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![Build Status](https://gitlab.com/pages/plain-html/badges/master/build.svg)
---
Write documentation using Jupyter Book for DISCO Beamline data processing
---
The webversion is available at: https://discosoleil.gitlab.io/doc/
The principal repository of is located at : https://gitlab.synchrotron-soleil.fr/disco-beamline/doc
The **gitlab.com** is a mirror repo don't push merge request here use the above repository to push request, issues, etc...
# Use GLOBUS
Globus intro
## Connect to Globus
## Install globus-connect on your computer
```{info}
You need to do that outside of the network of Soleil
```
# Introduction
TODO
\ No newline at end of file
# POLYPHEME Microscope
Data acquired using LabSpec6 software, exported as SPC and text files. One file that contains all spectra for each spatial points.
# TELEMOS Microscope
Data acquired using micro-manager software. Produce stack of 2d images saved as separate tiff files
\ No newline at end of file
Source diff could not be displayed: it is too large. Options to address this: view the blob.
%% Cell type:markdown id:fbf828cb-0fda-4f25-a3aa-4294319b621f tags:
# Read hyperspectral images from POLYPHEME microscope
TODO
%% Cell type:code id:42580539-ee7f-414e-928f-0e13d7c3f293 tags:
``` python
```
%% Cell type:markdown id:79969a1c-5e05-4920-a335-b38028b72f20 tags:
# Read images acquired with TELEMOS
TODO
%% Cell type:code id:767b4d31-dbdf-4b77-88f1-036670115cf0 tags:
``` python
```
# Welcome to the DISCO documentation for data-processing
This book is a test to write a clean documentation for users to help them to process their data obtain on the
[DISCO Beamline of the Synchrotron-SOLEIL](https://www.synchrotron-soleil.fr/en/beamlines/disco).
```{warning}
This is an early version of the documentation and a lot of things are missing.
Please feel free to send us your suggestions to improve this documentation.
```
Main idea:
- Give user guide to download their data using globus
- Give user guide to work on their data:
- Using the jupyter-notebook of grades via the remote.synchrotron-soleil.fr
- Using their own jupyter notebook (or lab) installation
- Using Their matlab
- Using ImageJ ?
%% Cell type:markdown id:5163879e tags:
# Notebooks with MyST Markdown
Jupyter Book also lets you write text-based notebooks using MyST Markdown.
See [the Notebooks with MyST Markdown documentation](https://jupyterbook.org/file-types/myst-notebooks.html) for more detailed instructions.
This page shows off a notebook written in MyST Markdown.
## An example cell
With MyST Markdown, you can define code cells with a directive like so:
%% Cell type:code id:9a22d3b9 tags:
``` python
print(2 + 2)
```
%% Output
4
%% Cell type:markdown id:0ddd6c2c tags:
When your book is built, the contents of any `{code-cell}` blocks will be
executed with your default Jupyter kernel, and their outputs will be displayed
in-line with the rest of your content.
```{seealso}
Jupyter Book uses [Jupytext](https://jupytext.readthedocs.io/en/latest/) to convert text-based files to notebooks, and can support [many other text-based notebook files](https://jupyterbook.org/file-types/jupytext.html).
```
## Create a notebook with MyST Markdown
MyST Markdown notebooks are defined by two things:
1. YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).
See the YAML at the top of this page for example.
2. The presence of `{code-cell}` directives, which will be executed with your book.
That's all that is needed to get started!
## Quickly add YAML metadata for MyST Notebooks
If you have a markdown file and you'd like to quickly add YAML metadata to it, so that Jupyter Book will treat it as a MyST Markdown Notebook, run the following command:
```
jupyter-book myst init path/to/markdownfile.md
```
---
jupytext:
formats: md:myst
text_representation:
extension: .md
format_name: myst
format_version: 0.13
jupytext_version: 1.11.5
kernelspec:
display_name: Python 3
language: python
name: python3
---
# Notebooks with MyST Markdown
Jupyter Book also lets you write text-based notebooks using MyST Markdown.
