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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 512dbb367b2d1501c30ac13c1b597739
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_sources/api.rst.txt b/docs/build/html/_sources/api.rst.txt
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+.. autosummary::
+ :toctree: generated
+
+ dartwrf
+
diff --git a/docs/build/html/_sources/example.rst.txt b/docs/build/html/_sources/example.rst.txt
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+
+
+## Workflow
+#### Configure your experiment
+Define simulation specific variables in [`config/cfg.py`](https://github.com/lkugler/DART-WRF/blob/master/config/cfg.py).
+Define paths for python, ncks, etc. in [`config/clusters.py`](https://github.com/lkugler/DART-WRF/blob/master/config/clusters.py).
+Dependencies are `numpy, pandas, scipy, xarray, netCDF4`. Install non-standard packages with `pip install docopt slurmpy --user`.
+Workflow is defined using meta-routines (functions) like `run_ENS` which are defined in `scheduler.py`.
+
+#### Prepare initial conditions (from input_sounding)
+1) Define starting time:
+`begin = dt.datetime(2008, 7, 30, 6)`
+2) WRF needs directories with certain files:
+`id = prepare_WRFrundir(begin)`
+3) Create 3D initial conditions from input_sounding etc.:
+`id = run_ideal(depends_on=id)`
+
+### Run free forecast
+Let's say you want to run a free forecast starting at 6z, which you want to use as prior for an assimilation at 9z. Then you need can use the above defined 3 steps to create initial conditions.
+Then you can run an ensemble forecast using:
+```
+id = run_ENS(begin=begin, # start integration from here
+ end=end, # integrate until here
+ input_is_restart=False,
+ output_restart_interval=(end-begin).total_seconds()/60,
+ depends_on=id)
+```
+where `begin` & `end` are `dt.datetime` objects.
+
+### Assimilation experiment
+#### Assimilate
+To assimilate observations at dt.datetime `time` use this command:
+
+`id = assimilate(time, prior_init_time, prior_valid_time, prior_path_exp, depends_on=id)`
+
+#### Update initial conditions from Data Assimilation
+In order to continue after assimilation you need the posterior = prior (1) + increments (2)
+
+1. Set prior with this function:
+
+`id = prepare_IC_from_prior(prior_path_exp, prior_init_time, prior_valid_time, depends_on=id)`
+
+where path is `str`, times are `dt.datetime`.
+
+2. To update the model state with assimilation increments, you need to update the WRF restart files by running
+
+`id = update_IC_from_DA(time, depends_on=id)`
+
+After this, the wrfrst files are updated with assimilation increments (filter_restart) and copied to the WRF's run directories so you can continue to run the ENS after assimilation using
+
+```
+id = run_ENS(begin=time, # start integration from here
+ end=time + timedelta_integrate, # integrate until here
+ restart_path=cluster.archivedir+prior_init_time.strftime('/%Y-%m-%d_%H:%M/'),
+ output_restart_interval=timedelta_btw_assim.total_seconds()/60,
+ depends_on=id)
+```
+where times are `dt.datetime`; `timedelta` variables are `dt.timedelta`.
+
+### Examples
+[`scheduler.py`](https://github.com/lkugler/DART-WRF/blob/master/scheduler.py)
+[`generate_free.py`](https://github.com/lkugler/DART-WRF/blob/master/generate_free.py)
+
+## Finally
+
+### SLURM submissions
+`scheduler.py` submits jobs into the SLURM queue with dependencies, so that SLURM starts the jobs itself as soon as resources are available. Most jobs need only one node, but model integration is done in a SLURM job array across e.g. 10 nodes:
+```
+$ squeue -u `whoami` --sort=i
+ JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
+ 1710274 mem_0384 prepwrfr lkugler PD 0:00 1 (Priority)
+ 1710275 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+ 1710276 mem_0384 Assim-42 lkugler PD 0:00 1 (Dependency)
+ 1710277 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+ 1710278 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
+ 1710279 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)
+ 1710280_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)
+ 1710281 mem_0384 pRTTOV-6 lkugler PD 0:00 1 (Dependency)
+ 1710282 mem_0384 Assim-3a lkugler PD 0:00 1 (Dependency)
+ 1710283 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+ 1710284 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
+ 1710285 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)
+ 1710286_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)
+ 1710287 mem_0384 pRTTOV-7 lkugler PD 0:00 1 (Dependency)
+```
+
+### Easily switch between clusters
+Define cluster specific variables in `config/clusters.py `:
+```python
+
+clusterA = ClusterConfig()
+clusterA.name = 'vsc'
+clusterA.userdir = '/home/pathA/myuser/'
+...
