repository on GitHub">
 <span class="docs-icon fa-brands">
 </span>
 <span class="docs-label is-hidden-touch">GitHub
@@ -245,8 +245,8 @@ <h1 id="Adapters">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="DafJL.Adapters" href="#DafJL.Adapters">
-<code>DafJL.Adapters
+<a class="docstring-binding" id="DataAxesFormats.Adapters" href="#DataAxesFormats.Adapters">
+<code>DataAxesFormats.Adapters
 </code>
 </a> — 
 <span class="docstring-category">Module
@@ -259,7 +259,7 @@ <h1 id="Adapters">
 <p>Adapt 
 <code>Daf
 </code> data to a 
-<a href="computations.html#DafJL.Computations.@computation">
+<a href="computations.html#DataAxesFormats.Computations.@computation">
 <code>@computation
 </code>
 </a>.
@@ -271,8 +271,8 @@ <h1 id="Adapters">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="DafJL.Adapters.adapter" href="#DafJL.Adapters.adapter">
-<code>DafJL.Adapters.adapter
+<a class="docstring-binding" id="DataAxesFormats.Adapters.adapter" href="#DataAxesFormats.Adapters.adapter">
+<code>DataAxesFormats.Adapters.adapter
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -329,19 +329,19 @@ <h1 id="Adapters">
 </code>. If the 
 <code>computation
 </code> was annotated by 
-<a href="computations.html#DafJL.Computations.@computation">
+<a href="computations.html#DataAxesFormats.Computations.@computation">
 <code>@computation
 </code>
 </a>, then its 
-<a href="contracts.html#DafJL.Contracts.Contract">
+<a href="contracts.html#DataAxesFormats.Contracts.Contract">
 <code>Contract
 </code>
 </a> will be explicitly documented so you will know exactly what to provide.
 </li>
 <li>Chain this read-only view with an empty 
 <code>capture
 </code> writable data set (by default, 
-<a href="memory_format.html#DafJL.MemoryFormat.MemoryDaf">
+<a href="memory_format.html#DataAxesFormats.MemoryFormat.MemoryDaf">
 <code>MemoryDaf
 </code>
 </a>) and pass the result to the 
@@ -357,7 +357,7 @@ <h1 id="Adapters">
 </code> to create a view of the output, and copy this subset to the original 
 <code>daf
 </code> data set, using (using 
-<a href="copies.html#DafJL.Copies.copy_all!">
+<a href="copies.html#DataAxesFormats.Copies.copy_all!">
 <code>copy_all!
 </code>
 </a>, 
@@ -396,7 +396,7 @@ <h1 id="Adapters">
 </code>
 </pre>
 <p>This idiom allows 
-<a href="computations.html#DafJL.Computations.@computation">
+<a href="computations.html#DataAxesFormats.Computations.@computation">
 <code>@computation
 </code>
 </a> functions to use clear generic names for their inputs and outputs, and still apply them to arbitrary data sets that use 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.