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Adapt to Julia 1.11.
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orenbenkiki committed Oct 9, 2024
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4 changes: 2 additions & 2 deletions Makefile
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Expand Up @@ -68,9 +68,9 @@ deps/.did.untested: deps/.did.coverage deps/untested_lines.sh
coverage: untested_lines line_coverage

.PHONY: docs
docs: docs/v0.1.1/index.html
docs: docs/v0.1.2/index.html

docs/v0.1.1/index.html: src/*.jl src/*.md deps/document.sh deps/document.jl docs/make.jl
docs/v0.1.2/index.html: src/*.jl src/*.md deps/document.sh deps/document.jl docs/make.jl
deps/document.sh

.PHONY: clean
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2 changes: 1 addition & 1 deletion Project.toml
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Expand Up @@ -29,7 +29,6 @@ StringViews = "354b36f9-a18e-4713-926e-db85100087ba"
URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"

[compat]
julia = "1.10"
CategoricalArrays = "0.1 - 0.10"
ConcurrentUtils = "0.1"
DataFrames = "1"
Expand All @@ -46,3 +45,4 @@ Statistics = "1"
StatsBase = "0.34"
StringViews = "1"
URIs = "1"
julia = "1.10"
2 changes: 1 addition & 1 deletion deps/clean.sh
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@@ -1,3 +1,3 @@
#!/bin/bash
set -e -o pipefail
rm -rf tracefile.info src/*.cov src/*/*.cov test/*.cov docs/build docs/assets docs/*.{html,js,cov} docs/v0.1.1 deps/.did.*
rm -rf tracefile.info src/*.cov src/*/*.cov test/*.cov docs/build docs/assets docs/*.{html,js,cov} docs/v0.1.2 deps/.did.*
2 changes: 1 addition & 1 deletion deps/document.sh
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@@ -1,5 +1,5 @@
#!/bin/bash
set -e -o pipefail
julia --color=no deps/document.jl
sed -i 's: on <span class="colophon-date" title="[^"]*">[^<]*</span>::;s:<:\n<:g' docs/v0.1.1/*html
sed -i 's: on <span class="colophon-date" title="[^"]*">[^<]*</span>::;s:<:\n<:g' docs/v0.1.2/*html
rm -rf docs/*/*.{cov,jl}
1 change: 0 additions & 1 deletion docs/v0.1.1/.documenter-siteinfo.json

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3 changes: 0 additions & 3 deletions docs/v0.1.1/search_index.js