+clusterB = ClusterConfig()
+clusterB.name = 'jet'
+clusterB.userdir = '/home/pathB/myuser/'
+```
+
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
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+Welcome to the DART-WRF documentation!
+===================================
+
+DART-WRF is a Python package to run an Ensemble Data Assimilation system with the software packages DART and WRF.
+
+- Why should I use it?
+ - It's pythonic: see what it does at first glance, modular, flexible
+ - It handles dependencies using SLURM without '`sleep` loops in the bash script'.
+Functions return a SLURM ID which can be used to trigger the start of another function (interface by [brentp/slurmpy](https://github.com/brentp/slurmpy)).
+
+- How does it work?
+ - There are two kinds of code/scripts: One that is run immediately and one that is run later on.
+ - The first one instructs the cluster (SLURM) to do the things you tell it - in the right order - using the right input.
+ - The latter kind of code actually does the things. Its code is not executed right away, but when there are resources assigned to you by SLURM.
+
+- Can I use it for real weather?
+ - Yes, but you need to [convert your observations into DART format.](https://docs.dart.ucar.edu)
+
+
+
+Contents
+--------
+
+.. toctree::
+
+ usage
+ api
+ docs/source/example
+
diff --git a/docs/build/html/_sources/index2.rst.txt b/docs/build/html/_sources/index2.rst.txt
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index 0000000000000000000000000000000000000000..993e6a3d7d8874f0d3c9ad84933439de14a57f7c
--- /dev/null
+++ b/docs/build/html/_sources/index2.rst.txt
@@ -0,0 +1,20 @@
+.. DART-WRF documentation master file, created by
+ sphinx-quickstart on Fri Feb 17 17:22:54 2023.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to DART-WRF's documentation!
+====================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
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+
+ .footer {
+ width: auto;
+ }
+
+ .github {
+ display: none;
+ }
+}
+
+
+/* misc. */
+
+.revsys-inline {
+ display: none!important;
+}
+
+/* Make nested-list/multi-paragraph items look better in Releases changelog
+ * pages. Without this, docutils' magical list fuckery causes inconsistent
+ * formatting between different release sub-lists.
+ */
+div#changelog > div.section > ul > li > p:only-child {
+ margin-bottom: 0;
+}
+
+/* Hide fugly table cell borders in ..bibliography:: directive output */
+table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
+ border: none;
+ /* Below needed in some edge cases; if not applied, bottom shadows appear */
+ -moz-box-shadow: none;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+
+
+/* relbar */
+
+.related {
+ line-height: 30px;
+ width: 100%;
+ font-size: 0.9rem;
+}
+
+.related.top {
+ border-bottom: 1px solid #EEE;
+ margin-bottom: 20px;
+}
+
+.related.bottom {
+ border-top: 1px solid #EEE;
+}
+
+.related ul {
+ padding: 0;
+ margin: 0;
+ list-style: none;
+}
+
+.related li {
+ display: inline;
+}
+
+nav#rellinks {
+ float: right;
+}
+
+nav#rellinks li+li:before {
+ content: "|";
+}
+
+nav#breadcrumbs li+li:before {
+ content: "\00BB";
+}
+
+/* Hide certain items when printing */
+@media print {
+ div.related {
+ display: none;
+ }
+}
\ No newline at end of file
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
new file mode 100644
index 0000000000000000000000000000000000000000..7577acb1ad176e3f58c15ddf9bf1f73525dfe7ed
--- /dev/null
+++ b/docs/build/html/_static/basic.css
@@ -0,0 +1,903 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2023 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: 230px;
+ 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: 360px;
+ 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;
+}
+
+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;
+}
+
+nav.contents,
+aside.topic,
+div.admonition, div.topic, blockquote {
+ clear: left;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
+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,
+nav.contents > :last-child,
+aside.topic > :last-child,
+div.topic > :last-child,
+div.admonition > :last-child {
+ margin-bottom: 0;
+}
+
+div.sidebar::after,
+aside.sidebar::after,
+nav.contents::after,
+aside.topic::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;
+}
+
+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;
+}
+
+aside.footnote > span,
+div.citation > span {
+ float: left;
+}
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+ padding-right: 0.5em;
+}
+aside.footnote > p {
+ margin-left: 2em;
+}
+div.citation > p {
+ margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
+ margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type: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 > 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
diff --git a/docs/build/html/_static/custom.css b/docs/build/html/_static/custom.css
new file mode 100644
index 0000000000000000000000000000000000000000..2a924f1d6a8bc930c5296bdb2d5c2d3e39b04a1c
--- /dev/null
+++ b/docs/build/html/_static/custom.css
@@ -0,0 +1 @@
+/* This file intentionally left blank. */
diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
new file mode 100644
index 0000000000000000000000000000000000000000..d06a71d7518041301a303697d2a3c372648eb7bf
--- /dev/null
+++ b/docs/build/html/_static/doctools.js
@@ -0,0 +1,156 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Base JavaScript utilities for all Sphinx HTML documentation.
