Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit 382360ff authored by Clément Haëck's avatar Clément Haëck
Browse files

Up docs

parent f8c477e9
......@@ -4,13 +4,14 @@ Collocate submesoscale fronts to phytoplankton levels using satellite imagery
## Content
- Compute: Process data, compute diagnostics,...
- docs: Documentation
- Download: Scripts for downloading data
- lib: Reusable code. Scripts for defining databases
- Compute: Process data, compute diagnostics,...
- Plots: Plotting scripts
## Doc
Some documentation is available in orgmode and html format. See ([./docs/index.org](Index)).
Some documentation is available in orgmode and html format. See ([./docs](docs)). Org files can be read directly in gitlab, though I recommend browsing the html files from a local clone of this repository.
......@@ -3,10 +3,10 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Args</title>
<title>Arguments</title>
<meta name="author" content="Clément Haëck" />
<meta name="generator" content="Org Mode" />
<style>
......@@ -197,7 +197,7 @@
</head>
<body>
<div id="content" class="content">
<h1 class="title">Args</h1>
<h1 class="title">Arguments</h1>
<div id="table-of-contents" role="doc-toc">
<h2>Table of Contents</h2>
<div id="text-table-of-contents" role="doc-toc">
......@@ -215,10 +215,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<p>
All scripts are written with a command-line use in mind.
To change some parameters, command-line arguments are retrieved. As always, things are quite automated.
......@@ -339,8 +335,7 @@ This system is a bit heavy but convenient, as the variable args can be passed to
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Args
#+TITLE: Arguments
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
All scripts are written with a command-line use in mind.
To change some parameters, command-line arguments are retrieved. As always, things are quite automated.
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Boxes</title>
......@@ -198,10 +198,6 @@
<body>
<div id="content" class="content">
<h1 class="title">Boxes</h1>
<p>
<a href="index.html">Index</a>
</p>
<p>
We sometime needs to define a rectangular area (a zone clean of clouds for instance).
<code>lib.box</code> defines several classes to help with this notion.
......@@ -209,8 +205,7 @@ With those, it is easy to define a rectangular area. It can be used to slice a d
</p>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Boxes
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
We sometime needs to define a rectangular area (a zone clean of clouds for instance).
~lib.box~ defines several classes to help with this notion.
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Datasets</title>
......@@ -221,9 +221,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<div id="outline-container-org44091ea" class="outline-2">
<h2 id="org44091ea"><span class="section-number-2">1.</span> Location</h2>
......@@ -321,8 +318,7 @@ We define some static &rsquo;zones&rsquo;, this dataset is quite special and hav
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Datasets
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
* Location
All data is found in ~$SUBMESOCOLOR_DATA_DIR/[Region]/[dataset name / abbreviation]~.
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Grids</title>
......@@ -212,10 +212,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<p>
Because of the datasets that I use, I currently uses 3 different grids.
</p>
......@@ -249,8 +245,7 @@ This was choosen recently, so for a time I dealt with 2 grids. This is why most
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Grids
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
Because of the datasets that I use, I currently uses 3 different grids.
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Hi</title>
......@@ -207,9 +207,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<div id="outline-container-org5d6fb5b" class="outline-2">
<h2 id="org5d6fb5b"><span class="section-number-2">1.</span> HI definition</h2>
......@@ -225,8 +222,7 @@ How it works (the script).
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Hi
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
* HI definition
* Compilation
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Histograms</title>
......@@ -206,9 +206,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<div id="outline-container-org70c6638" class="outline-2">
<h2 id="org70c6638"><span class="section-number-2">1.</span> Method of computation</h2>
......@@ -220,8 +217,7 @@ advantages / defaults of using xhistogram
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Histograms
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
* Method of computation
advantages / defaults of using xhistogram
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Index</title>
......@@ -203,19 +203,10 @@
<div id="text-table-of-contents" role="doc-toc">
<ul>
<li><a href="#orgc3f1908">1. Folders</a></li>
<li><a href="#org1a203af">2. Other</a>
<ul>
<li><a href="#orgaa5eb64">2.1. Setup</a></li>
<li><a href="#org442cfd6">2.2. Workflow</a></li>
</ul>
</li>
<li><a href="#org7ad4688">2. Index</a></li>
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<p>
This is this project documentation.
It is far from covering everything but should put you on the right track.
......@@ -234,21 +225,26 @@ It is far from covering everything but should put you on the right track.