See [the Notebooks with MyST Markdown documentation](https://jupyterbook.org/file-types/myst-notebooks.html) for more detailed instructions.
This page shows off a notebook written in MyST Markdown.
## An example cell
With MyST Markdown, you can define code cells with a directive like so:
```{code-cell}
print(2 + 2)
```
When your book is built, the contents of any `{code-cell}` blocks will be
executed with your default Jupyter kernel, and their outputs will be displayed
in-line with the rest of your content.
```{seealso}
Jupyter Book uses [Jupytext](https://jupytext.readthedocs.io/en/latest/) to convert text-based files to notebooks, and can support [many other text-based notebook files](https://jupyterbook.org/file-types/jupytext.html).
```
## Create a notebook with MyST Markdown
MyST Markdown notebooks are defined by two things:
1. YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).
See the YAML at the top of this page for example.
2. The presence of `{code-cell}` directives, which will be executed with your book.
That's all that is needed to get started!
## Quickly add YAML metadata for MyST Notebooks
If you have a markdown file and you'd like to quickly add YAML metadata to it, so that Jupyter Book will treat it as a MyST Markdown Notebook, run the following command:
```
jupyter-book myst init path/to/markdownfile.md
```
# Markdown Files
Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or
in regular markdown files (`.md`), you'll write in the same flavor of markdown
called **MyST Markdown**.
This is a simple file to help you get started and show off some syntax.
## What is MyST?
MyST stands for "Markedly Structured Text". It
is a slight variation on a flavor of markdown called "CommonMark" markdown,
with small syntax extensions to allow you to write **roles** and **directives**
in the Sphinx ecosystem.
For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html).
## Sample Roles and Directives
Roles and directives are two of the most powerful tools in Jupyter Book. They
are kind of like functions, but written in a markup language. They both
serve a similar purpose, but **roles are written in one line**, whereas
**directives span many lines**. They both accept different kinds of inputs,
and what they do with those inputs depends on the specific role or directive
that is being called.
Here is a "note" directive:
```{note}
Here is a note
```
It will be rendered in a special box when you build your book.
Here is an inline directive to refer to a document: {doc}`markdown-notebooks`.
## Citations
You can also cite references that are stored in a `bibtex` file. For example,
the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like
this: {cite}`holdgraf_evidence_2014`.
Moreover, you can insert a bibliography into your page with this syntax:
The `{bibliography}` directive must be used for all the `{cite}` roles to
render properly.
For example, if the references for your book are stored in `references.bib`,
then the bibliography is inserted with:
```{bibliography}
```
## Learn more
This is just a simple starter to get you started.
You can learn a lot more at [jupyterbook.org](https://jupyterbook.org).
%% Cell type:markdown id: tags:
# Content with notebooks
You can also create content with Jupyter Notebooks. This means that you can include
code blocks and their outputs in your book.
## Markdown + notebooks
As it is markdown, you can embed images, HTML, etc into your posts!
![](https://myst-parser.readthedocs.io/en/latest/_static/logo-wide.svg)
You can also $add_{math}$ and
$$
math^{blocks}
$$
or
$$
\begin{aligned}
\mbox{mean} la_{tex} \\ \\
math blocks
\end{aligned}
$$
But make sure you \$Escape \$your \$dollar signs \$you want to keep!
## MyST markdown
MyST markdown works in Jupyter Notebooks as well. For more information about MyST markdown, check
out [the MyST guide in Jupyter Book](https://jupyterbook.org/content/myst.html),
or see [the MyST markdown documentation](https://myst-parser.readthedocs.io/en/latest/).
## Code blocks and outputs
Jupyter Book will also embed your code blocks and output in your book.