+ *
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+"use strict";
+
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+ "TEXTAREA",
+ "INPUT",
+ "SELECT",
+ "BUTTON",
+]);
+
+const _ready = (callback) => {
+ if (document.readyState !== "loading") {
+ callback();
+ } else {
+ document.addEventListener("DOMContentLoaded", callback);
+ }
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const Documentation = {
+ init: () => {
+ Documentation.initDomainIndexTable();
+ Documentation.initOnKeyListeners();
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS: {},
+ PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
+ LOCALE: "unknown",
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext: (string) => {
+ const translated = Documentation.TRANSLATIONS[string];
+ switch (typeof translated) {
+ case "undefined":
+ return string; // no translation
+ case "string":
+ return translated; // translation exists
+ default:
+ return translated[0]; // (singular, plural) translation tuple exists
+ }
+ },
+
+ ngettext: (singular, plural, n) => {
+ const translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated !== "undefined")
+ return translated[Documentation.PLURAL_EXPR(n)];
+ return n === 1 ? singular : plural;
+ },
+
+ addTranslations: (catalog) => {
+ Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+ Documentation.PLURAL_EXPR = new Function(
+ "n",
+ `return (${catalog.plural_expr})`
+ );
+ Documentation.LOCALE = catalog.locale;
+ },
+
+ /**
+ * helper function to focus on search bar
+ */
+ focusSearchBar: () => {
+ document.querySelectorAll("input[name=q]")[0]?.focus();
+ },
+
+ /**
+ * Initialise the domain index toggle buttons
+ */
+ initDomainIndexTable: () => {
+ const toggler = (el) => {
+ const idNumber = el.id.substr(7);
+ const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+ if (el.src.substr(-9) === "minus.png") {
+ el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+ toggledRows.forEach((el) => (el.style.display = "none"));
+ } else {
+ el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+ toggledRows.forEach((el) => (el.style.display = ""));
+ }
+ };
+
+ const togglerElements = document.querySelectorAll("img.toggler");
+ togglerElements.forEach((el) =>
+ el.addEventListener("click", (event) => toggler(event.currentTarget))
+ );
+ togglerElements.forEach((el) => (el.style.display = ""));
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+ },
+
+ initOnKeyListeners: () => {
+ // only install a listener if it is really needed
+ if (
+ !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+ !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+ )
+ return;
+
+ document.addEventListener("keydown", (event) => {
+ // bail for input elements
+ if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+ // bail with special keys
+ if (event.altKey || event.ctrlKey || event.metaKey) return;
+
+ if (!event.shiftKey) {
+ switch (event.key) {
+ case "ArrowLeft":
+ if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+ const prevLink = document.querySelector('link[rel="prev"]');
+ if (prevLink && prevLink.href) {
+ window.location.href = prevLink.href;
+ event.preventDefault();
+ }
+ break;
+ case "ArrowRight":
+ if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+ const nextLink = document.querySelector('link[rel="next"]');
+ if (nextLink && nextLink.href) {
+ window.location.href = nextLink.href;
+ event.preventDefault();
+ }
+ break;
+ }
+ }
+
+ // some keyboard layouts may need Shift to get /
+ switch (event.key) {
+ case "/":
+ if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+ Documentation.focusSearchBar();
+ event.preventDefault();
+ }
+ });
+ },
+};
+
+// quick alias for translations
+const _ = Documentation.gettext;
+
+_ready(Documentation.init);
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
new file mode 100644
index 0000000000000000000000000000000000000000..3e3a2bb802753f8a2a3f47c757a88324b6914ee1
--- /dev/null
+++ b/docs/build/html/_static/documentation_options.js
@@ -0,0 +1,14 @@
+var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+ VERSION: '2023.2.17',
+ LANGUAGE: 'en',
+ COLLAPSE_INDEX: false,
+ BUILDER: 'html',
+ FILE_SUFFIX: '.html',
+ LINK_SUFFIX: '.html',
+ HAS_SOURCE: true,
+ SOURCELINK_SUFFIX: '.txt',
+ NAVIGATION_WITH_KEYS: false,
+ SHOW_SEARCH_SUMMARY: true,
+ ENABLE_SEARCH_SHORTCUTS: true,
+};
\ No newline at end of file
diff --git a/docs/build/html/_static/file.png b/docs/build/html/_static/file.png
new file mode 100644
