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‎docs/.buildinfo‎

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: ebf22e7606a0334f8865defd258a74c5
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config: b0bb638516d5929555228a8219f6cc18
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎docs/_sources/citing.rst.txt‎

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If you use this software in a scientific publication, please cite using the following Zenodo reference.
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**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.3.2). Zenodo. https://doi.org/10.5281/zenodo.7863308**
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**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.7863308**

‎docs/_sources/examples/visium.rst.txt‎

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.. code-block:: shell
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:caption: Input
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ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2
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ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0
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.. code-block:: shell
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:caption: Output
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.. code-block:: shell
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:caption: Input
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npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2 --port 3000 --cors
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npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0 --port 3000 --cors
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.. code-block:: shell
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:caption: Output

‎docs/_sources/examples/xenium.rst.txt‎

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.. code-block:: shell
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:caption: Input
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ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.3.2
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ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0
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.. code-block:: shell
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:caption: Output
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.. code-block:: shell
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:caption: Input
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npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.3.2 --port 3000 --cors
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npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0 --port 3000 --cors
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.. code-block:: shell
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:caption: Output

‎docs/_sources/installation.rst.txt‎

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.. code-block:: shell
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:caption: Input
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wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.3.2.tar.gz
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wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.4.0.tar.gz
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.. code-block:: shell
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:caption: Expected Output
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Resolving github.com (github.com)... 140.82.121.3
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Connecting to github.com (github.com)|140.82.121.3|:443... connected.
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HTTP request sent, awaiting response... 302 Found
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Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.3.2 [following]
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--2023-05-18 09:30:15-- https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.3.2
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Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.4.0 [following]
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--2023-05-18 09:30:15-- https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.4.0
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Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
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Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
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HTTP request sent, awaiting response... 200 OK
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Length: unspecified [application/x-gzip]
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Saving to: ‘v0.3.2.tar.gz’
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Saving to: ‘v0.4.0.tar.gz’
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v0.3.2.tar.gz [ <=> ] 2.70M 9.12MB/s in 0.3s
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v0.4.0.tar.gz [ <=> ] 2.70M 9.12MB/s in 0.3s
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2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.3.2.tar.gz’ saved [2835534]
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2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.4.0.tar.gz’ saved [2835534]
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Extract the WebAtlas compressed tag and change directory into the new repo.
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.. code-block:: shell
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tar -xzvf ./v0.3.2.tar.gz
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cd webatlas-pipeline-0.3.2
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tar -xzvf ./v0.4.0.tar.gz
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cd webatlas-pipeline-0.4.0
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.. code-block:: shell
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:caption: Expected Output
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webatlas-pipeline-0.3.2/
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webatlas-pipeline-0.3.2/.github/
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webatlas-pipeline-0.4.0/
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webatlas-pipeline-0.4.0/.github/
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...
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...
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webatlas-pipeline-0.3.2/tests/input/simple_config.json
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webatlas-pipeline-0.3.2/tests/test_class.py
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webatlas-pipeline-0.4.0/tests/input/simple_config.json
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webatlas-pipeline-0.4.0/tests/test_class.py
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.. _environment:
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‎docs/_static/documentation_options.js‎

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const DOCUMENTATION_OPTIONS = {
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VERSION: '0.3.2',
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VERSION: '0.4.0',
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LANGUAGE: 'en',
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COLLAPSE_INDEX: false,
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BUILDER: 'html',

‎docs/citing.html‎

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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Citation &mdash; WebAtlas 0.3.2 documentation</title>
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<title>Citation &mdash; WebAtlas 0.4.0 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<script src="_static/jquery.js?v=5d32c60e"></script>
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<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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<script src="_static/documentation_options.js?v=71d9d8e6"></script>
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<script src="_static/documentation_options.js?v=6c02275b"></script>
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<script src="_static/doctools.js?v=888ff710"></script>
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<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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<span id="citing"></span><h1>Citation<a class="headerlink" href="#citation" title="Link to this heading"></a></h1>
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<p><a class="reference external" href="https://doi.org/10.5281/zenodo.7405818"><img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.7405818.svg" /></a></p>
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<p>If you use this software in a scientific publication, please cite using the following Zenodo reference.</p>
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<p><strong>Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, &amp; Iolo, Squires. (2023). WebAtlas Pipeline (v0.3.2). Zenodo. https://doi.org/10.5281/zenodo.7863308</strong></p>
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<p><strong>Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, &amp; Iolo, Squires. (2023). WebAtlas Pipeline (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.7863308</strong></p>
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‎docs/configuration.html‎

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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Configuration &mdash; WebAtlas 0.3.2 documentation</title>
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<title>Configuration &mdash; WebAtlas 0.4.0 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<script src="_static/jquery.js?v=5d32c60e"></script>
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<script src="_static/documentation_options.js?v=71d9d8e6"></script>
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<script src="_static/documentation_options.js?v=6c02275b"></script>
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<script src="_static/js/theme.js"></script>

‎docs/examples/visium.html‎

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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Visium &mdash; WebAtlas 0.3.2 documentation</title>
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<title>Visium &mdash; WebAtlas 0.4.0 documentation</title>
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<script src="../_static/documentation_options.js?v=6c02275b"></script>
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>ls<span class="w"> </span>-l<span class="w"> </span>output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>ls<span class="w"> </span>-l<span class="w"> </span>output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>npx<span class="w"> </span>http-server<span class="w"> </span>output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2<span class="w"> </span>--port<span class="w"> </span><span class="m">3000</span><span class="w"> </span>--cors
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>npx<span class="w"> </span>http-server<span class="w"> </span>output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0<span class="w"> </span>--port<span class="w"> </span><span class="m">3000</span><span class="w"> </span>--cors
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‎docs/examples/xenium.html‎

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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Xenium &mdash; WebAtlas 0.3.2 documentation</title>
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<title>Xenium &mdash; WebAtlas 0.4.0 documentation</title>
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>ls<span class="w"> </span>-l<span class="w"> </span>output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>npx<span class="w"> </span>http-server<span class="w"> </span>output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.3.2<span class="w"> </span>--port<span class="w"> </span><span class="m">3000</span><span class="w"> </span>--cors
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<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>npx<span class="w"> </span>http-server<span class="w"> </span>output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0<span class="w"> </span>--port<span class="w"> </span><span class="m">3000</span><span class="w"> </span>--cors
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