build based on 894816d

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-05T08:10:12","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-11T06:29:14","documenter_version":"1.7.0"}}

dev/index.html

@@ -17,9 +17,10 @@
 directoryname = "/tmp/test-zarr"
 ds = ZarrDataset(directoryname)
 data = ds["varname"][:,:]
-data_units = ds[&quot;varname&quot;].attrib[&quot;units&quot;]</code></pre><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="ZarrDatasets.ZarrDataset" href="#ZarrDatasets.ZarrDataset"><code>ZarrDatasets.ZarrDataset</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">ds = ZarrDataset(url::AbstractString,mode = &quot;r&quot;;
+data_units = ds[&quot;varname&quot;].attrib[&quot;units&quot;]</code></pre><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="ZarrDatasets.ZarrDataset" href="#ZarrDatasets.ZarrDataset"><code>ZarrDatasets.ZarrDataset</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">ds = ZarrDataset(url::AbstractString,mode = &quot;r&quot;;
                  _omitcode = [404,403],
                  maskingvalue = missing)
+ZarrDataset(zg::Zarr.ZGroup; _omitcode, maskingvalue)
 ZarrDataset(f::Function,url::AbstractString,mode = &quot;r&quot;;
                  maskingvalue = missing)</code></pre><p>Open the zarr dataset at the url or path <code>url</code>. The mode can only be <code>&quot;r&quot;</code> (read-only) or <code>&quot;c&quot;</code> (create). <code>ds</code> supports the API of the <a href="https://github.com/JuliaGeo/CommonDataModel.jl">JuliaGeo/CommonDataModel.jl</a>. The experimental <code>_omitcode</code> allows to define which HTTP error code should be used for missing chunks. For compatibility with python&#39;s Zarr, the HTTP error 403 (permission denied) is also used to missing chunks in addition to 404 (not found).</p><p>The parameter <code>maskingvalue</code> allows to define which special value should be used as replacement for fill values. The default is <code>missing</code>.</p><p>Example:</p><pre><code class="language-julia hljs">using ZarrDatasets
 url = &quot;https://s3.waw3-1.cloudferro.com/mdl-arco-time-035/arco/MEDSEA_MULTIYEAR_PHY_006_004/med-cmcc-ssh-rean-d_202012/timeChunked.zarr&quot;
@@ -39,4 +40,4 @@
 