For example, here's some sample Matplotlib code:
%% Cell type:code id: tags:
``` python
from matplotlib import rcParams, cycler
import matplotlib.pyplot as plt
import numpy as np
plt.ion()
```
%% Cell type:code id: tags:
``` python
# Fixing random state for reproducibility
np.random.seed(19680801)
N = 10
data = [np.logspace(0, 1, 100) + np.random.randn(100) + ii for ii in range(N)]
data = np.array(data).T
cmap = plt.cm.coolwarm
rcParams['axes.prop_cycle'] = cycler(color=cmap(np.linspace(0, 1, N)))
from matplotlib.lines import Line2D
custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),
Line2D([0], [0], color=cmap(.5), lw=4),
Line2D([0], [0], color=cmap(1.), lw=4)]
fig, ax = plt.subplots(figsize=(10, 5))
lines = ax.plot(data)
ax.legend(custom_lines, ['Cold', 'Medium', 'Hot']);
```
%% Cell type:markdown id: tags:
There is a lot more that you can do with outputs (such as including interactive outputs)
with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)
# Introduction
TODO
var sd_labels_by_text = {};
function ready() {
const li = document.getElementsByClassName("sd-tab-label");
for (const label of li) {
syncId = label.getAttribute("data-sync-id");
if (syncId) {
label.onclick = onLabelClick;
if (!sd_labels_by_text[syncId]) {
sd_labels_by_text[syncId] = [];
}
sd_labels_by_text[syncId].push(label);
}
}
}
function onLabelClick() {
// Activate other inputs with the same sync id.
syncId = this.getAttribute("data-sync-id");
for (label of sd_labels_by_text[syncId]) {
if (label === this) continue;
label.previousElementSibling.checked = true;
}
window.localStorage.setItem("sphinx-design-last-tab", syncId);
}
document.addEventListener("DOMContentLoaded", ready, false);
/*
* basic.css
* ~~~~~~~~~
*
* Sphinx stylesheet -- basic theme.
*
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
/* -- main layout ----------------------------------------------------------- */
div.clearer {
clear: both;
}
div.section::after {
display: block;
content: '';
clear: left;
}
/* -- relbar ---------------------------------------------------------------- */
div.related {
width: 100%;
font-size: 90%;
}
div.related h3 {
display: none;
}
div.related ul {
margin: 0;
padding: 0 0 0 10px;
list-style: none;
}
div.related li {
display: inline;
}
div.related li.right {
float: right;
margin-right: 5px;
}
/* -- sidebar --------------------------------------------------------------- */
div.sphinxsidebarwrapper {
padding: 10px 5px 0 10px;
}
div.sphinxsidebar {
float: left;
width: 270px;
margin-left: -100%;
font-size: 90%;
word-wrap: break-word;
overflow-wrap : break-word;
}
div.sphinxsidebar ul {
list-style: none;
}
div.sphinxsidebar ul ul,
div.sphinxsidebar ul.want-points {
margin-left: 20px;
list-style: square;
}
div.sphinxsidebar ul ul {
margin-top: 0;
margin-bottom: 0;
}
div.sphinxsidebar form {
margin-top: 10px;
}
div.sphinxsidebar input {
border: 1px solid #98dbcc;
font-family: sans-serif;
font-size: 1em;
}
div.sphinxsidebar #searchbox form.search {
overflow: hidden;
}
div.sphinxsidebar #searchbox input[type="text"] {
float: left;
width: 80%;
padding: 0.25em;
box-sizing: border-box;
}
div.sphinxsidebar #searchbox input[type="submit"] {
float: left;
width: 20%;
border-left: none;
padding: 0.25em;
box-sizing: border-box;
}
img {
border: 0;
max-width: 100%;
}
/* -- search page ----------------------------------------------------------- */
ul.search {
margin: 10px 0 0 20px;
padding: 0;
}
ul.search li {
padding: 5px 0 5px 20px;
background-image: url(file.png);
background-repeat: no-repeat;
background-position: 0 7px;
}
ul.search li a {
font-weight: bold;
}
ul.search li p.context {
color: #888;
margin: 2px 0 0 30px;
text-align: left;
}
ul.keywordmatches li.goodmatch a {
