Skip to content

Commit

Permalink
deploy: 6954bb1
Browse files Browse the repository at this point in the history
  • Loading branch information
nullnik-0 committed Jun 26, 2024
1 parent 2a58c33 commit 5dd19e3
Show file tree
Hide file tree
Showing 145 changed files with 2,971 additions and 1,913 deletions.
31 changes: 17 additions & 14 deletions README.html
Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,12 @@
</script>

<!-- Loaded before other Sphinx assets -->
<link href="_static/styles/theme.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />


<link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
Expand All @@ -34,9 +34,9 @@
<link rel="stylesheet" type="text/css" href="_static/theme.css?v=ec48f040" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
<script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
<script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>

<script src="_static/documentation_options.js?v=c607423c"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
Expand Down Expand Up @@ -127,6 +127,8 @@
<div class="sidebar-primary-item">





<a class="navbar-brand logo" href="#">

Expand Down Expand Up @@ -229,6 +231,7 @@
</details></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="data/dataset-curation.html">Dataset curation</a></li>
<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
<li class="toctree-l2"><a class="reference internal" href="data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
Expand Down Expand Up @@ -410,18 +413,18 @@

<script>
document.write(`
<button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
<button class="btn btn-sm nav-link pst-navbar-icon theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="theme-switch fa-solid fa-sun fa-lg" data-mode="light"></i>
<i class="theme-switch fa-solid fa-moon fa-lg" data-mode="dark"></i>
<i class="theme-switch fa-solid fa-circle-half-stroke fa-lg" data-mode="auto"></i>
</button>
`);
</script>


<script>
document.write(`
<button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<button class="btn btn-sm pst-navbar-icon search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass fa-lg"></i>
</button>
`);
Expand Down Expand Up @@ -533,8 +536,8 @@ <h1><span>⚗️</span> Lab Manual<a class="headerlink" href="#lab-manual" title
</div>

<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341"></script>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341"></script>
<script src="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b"></script>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b"></script>

<footer class="bd-footer">
</footer>
Expand Down
11 changes: 10 additions & 1 deletion _sources/data/README.md
Original file line number Diff line number Diff line change
@@ -1,10 +1,19 @@
# <span>💾</span> Data

For the details of how we structure datasets at the lab, see:

```{toctree}
:maxdepth: 1
dataset-curation
```

For instructions on how to do various admin tasks on our data server, see:

```{toctree}
:maxdepth: 1
admin-guide
```

MRI, microscopy and other research data are stored in the following servers:

```{toctree}
Expand All @@ -14,4 +23,4 @@ duke
django
```

[Here](https://docs.google.com/spreadsheets/d/1yjcA8Z0COn4OZxusIDHjStH2DpeXvscsj-aWE2X-_sg) useful list of MRI data to use for various projects.
[Here](https://docs.google.com/spreadsheets/d/1yjcA8Z0COn4OZxusIDHjStH2DpeXvscsj-aWE2X-_sg) is a useful list of MRI data to use for various projects.
29 changes: 29 additions & 0 deletions _sources/data/admin-guide.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
# Dataset admin guide

TODO: list the places where we have datasets (data.neuro.polymtl.ca, github, aws, compute canada, spineimage.ca)

TODO: describe our current access rules

TODO: give some API examples/scripts

See also: [the user guide](git-datasets.md)

## New repository

We have a [dataset template](https://data.neuro.polymtl.ca/datasets/template) that we use for new repositories. When someone at the lab asks for a new dataset on <https://data.neuro.polymtl.ca/>, the steps to take are:

1. Make sure they've opened [an issue in data-management](https://github.com/neuropoly/data-management/issues) with the name they want. Note that we only use **lowercase letters** and **hyphens** (no underscores).
2. Log in to Neurogitea and go to [the repository creation page](https://data.neuro.polymtl.ca/repo/create?org=2). Then:
1. Select the organization "NeuroPoly datasets" as owner.
2. Fill in the repository name.
3. "Make Repository Private" should already be checked.
4. Select "datasets/template" as the template.
5. For template items, check the box for "Git Content (Default Branch)".
6. Click "Create Repository".
3. In the new repository, click "Watch" so that at least one admin gets notifications (that is, you).
4. Give write access to the requesting student:
1. Go to the repository's "Settings" tab.
2. Select "Collaborators" from the left-hand menu.
3. Search for the student's name and click "Add Collaborator".
4. Make sure the student's Neurogitea user account contains their actual human-readable name ("Site Administration" -> "User Accounts" -> search for the user -> edit).
5. Reply on the original [data-management issue](https://github.com/neuropoly/data-management/issues) that you've created the repo and given them write access, with a link to the repo.
2 changes: 1 addition & 1 deletion _static/scripts/pydata-sphinx-theme.js

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion _static/scripts/pydata-sphinx-theme.js.map

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion _static/styles/pydata-sphinx-theme.css

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion _static/styles/pydata-sphinx-theme.css.map

Large diffs are not rendered by default.