 zos1 = ZarrDataset(url) do ds
   ds[&quot;zos&quot;][:,:,end,1]
-end # implicit call to close(ds)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaGeo/ZarrDatasets.jl/blob/5dc7251fbd2db1afa3fe2a4681d76881ab13d873/src/dataset.jl#L82-L129">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="CommonDataModel.defVar-Tuple{ZarrDatasets.ZarrDataset, Union{AbstractString, Symbol}, DataType, Any}" href="#CommonDataModel.defVar-Tuple{ZarrDatasets.ZarrDataset, Union{AbstractString, Symbol}, DataType, Any}"><code>CommonDataModel.defVar</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">defVar(ds::ZarrDataset,name::SymbolOrString,vtype::DataType,dimensionnames; chunksizes=nothing, attrib = Dict(), fillvalue = nothing)</code></pre><p>Create a variable <code>name</code> in the dataset <code>ds</code> with the type <code>vtype</code> and the dimension <code>dimensionnames</code>.</p><p>For coordinate variables, fill values will be used a background value of undefined chunks and not as missing value as coordinate variables cannot have the <code>_FillValues</code> in the CF convension as in Zarr v2 format a <code>fill_value</code> does not necessarily indicate a missing value.</p><p>See also <code>CommonDataModel.defVar</code> for more information.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaGeo/ZarrDatasets.jl/blob/5dc7251fbd2db1afa3fe2a4681d76881ab13d873/src/variable.jl#L55-L65">source</a></section></article><h3 id="Differences-between-Zarr-and-NetCDF-files"><a class="docs-heading-anchor" href="#Differences-between-Zarr-and-NetCDF-files">Differences between Zarr and NetCDF files</a><a id="Differences-between-Zarr-and-NetCDF-files-1"></a><a class="docs-heading-anchor-permalink" href="#Differences-between-Zarr-and-NetCDF-files" title="Permalink"></a></h3><ul><li>All metadata (in particular attributes) is stored in JSON files for the Zarr format with the following implications:<ul><li>JSON does not distinguish between integers and real numbers. They are all considered as generic numbers. Whole numbers are loaded as <code>Int64</code> and real numbers <code>Float64</code>. It is not possible to store the number <code>1.0</code> as a real number.</li><li>The order of keys in a JSON document is undefined. It is therefore not possible to have a consistent ordering of the attributes or variables.</li><li>The JSON standard does not allow the values NaN, +Inf, -Inf which is problematic for attributes (<a href="https://github.com/zarr-developers/zarr-python/issues/412">zarr-python #412</a>,   <a href="https://github.com/zarr-developers/zarr-specs/issues/81">zarr-specs #81</a>). However, there is a special case for the fill-value to handle NaN, +Inf and -Inf.</li></ul></li><li>All dimensions must be associated to Zarr variables.</li></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 5 August 2024 08:10">Monday 5 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end # implicit call to close(ds)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaGeo/ZarrDatasets.jl/blob/894816d94229ca7a6fe3aaa5218dec1385e950eb/src/dataset.jl#L82-L130">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="CommonDataModel.defVar-Tuple{ZarrDatasets.ZarrDataset, Union{AbstractString, Symbol}, DataType, Any}" href="#CommonDataModel.defVar-Tuple{ZarrDatasets.ZarrDataset, Union{AbstractString, Symbol}, DataType, Any}"><code>CommonDataModel.defVar</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">defVar(ds::ZarrDataset,name::SymbolOrString,vtype::DataType,dimensionnames; chunksizes=nothing, attrib = Dict(), fillvalue = nothing)</code></pre><p>Create a variable <code>name</code> in the dataset <code>ds</code> with the type <code>vtype</code> and the dimension <code>dimensionnames</code>.</p><p>For coordinate variables, fill values will be used a background value of undefined chunks and not as missing value as coordinate variables cannot have the <code>_FillValues</code> in the CF convension as in Zarr v2 format a <code>fill_value</code> does not necessarily indicate a missing value.</p><p>See also <code>CommonDataModel.defVar</code> for more information.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaGeo/ZarrDatasets.jl/blob/894816d94229ca7a6fe3aaa5218dec1385e950eb/src/variable.jl#L55-L65">source</a></section></article><h3 id="Differences-between-Zarr-and-NetCDF-files"><a class="docs-heading-anchor" href="#Differences-between-Zarr-and-NetCDF-files">Differences between Zarr and NetCDF files</a><a id="Differences-between-Zarr-and-NetCDF-files-1"></a><a class="docs-heading-anchor-permalink" href="#Differences-between-Zarr-and-NetCDF-files" title="Permalink"></a></h3><ul><li>All metadata (in particular attributes) is stored in JSON files for the Zarr format with the following implications:<ul><li>JSON does not distinguish between integers and real numbers. They are all considered as generic numbers. Whole numbers are loaded as <code>Int64</code> and real numbers <code>Float64</code>. It is not possible to store the number <code>1.0</code> as a real number.</li><li>The order of keys in a JSON document is undefined. It is therefore not possible to have a consistent ordering of the attributes or variables.</li><li>The JSON standard does not allow the values NaN, +Inf, -Inf which is problematic for attributes (<a href="https://github.com/zarr-developers/zarr-python/issues/412">zarr-python #412</a>,   <a href="https://github.com/zarr-developers/zarr-specs/issues/81">zarr-specs #81</a>). However, there is a special case for the fill-value to handle NaN, +Inf and -Inf.</li></ul></li><li>All dimensions must be associated to Zarr variables.</li></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 06:29">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>