font-weight: bold;
}
/* -- index page ------------------------------------------------------------ */
table.contentstable {
width: 90%;
margin-left: auto;
margin-right: auto;
}
table.contentstable p.biglink {
line-height: 150%;
}
a.biglink {
font-size: 1.3em;
}
span.linkdescr {
font-style: italic;
padding-top: 5px;
font-size: 90%;
}
/* -- general index --------------------------------------------------------- */
table.indextable {
width: 100%;
}
table.indextable td {
text-align: left;
vertical-align: top;
}
table.indextable ul {
margin-top: 0;
margin-bottom: 0;
list-style-type: none;
}
table.indextable > tbody > tr > td > ul {
padding-left: 0em;
}
table.indextable tr.pcap {
height: 10px;
}
table.indextable tr.cap {
margin-top: 10px;
background-color: #f2f2f2;
}
img.toggler {
margin-right: 3px;
margin-top: 3px;
cursor: pointer;
}
div.modindex-jumpbox {
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
margin: 1em 0 1em 0;
padding: 0.4em;
}
div.genindex-jumpbox {
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
margin: 1em 0 1em 0;
padding: 0.4em;
}
/* -- domain module index --------------------------------------------------- */
table.modindextable td {
padding: 2px;
border-collapse: collapse;
}
/* -- general body styles --------------------------------------------------- */
div.body {
min-width: 450px;
max-width: 800px;
}
div.body p, div.body dd, div.body li, div.body blockquote {
-moz-hyphens: auto;
-ms-hyphens: auto;
-webkit-hyphens: auto;
hyphens: auto;
}
a.headerlink {
visibility: hidden;
}
a.brackets:before,
span.brackets > a:before{
content: "[";
}
a.brackets:after,
span.brackets > a:after {
content: "]";
}
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
h4:hover > a.headerlink,
h5:hover > a.headerlink,
h6:hover > a.headerlink,
dt:hover > a.headerlink,
caption:hover > a.headerlink,
p.caption:hover > a.headerlink,
div.code-block-caption:hover > a.headerlink {
visibility: visible;
}
div.body p.caption {
text-align: inherit;
}
div.body td {
text-align: left;
}
.first {
margin-top: 0 !important;
}
p.rubric {
margin-top: 30px;
font-weight: bold;
}
img.align-left, figure.align-left, .figure.align-left, object.align-left {
clear: left;
float: left;
margin-right: 1em;
}
img.align-right, figure.align-right, .figure.align-right, object.align-right {
clear: right;
float: right;
margin-left: 1em;
}
img.align-center, figure.align-center, .figure.align-center, object.align-center {
display: block;
margin-left: auto;
margin-right: auto;
}
img.align-default, figure.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
}
.align-left {
text-align: left;
}
.align-center {
text-align: center;
}
.align-default {
text-align: center;
}
.align-right {
text-align: right;
}
/* -- sidebars -------------------------------------------------------------- */
div.sidebar,
aside.sidebar {
margin: 0 0 0.5em 1em;
border: 1px solid #ddb;
padding: 7px;
background-color: #ffe;
width: 40%;
float: right;
clear: right;
overflow-x: auto;
}
p.sidebar-title {
font-weight: bold;
}
div.admonition, div.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
div.topic {
border: 1px solid #ccc;
padding: 7px;
margin: 10px 0 10px 0;
}
p.topic-title {
font-size: 1.1em;
font-weight: bold;
margin-top: 10px;
}
/* -- admonitions ----------------------------------------------------------- */
div.admonition {
margin-top: 10px;
margin-bottom: 10px;
padding: 7px;
}
div.admonition dt {
font-weight: bold;
}
p.admonition-title {
margin: 0px 10px 5px 0px;
font-weight: bold;
}
div.body p.centered {
text-align: center;
margin-top: 25px;
}
/* -- content of sidebars/topics/admonitions -------------------------------- */
div.sidebar > :last-child,
aside.sidebar > :last-child,