18 changes: 9 additions & 9 deletions _static/webpack-macros.html
Original file line number Diff line number Diff line change
Expand Up @@ -4,28 +4,28 @@
-->
{# Load FontAwesome icons #}
{% macro head_pre_icons() %}
<link href="{{ pathto('_static/vendor/fontawesome/6.5.2/css/all.min.css', 1) }}?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="{{ pathto('_static/vendor/fontawesome/6.5.2/css/all.min.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2', 1) }}" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2', 1) }}" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2', 1) }}" />
{% endmacro %}

{% macro head_pre_assets() %}
<!-- Loaded before other Sphinx assets -->
<link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
{% endmacro %}

{% macro head_js_preload() %}
<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=3ee479438cf8b5e0d341" />
<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=3ee479438cf8b5e0d341" />
<script src="{{ pathto('_static/vendor/fontawesome/6.5.2/js/all.min.js', 1) }}?digest=3ee479438cf8b5e0d341"></script>
<link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
<script src="{{ pathto('_static/vendor/fontawesome/6.5.2/js/all.min.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
{% endmacro %}

{% macro body_post() %}
<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=3ee479438cf8b5e0d341"></script>
<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=3ee479438cf8b5e0d341"></script>
<script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
{% endmacro %}
31 changes: 17 additions & 14 deletions agenda-and-calendar.html
Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,12 @@
</script>

<!-- Loaded before other Sphinx assets -->
<link href="_static/styles/theme.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/styles/theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="_static/styles/bootstrap.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link href="_static/styles/pydata-sphinx-theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />


<link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=3ee479438cf8b5e0d341" rel="stylesheet" />
<link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
Expand All @@ -34,9 +34,9 @@
<link rel="stylesheet" type="text/css" href="_static/theme.css?v=ec48f040" />

<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341" />
<script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=3ee479438cf8b5e0d341"></script>
<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
<script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>

<script src="_static/documentation_options.js?v=c607423c"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
Expand Down Expand Up @@ -126,6 +126,8 @@
<div class="sidebar-primary-item">





<a class="navbar-brand logo" href="README.html">

Expand Down Expand Up @@ -228,6 +230,7 @@
</details></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="data/README.html"><span>💾</span> Data</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="data/dataset-curation.html">Dataset curation</a></li>
<li class="toctree-l2"><a class="reference internal" href="data/admin-guide.html">Dataset admin guide</a></li>
<li class="toctree-l2"><a class="reference internal" href="data/git-datasets.html"><code class="docutils literal notranslate"><span class="pre">data.neuro.polymtl.ca</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="data/duke.html"><code class="docutils literal notranslate"><span class="pre">duke</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="data/django.html"><code class="docutils literal notranslate"><span class="pre">django</span></code></a></li>
Expand Down Expand Up @@ -409,18 +412,18 @@

<script>
document.write(`
<button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
<span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
<button class="btn btn-sm nav-link pst-navbar-icon theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="theme-switch fa-solid fa-sun fa-lg" data-mode="light"></i>
<i class="theme-switch fa-solid fa-moon fa-lg" data-mode="dark"></i>
<i class="theme-switch fa-solid fa-circle-half-stroke fa-lg" data-mode="auto"></i>
</button>
`);
</script>


<script>
document.write(`
<button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<button class="btn btn-sm pst-navbar-icon search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass fa-lg"></i>
</button>
`);
Expand Down Expand Up @@ -759,8 +762,8 @@ <h2>Book a room<a class="headerlink" href="#book-a-room" title="Link to this hea
</div>

<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script src="_static/scripts/bootstrap.js?digest=3ee479438cf8b5e0d341"></script>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=3ee479438cf8b5e0d341"></script>
<script src="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b"></script>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b"></script>

<footer class="bd-footer">
</footer>
Expand Down
Loading

0 comments on commit 5dd19e3

Please sign in to comment.