</ul>
</div>
</div>
<div id="outline-container-org1a203af" class="outline-2">
<h2 id="org1a203af"><span class="section-number-2">2.</span> Other</h2>
<div id="outline-container-org7ad4688" class="outline-2">
<h2 id="org7ad4688"><span class="section-number-2">2.</span> Index</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgaa5eb64" class="outline-3">
<h3 id="orgaa5eb64"><span class="section-number-3">2.1.</span> <a href="setup.html">Setup</a></h3>
</div>
<div id="outline-container-org442cfd6" class="outline-3">
<h3 id="org442cfd6"><span class="section-number-3">2.2.</span> <a href="workflow.html">Workflow</a></h3>
<ul class="org-ul">
<li><a href="args.html">Arguments</a></li>
<li><a href="boxes.html">Boxes</a></li>
<li><a href="datasets.html">Datasets</a></li>
<li><a href="grids.html">Grids</a></li>
<li><a href="hi.html">Heterogeneity-Index</a></li>
<li><a href="histograms.html">Histograms</a></li>
<li><a href="setup.html">Setup</a></li>
<li><a href="workflow.html">Workflow</a></li>
<li><a href="zones.html">Zones</a></li>
</ul>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Index
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
This is this project documentation.
It is far from covering everything but should put you on the right track.
......@@ -12,6 +11,14 @@ It is far from covering everything but should put you on the right track.
- lib: General modules
- lib/data: [[file:datasets.org][Datasets]]
- Plots: Folder is a hot mess. Lot of scripts are not kept up to date. Use at your own risk.
* Other
** [[file:setup.org][Setup]]
** [[file:workflow.org][Workflow]]
* Index
- [[file:args.org][Arguments]]
- [[file:boxes.org][Boxes]]
- [[file:datasets.org][Datasets]]
- [[file:grids.org][Grids]]
- [[file:hi.org][Heterogeneity-Index]]
- [[file:histograms.org][Histograms]]
- [[file:setup.org][Setup]]
- [[file:workflow.org][Workflow]]
- [[file:zones.org][Zones]]
......@@ -13,7 +13,9 @@
:recursive t
:publishing-function #'org-html-publish-to-html
:headline-levels 4
:auto-preamble t)))
:auto-preamble t
:html-postamble "<a href=index.html>Index</a>"
)))
(setq org-export-html-style
"<link rel=\"stylesheet\" type=\"text/css\" href=\"org-style.css\" />")
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:46 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Setup</title>
......@@ -212,10 +212,6 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<p>
First step is to clone this repository into a folder of your choice.
</p>
......@@ -284,8 +280,7 @@ On ciclad, python script must be executed by using <a href="../launch_python.sh"
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:46</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Setup
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
First step is to clone this repository into a folder of your choice.
......
......@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-06 jeu. 13:48 -->
<!-- 2022-01-06 jeu. 13:58 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Workflow</title>
......@@ -226,16 +226,12 @@
</ul>
</div>
</div>
<p>
<a href="index.html">Index</a>
</p>
<p>
This describes the important scripts, the order and the manner they should be executed to obtain results.
</p>
<p>
Most scripts work on a single year passed by the argument &rsquo;-year&rsquo; (see <a href="args.html">Args</a>).
Most scripts work on a single year passed by the argument &rsquo;-year&rsquo; (see <a href="args.html">Arguments</a>).
</p>
<div id="outline-container-org30869bd" class="outline-2">
......@@ -364,8 +360,7 @@ Processed file are <code>SST_processed_[date].nc</code>, original files are to b
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Clément Haëck</p>
<p class="date">Created: 2022-01-06 jeu. 13:48</p>
<a href=index.html>Index</a>
</div>
</body>
</html>
#+TITLE: Workflow
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="stylesheet.css"/>
[[file:index.org][Index]]
This describes the important scripts, the order and the manner they should be executed to obtain results.
Most scripts work on a single year passed by the argument '-year' (see [[file:args.org][Args]]).
Most scripts work on a single year passed by the argument '-year' (see [[file:args.org][Arguments]]).
* Python scripts execution
Most of the script are python. The packages must be defined, see [[file:setup.org::Requirements][Setup::Requirements]]. I recommend an anaconda environment.
......@@ -62,3 +61,12 @@ Processed file are ~SST_processed_[date].nc~, original files are to be deleted m
#+begin_src bash
year=2007; echo "bash DIR/Download/process_ostia_sst.py $year" | qsub -N process_sst_$year -q short
#+end_src
* Computing HI
* Computing Climatology
* Using Histograms
why hists
** Computing histograms
** Extract values
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