div.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
}
div.sidebar::after,
aside.sidebar::after,
div.topic::after,
div.admonition::after,
blockquote::after {
display: block;
content: '';
clear: both;
}
/* -- tables ---------------------------------------------------------------- */
table.docutils {
margin-top: 10px;
margin-bottom: 10px;
border: 0;
border-collapse: collapse;
}
table.align-center {
margin-left: auto;
margin-right: auto;
}
table.align-default {
margin-left: auto;
margin-right: auto;
}
table caption span.caption-number {
font-style: italic;
}
table caption span.caption-text {
}
table.docutils td, table.docutils th {
padding: 1px 8px 1px 5px;
border-top: 0;
border-left: 0;
border-right: 0;
border-bottom: 1px solid #aaa;
}
table.footnote td, table.footnote th {
border: 0 !important;
}
th {
text-align: left;
padding-right: 5px;
}
table.citation {
border-left: solid 1px gray;
margin-left: 1px;
}
table.citation td {
border-bottom: none;
}
th > :first-child,
td > :first-child {
margin-top: 0px;
}
th > :last-child,
td > :last-child {
margin-bottom: 0px;
}
/* -- figures --------------------------------------------------------------- */
div.figure, figure {
margin: 0.5em;
padding: 0.5em;
}
div.figure p.caption, figcaption {
padding: 0.3em;
}
div.figure p.caption span.caption-number,
figcaption span.caption-number {
font-style: italic;
}
div.figure p.caption span.caption-text,
figcaption span.caption-text {
}
/* -- field list styles ----------------------------------------------------- */
table.field-list td, table.field-list th {
border: 0 !important;
}
.field-list ul {
margin: 0;
padding-left: 1em;
}
.field-list p {
margin: 0;
}
.field-name {
-moz-hyphens: manual;
-ms-hyphens: manual;
-webkit-hyphens: manual;
hyphens: manual;
}
/* -- hlist styles ---------------------------------------------------------- */
table.hlist {
margin: 1em 0;
}
table.hlist td {
vertical-align: top;
}
/* -- object description styles --------------------------------------------- */
.sig {
font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
}
.sig-name, code.descname {
background-color: transparent;
font-weight: bold;
}
.sig-name {
font-size: 1.1em;
}
code.descname {
font-size: 1.2em;
}
.sig-prename, code.descclassname {
background-color: transparent;
}
.optional {
font-size: 1.3em;
}
.sig-paren {
font-size: larger;
}
.sig-param.n {
font-style: italic;
}
/* C++ specific styling */
.sig-inline.c-texpr,
.sig-inline.cpp-texpr {
font-family: unset;
}
.sig.c .k, .sig.c .kt,
.sig.cpp .k, .sig.cpp .kt {
color: #0033B3;
}
.sig.c .m,
.sig.cpp .m {
color: #1750EB;
}
.sig.c .s, .sig.c .sc,
.sig.cpp .s, .sig.cpp .sc {
color: #067D17;
}
/* -- other body styles ----------------------------------------------------- */
ol.arabic {
list-style: decimal;
}
ol.loweralpha {
list-style: lower-alpha;
}
ol.upperalpha {
list-style: upper-alpha;
}
ol.lowerroman {
list-style: lower-roman;
}
ol.upperroman {
list-style: upper-roman;
}
:not(li) > ol > li:first-child > :first-child,
:not(li) > ul > li:first-child > :first-child {
margin-top: 0px;
}
:not(li) > ol > li:last-child > :last-child,
:not(li) > ul > li:last-child > :last-child {
margin-bottom: 0px;
}
ol.simple ol p,
ol.simple ul p,
ul.simple ol p,
ul.simple ul p {
margin-top: 0;
}
ol.simple > li:not(:first-child) > p,
ul.simple > li:not(:first-child) > p {
margin-top: 0;
}
ol.simple p,
ul.simple p {
margin-bottom: 0;
}
dl.footnote > dt,
dl.citation > dt {
float: left;
margin-right: 0.5em;
}
dl.footnote > dd,
dl.citation > dd {
margin-bottom: 0em;
}
dl.footnote > dd:after,
dl.citation > dd:after {
content: "";
clear: both;
}
dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
}
dl.field-list > dt {
