Rename the module to DafJL to satisfy Julia package name requirement.

tanaylab · Sep 20, 2024 · 0d36c37 · 0d36c37
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "Daf"
+name = "DafJL"
 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 `Daf.jl` package provides a uniform generic interface for accessing 1D and 2D data arranged along some set of axes.
+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.`
+were the driving force for the development of `Daf`.
 
 The key features of `Daf` are:
 
@@ -26,13 +26,13 @@ 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 [Daf.py](https://pypi.org/project/daf/) Python package, which
-    is a thin wrapper around `Daf.jl` 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 `DafJL` 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 `Daf.jl` from R
+    [JuliaCall](https://libraries.io/cran/JuliaCall) to allow direct access to `DafJL` from R
     code.
 
-See the [v0.1.0 documentation](https://tanaylab.github.io/Daf.jl/v0.1.0) for details.
+See the [v0.1.0 documentation](https://tanaylab.github.io/DafJL/v0.1.0) for details.
 
 ## Status
 
@@ -125,9 +125,9 @@ interoperability with legacy computation pipelines.
 
 ## Installation
 
-Just `Pkg.add("Daf")`, like installing any other Julia package.
+Just `Pkg.add("DafJ")`, like installing any other Julia package.
 
-To install the Python `Daf` [package](https://github.com/tanaylab/Daf.py), just `pip install daf`, like installing any
+To install the Python `Daf` [package](https://github.com/tanaylab/DafPY), just `pip install dafpy`, like installing any
 other Python package.
 
 TODO: To install the R wrappers...

diff --git a/deps/aqua.jl b/deps/aqua.jl
@@ -1,6 +1,6 @@
 push!(LOAD_PATH, ".")
 
 using Aqua
-using Daf
-Aqua.test_ambiguities([Daf])
-Aqua.test_all(Daf; ambiguities = false, unbound_args = false, deps_compat = false)
+using DafJL
+Aqua.test_ambiguities([DafJL])
+Aqua.test_all(DafJL; ambiguities = false, unbound_args = false, deps_compat = false)
diff --git a/deps/build.jl b/deps/build.jl
@@ -1 +1 @@
-println("Building Daf...")
+println("Building DafJL...")
diff --git a/deps/document.jl b/deps/document.jl
@@ -20,7 +20,7 @@ global_logger(detect_problems)
 
 push!(LOAD_PATH, ".")
 
-using Daf
+using DafJL
 using Pkg
 
 PROJECT_TOML = Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))
@@ -36,7 +36,7 @@ makedocs(;
     source = "../src",
     clean = true,
     doctest = true,
-    modules = [Daf],
+    modules = [DafJL],
     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 Daf
+using DafJL
 
-println(report_package("Daf"))
+println(report_package("DafJL"))
 
 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/Daf.jl"))
+file = StaticLint.loadfile(language_server, abspath("src/DafJL.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":"1.10.4","generation_timestamp":"2024-09-20T10:36:03","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-09-20T12:57:28","documenter_version":"1.5.0"}}
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 · Daf.jl v0.1.0
+<title>Adapters · DafJL.jl v0.1.0
 </title>
-<meta name="title" content="Adapters · Daf.jl v0.1.0"/>
-<meta property="og:title" content="Adapters · Daf.jl v0.1.0"/>
-<meta property="twitter:title" content="Adapters · Daf.jl v0.1.0"/>
-<meta name="description" content="Documentation for Daf.jl v0.1.0."/>
-<meta property="og:description" content="Documentation for Daf.jl v0.1.0."/>
-<meta property="twitter:description" content="Documentation for Daf.jl v0.1.0."/>
+<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."/>
 <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="Daf.jl v0.1.0 logo"/>
+<img src="assets/logo.svg" alt="DafJL.jl v0.1.0 logo"/>
 </a>
 <div class="docs-package-name">
 <span class="docs-autofit">
-<a href="index.html">Daf.jl v0.1.0
+<a href="index.html">DafJL.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/Daf.jl/blob/main{path}?plain=1#L{line}" title="View the repository on GitHub">
+<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">
 <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="Daf.Adapters" href="#Daf.Adapters">
-<code>Daf.Adapters
+<a class="docstring-binding" id="DafJL.Adapters" href="#DafJL.Adapters">
+<code>DafJL.Adapters
 </code>
 </a> — 
 <span class="docstring-category">Module
@@ -257,7 +257,7 @@ <h1 id="Adapters">
 <p>Adapt 
 <code>Daf
 </code> data to a 
-<a href="computations.html#Daf.Computations.@computation">
+<a href="computations.html#DafJL.Computations.@computation">
 <code>@computation
 </code>
 </a>.
@@ -269,8 +269,8 @@ <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="Daf.Adapters.adapter" href="#Daf.Adapters.adapter">
-<code>Daf.Adapters.adapter
+<a class="docstring-binding" id="DafJL.Adapters.adapter" href="#DafJL.Adapters.adapter">
+<code>DafJL.Adapters.adapter
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -325,19 +325,19 @@ <h1 id="Adapters">
 </code>. If the 
 <code>computation
 </code> was annotated by 
-<a href="computations.html#Daf.Computations.@computation">
+<a href="computations.html#DafJL.Computations.@computation">
 <code>@computation
 </code>
 </a>, then its 
-<a href="contracts.html#Daf.Contracts.Contract">
+<a href="contracts.html#DafJL.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#Daf.MemoryFormat.MemoryDaf">
+<a href="memory_format.html#DafJL.MemoryFormat.MemoryDaf">
 <code>MemoryDaf
 </code>
 </a>) and pass the result to the 
@@ -353,7 +353,7 @@ <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#Daf.Copies.copy_all!">
+<a href="copies.html#DafJL.Copies.copy_all!">
 <code>copy_all!
 </code>
 </a>, 
@@ -392,7 +392,7 @@ <h1 id="Adapters">
 </code>
 </pre>
 <p>This idiom allows 
-<a href="computations.html#Daf.Computations.@computation">
+<a href="computations.html#DafJL.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.