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1 change: 1 addition & 0 deletions docs/v0.1.2/.documenter-siteinfo.json
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@@ -0,0 +1 @@
{"documenter":{"julia_version":"1.11.0","generation_timestamp":"2024-10-09T15:21:49","documenter_version":"1.7.0"}}
20 changes: 10 additions & 10 deletions docs/v0.1.1/adapters.html → docs/v0.1.2/adapters.html
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<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Adapters · DataAxesFormats.jl v0.1.1
<title>Adapters · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Adapters · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Adapters · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="Adapters · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta name="title" content="Adapters · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Adapters · DataAxesFormats.jl v0.1.2"/>
<meta property="twitter:title" content="Adapters · DataAxesFormats.jl v0.1.2"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<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"/>
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<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -466,7 +466,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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40 changes: 14 additions & 26 deletions docs/v0.1.1/anndata_format.html → docs/v0.1.2/anndata_format.html
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Expand Up @@ -5,14 +5,14 @@
<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>AnnData Format · DataAxesFormats.jl v0.1.1
<title>AnnData Format · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="AnnData Format · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="AnnData Format · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="AnnData Format · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta name="title" content="AnnData Format · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="AnnData Format · DataAxesFormats.jl v0.1.2"/>
<meta property="twitter:title" content="AnnData Format · DataAxesFormats.jl v0.1.2"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<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"/>
Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -260,6 +260,10 @@ <h1 id="AnnData-Format">
<code>Daf
</code> data from/to
<a href="https://pypi.org/project/anndata/">AnnData
</a>. We use the
<code>AnnData
</code> Julia implementation from
<a href="https://github.com/scverse/Muon.jl">Muon.jl
</a>.
</p>
<p>Due to the different data models, not all the content of
Expand All @@ -268,22 +272,6 @@ <h1 id="AnnData-Format">
<code>Daf
</code>, and vice-versa. However, &quot;most&quot; of the data can be automatically converted from one form to the other. In both directions, conversion is zero-copy; that is, we merely create a different view for the same vectors and matrices. We also use memory-mapping whenever possible for increased performance.
</p>
<div class="admonition is-info">
<header class="admonition-header">Note
</header>
<div class="admonition-body">
<p>We use the
<code>AnnData
</code> Julia implementation from
<a href="https://docs.juliahub.com/Muon/QfqCh/0.1.1/">Muon.jl
</a>. The last published released for this package is from 2021, and lacks features added over the years, which we use. Therefore, currently
<code>Daf
</code> uses the head revision of Muon from
<a href="https://github.com/scverse/Muon.jl">github
</a>, with all that implies. We&#39;ll change this to a proper registry dependency if/when a new Muon version is released.
</p>
</div>
</div>
<p>The following
<code>Daf
</code> data can&#39;t be naively stored in
Expand Down Expand Up @@ -678,7 +666,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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20 changes: 10 additions & 10 deletions docs/v0.1.1/chains.html → docs/v0.1.2/chains.html
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Expand Up @@ -5,14 +5,14 @@
<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Chains · DataAxesFormats.jl v0.1.1
<title>Chains · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Chains · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Chains · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="Chains · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta name="title" content="Chains · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Chains · DataAxesFormats.jl v0.1.2"/>
<meta property="twitter:title" content="Chains · DataAxesFormats.jl v0.1.2"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<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"/>
Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -527,7 +527,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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20 changes: 10 additions & 10 deletions docs/v0.1.1/computations.html → docs/v0.1.2/computations.html
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Expand Up @@ -5,14 +5,14 @@
<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Computations · DataAxesFormats.jl v0.1.1
<title>Computations · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Computations · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Computations · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="Computations · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta name="title" content="Computations · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Computations · DataAxesFormats.jl v0.1.2"/>
<meta property="twitter:title" content="Computations · DataAxesFormats.jl v0.1.2"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<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"/>
Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -715,7 +715,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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20 changes: 10 additions & 10 deletions docs/v0.1.1/concat.html → docs/v0.1.2/concat.html
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<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Concat · DataAxesFormats.jl v0.1.1
<title>Concat · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Concat · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Concat · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="Concat · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
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<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
<meta name="title" content="Concat · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Concat · DataAxesFormats.jl v0.1.2"/>
<meta property="twitter:title" content="Concat · DataAxesFormats.jl v0.1.2"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="og:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<meta property="twitter:description" content="Documentation for DataAxesFormats.jl v0.1.2."/>
<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"/>
Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -592,7 +592,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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20 changes: 10 additions & 10 deletions docs/v0.1.1/contracts.html → docs/v0.1.2/contracts.html
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<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Contracts · DataAxesFormats.jl v0.1.1
<title>Contracts · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Contracts · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Contracts · DataAxesFormats.jl v0.1.1"/>
<meta property="twitter:title" content="Contracts · DataAxesFormats.jl v0.1.1"/>
<meta name="description" content="Documentation for DataAxesFormats.jl v0.1.1."/>
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<meta name="title" content="Contracts · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Contracts · DataAxesFormats.jl v0.1.2"/>
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</script>
<link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/>
Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -822,7 +822,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
<footer class="modal-card-foot">
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20 changes: 10 additions & 10 deletions docs/v0.1.1/copies.html → docs/v0.1.2/copies.html
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<head>
<meta charset="UTF-8"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
<title>Copies · DataAxesFormats.jl v0.1.1
<title>Copies · DataAxesFormats.jl v0.1.2
</title>
<meta name="title" content="Copies · DataAxesFormats.jl v0.1.1"/>
<meta property="og:title" content="Copies · DataAxesFormats.jl v0.1.1"/>
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<meta name="title" content="Copies · DataAxesFormats.jl v0.1.2"/>
<meta property="og:title" content="Copies · DataAxesFormats.jl v0.1.2"/>
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Expand Down Expand Up @@ -44,11 +44,11 @@
<div id="documenter">
<nav class="docs-sidebar">
<a class="docs-logo" href="index.html">
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.1 logo"/>
<img src="assets/logo.svg" alt="DataAxesFormats.jl v0.1.2 logo"/>
</a>
<div class="docs-package-name">
<span class="docs-autofit">
<a href="index.html">DataAxesFormats.jl v0.1.1
<a href="index.html">DataAxesFormats.jl v0.1.2
</a>
</span>
</div>
Expand Down Expand Up @@ -901,7 +901,7 @@ <h2 id="Index">
<hr/>
<p>This document was generated with
<a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl
</a> version 1.7.0. Using Julia version 1.10.5.
</a> version 1.7.0. Using Julia version 1.11.0.
</p>
</section>
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