font-weight: bold;
word-break: break-word;
padding-left: 0.5em;
padding-right: 5px;
}
dl.field-list > dt:after {
content: ":";
}
dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
margin-left: 0em;
margin-bottom: 0em;
}
dl {
margin-bottom: 15px;
}
dd > :first-child {
margin-top: 0px;
}
dd ul, dd table {
margin-bottom: 10px;
}
dd {
margin-top: 3px;
margin-bottom: 10px;
margin-left: 30px;
}
dl > dd:last-child,
dl > dd:last-child > :last-child {
margin-bottom: 0;
}
dt:target, span.highlighted {
background-color: #fbe54e;
}
rect.highlighted {
fill: #fbe54e;
}
dl.glossary dt {
font-weight: bold;
font-size: 1.1em;
}
.versionmodified {
font-style: italic;
}
.system-message {
background-color: #fda;
padding: 5px;
border: 3px solid red;
}
.footnote:target {
background-color: #ffa;
}
.line-block {
display: block;
margin-top: 1em;
margin-bottom: 1em;
}
.line-block .line-block {
margin-top: 0;
margin-bottom: 0;
margin-left: 1.5em;
}
.guilabel, .menuselection {
font-family: sans-serif;
}
.accelerator {
text-decoration: underline;
}
.classifier {
font-style: oblique;
}
.classifier:before {
font-style: normal;
margin: 0 0.5em;
content: ":";
display: inline-block;
}
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
}
/* -- code displays --------------------------------------------------------- */
pre {
overflow: auto;
overflow-y: hidden; /* fixes display issues on Chrome browsers */
}
pre, div[class*="highlight-"] {
clear: both;
}
span.pre {
-moz-hyphens: none;
-ms-hyphens: none;
-webkit-hyphens: none;
hyphens: none;
white-space: nowrap;
}
div[class*="highlight-"] {
margin: 1em 0;
}
td.linenos pre {
border: 0;
background-color: transparent;
color: #aaa;
}
table.highlighttable {
display: block;
}
table.highlighttable tbody {
display: block;
}
table.highlighttable tr {
display: flex;
}
table.highlighttable td {
margin: 0;
padding: 0;
}
table.highlighttable td.linenos {
padding-right: 0.5em;
}
table.highlighttable td.code {
flex: 1;
overflow: hidden;
}
.highlight .hll {
display: block;
}
div.highlight pre,
table.highlighttable pre {
margin: 0;
}
div.code-block-caption + div {
margin-top: 0;
}
div.code-block-caption {
margin-top: 1em;
padding: 2px 5px;
font-size: small;
}
div.code-block-caption code {
background-color: transparent;
}
table.highlighttable td.linenos,
span.linenos,
div.highlight span.gp { /* gp: Generic.Prompt */
user-select: none;
-webkit-user-select: text; /* Safari fallback only */
-webkit-user-select: none; /* Chrome/Safari */
-moz-user-select: none; /* Firefox */
-ms-user-select: none; /* IE10+ */
}
div.code-block-caption span.caption-number {
padding: 0.1em 0.3em;
font-style: italic;
}
div.code-block-caption span.caption-text {
}
div.literal-block-wrapper {
margin: 1em 0;
}
code.xref, a code {
background-color: transparent;
font-weight: bold;
}
h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
background-color: transparent;
}
.viewcode-link {
float: right;
}
.viewcode-back {
float: right;
font-family: sans-serif;
}
div.viewcode-block:target {
margin: -1px -10px;
padding: 0 10px;
}
/* -- math display ---------------------------------------------------------- */
img.math {
vertical-align: middle;
}
div.body div.math p {
text-align: center;
}
span.eqno {
float: right;
}
span.eqno a.headerlink {
position: absolute;
z-index: 1;
}
div.math:hover a.headerlink {
visibility: visible;
}
/* -- printout stylesheet --------------------------------------------------- */
@media print {
div.document,
div.documentwrapper,
div.bodywrapper {
margin: 0 !important;
width: 100%;
}
div.sphinxsidebar,
div.related,
div.footer,
#top-link {
display: none;
}
}
\ No newline at end of file
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