diff --git a/docs/v0.1.0/anndata_format.html b/docs/v0.1.0/anndata_format.html
@@ -5,14 +5,14 @@
 <head>
 <meta charset="UTF-8"/>
 <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
-<title>AnnData Format · Daf.jl v0.1.0
+<title>AnnData Format · DafJL.jl v0.1.0
 </title>
-<meta name="title" content="AnnData Format · Daf.jl v0.1.0"/>
-<meta property="og:title" content="AnnData Format · Daf.jl v0.1.0"/>
-<meta property="twitter:title" content="AnnData Format · Daf.jl v0.1.0"/>
-<meta name="description" content="Documentation for Daf.jl v0.1.0."/>
-<meta property="og:description" content="Documentation for Daf.jl v0.1.0."/>
-<meta property="twitter:description" content="Documentation for Daf.jl v0.1.0."/>
+<meta name="title" content="AnnData Format · DafJL.jl v0.1.0"/>
+<meta property="og:title" content="AnnData Format · DafJL.jl v0.1.0"/>
+<meta property="twitter:title" content="AnnData Format · 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."/>
 <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="Daf.jl v0.1.0 logo"/>
+<img src="assets/logo.svg" alt="DafJL.jl v0.1.0 logo"/>
 </a>
 <div class="docs-package-name">
 <span class="docs-autofit">
-<a href="index.html">Daf.jl v0.1.0
+<a href="index.html">DafJL.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/Daf.jl/blob/main{path}?plain=1#L{line}" title="View the repository on GitHub">
+<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">
 <span class="docs-icon fa-brands">
 </span>
 <span class="docs-label is-hidden-touch">GitHub
@@ -245,8 +245,8 @@ <h1 id="AnnData-Format">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="Daf.AnnDataFormat" href="#Daf.AnnDataFormat">
-<code>Daf.AnnDataFormat
+<a class="docstring-binding" id="DafJL.AnnDataFormat" href="#DafJL.AnnDataFormat">
+<code>DafJL.AnnDataFormat
 </code>
 </a> — 
 <span class="docstring-category">Module
@@ -313,7 +313,7 @@ <h1 id="AnnData-Format">
 </code> data as 
 <code>AnnData
 </code>, we pick two specific axes and rename them to &quot;obs&quot; and &quot;var&quot;, pick a specific matrix property of these axes and rename it to &quot;X&quot;, and 
-<a href="matrix_layouts.html#Daf.MatrixLayouts.relayout!">
+<a href="matrix_layouts.html#DafJL.MatrixLayouts.relayout!">
 <code>relayout!
 </code>
 </a> it if needed so 
@@ -400,21 +400,21 @@ <h1 id="AnnData-Format">
 </code> invariant that all accessed data is column-major, at least for square matrices. This is bad because the invariant greatly simplifies 
 <code>Daf
 </code> client code. Forcing clients to check the data layout and calling 
-<a href="matrix_layouts.html#Daf.MatrixLayouts.relayout!">
+<a href="matrix_layouts.html#DafJL.MatrixLayouts.relayout!">
 <code>relayout!
 </code>
 </a> would add a lot of error-prone boilerplate to our users.
 </li>
 <li>We can 
-<a href="matrix_layouts.html#Daf.MatrixLayouts.relayout!">
+<a href="matrix_layouts.html#DafJL.MatrixLayouts.relayout!">
 <code>relayout!
 </code>
 </a> the data when copying it between 
 <code>AnnData
 </code> and 
 <code>Daf
 </code>. This is bad because it would force us to duplicate the data. More importantly, there is typically a good reason for the layout of the data. For example, assume a directed graph between cells. A common way to store is is to have a square matrix where each row contains the weights of the edges originating in one cell, connecting it to all other cells. This allows code to efficiently &quot;loop on all cells; loop on all outgoing edges&quot;. If we 
-<a href="matrix_layouts.html#Daf.MatrixLayouts.relayout!">
+<a href="matrix_layouts.html#DafJL.MatrixLayouts.relayout!">
 <code>relayout!
 </code>
 </a> the data, then such a loop would become extremely inefficient.
@@ -441,7 +441,7 @@ <h1 id="AnnData-Format">
 </code> with the row-major data from 
 <code>AnnData
 </code> and if asked for the outher layout, will 
-<a href="matrix_layouts.html#Daf.MatrixLayouts.relayout!">
+<a href="matrix_layouts.html#DafJL.MatrixLayouts.relayout!">
 <code>relayout!
 </code>
 </a> it (and store/cache the result).
@@ -453,8 +453,8 @@ <h1 id="AnnData-Format">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="Daf.AnnDataFormat.anndata_as_daf" href="#Daf.AnnDataFormat.anndata_as_daf">
-<code>Daf.AnnDataFormat.anndata_as_daf
+<a class="docstring-binding" id="DafJL.AnnDataFormat.anndata_as_daf" href="#DafJL.AnnDataFormat.anndata_as_daf">
+<code>DafJL.AnnDataFormat.anndata_as_daf
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -478,7 +478,7 @@ <h1 id="AnnData-Format">
 </code> as a 
 <code>Daf
 </code> data set, specifically using a 
-<a href="memory_format.html#Daf.MemoryFormat.MemoryDaf">
+<a href="memory_format.html#DafJL.MemoryFormat.MemoryDaf">
 <code>MemoryDaf
 </code>
 </a>. This doesn&#39;t duplicate matrices or vectors, but acts as a view containing references to the same ones. Adding and/or deleting data in the view using the 
@@ -530,8 +530,8 @@ <h1 id="AnnData-Format">
 <header>
 <a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
 </a>
-<a class="docstring-binding" id="Daf.AnnDataFormat.daf_as_anndata" href="#Daf.AnnDataFormat.daf_as_anndata">
-<code>Daf.AnnDataFormat.daf_as_anndata
+<a class="docstring-binding" id="DafJL.AnnDataFormat.daf_as_anndata" href="#DafJL.AnnDataFormat.daf_as_anndata">
+<code>DafJL.AnnDataFormat.daf_as_anndata
 </code>
 </a> — 
 <span class="docstring-category">Function
@@ -600,20 +600,20 @@ <h2 id="Index">
 </h2>
 <ul>
 <li>
-<a href="anndata_format.html#Daf.AnnDataFormat">
-<code>Daf.AnnDataFormat
+<a href="anndata_format.html#DafJL.AnnDataFormat">
+<code>DafJL.AnnDataFormat
 </code>
 </a>
 </li>
 <li>
-<a href="anndata_format.html#Daf.AnnDataFormat.anndata_as_daf">
-<code>Daf.AnnDataFormat.anndata_as_daf
+<a href="anndata_format.html#DafJL.AnnDataFormat.anndata_as_daf">
+<code>DafJL.AnnDataFormat.anndata_as_daf
 </code>
 </a>
 </li>
 <li>
-<a href="anndata_format.html#Daf.AnnDataFormat.daf_as_anndata">
-<code>Daf.AnnDataFormat.daf_as_anndata
+<a href="anndata_format.html#DafJL.AnnDataFormat.daf_as_anndata">
+<code>DafJL.AnnDataFormat.daf_as_anndata
 </code>
 </a>
 </li>