index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3
Binary files /dev/null and b/docs/build/html/_static/file.png differ
diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
new file mode 100644
index 0000000000000000000000000000000000000000..250f5665fa64b70c822190199b3b804b10f8b9d8
--- /dev/null
+++ b/docs/build/html/_static/language_data.js
@@ -0,0 +1,199 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
+
+
+/* Non-minified version is copied as a separate JS file, is available */
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
diff --git a/docs/build/html/_static/minus.png b/docs/build/html/_static/minus.png
new file mode 100644
index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d
Binary files /dev/null and b/docs/build/html/_static/minus.png differ
diff --git a/docs/build/html/_static/plus.png b/docs/build/html/_static/plus.png
new file mode 100644
index 0000000000000000000000000000000000000000..7107cec93a979b9a5f64843235a16651d563ce2d
Binary files /dev/null and b/docs/build/html/_static/plus.png differ
diff --git a/docs/build/html/_static/pygments.css b/docs/build/html/_static/pygments.css
new file mode 100644
index 0000000000000000000000000000000000000000..9abe04ba552e93102be60b10311b288fbc57ab51
--- /dev/null
+++ b/docs/build/html/_static/pygments.css
@@ -0,0 +1,83 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #f8f8f8; }
+.highlight .c { color: #8f5902; font-style: italic } /* Comment */
+.highlight .err { color: #a40000; border: 1px solid #ef2929 } /* Error */
+.highlight .g { color: #000000 } /* Generic */
+.highlight .k { color: #004461; font-weight: bold } /* Keyword */
+.highlight .l { color: #000000 } /* Literal */
+.highlight .n { color: #000000 } /* Name */
+.highlight .o { color: #582800 } /* Operator */
+.highlight .x { color: #000000 } /* Other */
+.highlight .p { color: #000000; font-weight: bold } /* Punctuation */
+.highlight .ch { color: #8f5902; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #8f5902; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #8f5902 } /* Comment.Preproc */
+.highlight .cpf { color: #8f5902; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #8f5902; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #8f5902; font-style: italic } /* Comment.Special */
+.highlight .gd { color: #a40000 } /* Generic.Deleted */
+.highlight .ge { color: #000000; font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #ef2929 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #888888 } /* Generic.Output */
+.highlight .gp { color: #745334 } /* Generic.Prompt */
+.highlight .gs { color: #000000; font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #a40000; font-weight: bold } /* Generic.Traceback */
+.highlight .kc { color: #004461; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #004461; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #004461; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #004461; font-weight: bold } /* Keyword.Pseudo */
+.highlight .kr { color: #004461; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #004461; font-weight: bold } /* Keyword.Type */
+.highlight .ld { color: #000000 } /* Literal.Date */
+.highlight .m { color: #990000 } /* Literal.Number */
+.highlight .s { color: #4e9a06 } /* Literal.String */
+.highlight .na { color: #c4a000 } /* Name.Attribute */
+.highlight .nb { color: #004461 } /* Name.Builtin */
+.highlight .nc { color: #000000 } /* Name.Class */
+.highlight .no { color: #000000 } /* Name.Constant */
+.highlight .nd { color: #888888 } /* Name.Decorator */
+.highlight .ni { color: #ce5c00 } /* Name.Entity */
+.highlight .ne { color: #cc0000; font-weight: bold } /* Name.Exception */
+.highlight .nf { color: #000000 } /* Name.Function */
+.highlight .nl { color: #f57900 } /* Name.Label */
+.highlight .nn { color: #000000 } /* Name.Namespace */
+.highlight .nx { color: #000000 } /* Name.Other */
+.highlight .py { color: #000000 } /* Name.Property */
+.highlight .nt { color: #004461; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #000000 } /* Name.Variable */
+.highlight .ow { color: #004461; font-weight: bold } /* Operator.Word */
+.highlight .pm { color: #000000; font-weight: bold } /* Punctuation.Marker */
+.highlight .w { color: #f8f8f8; text-decoration: underline } /* Text.Whitespace */
+.highlight .mb { color: #990000 } /* Literal.Number.Bin */
+.highlight .mf { color: #990000 } /* Literal.Number.Float */
+.highlight .mh { color: #990000 } /* Literal.Number.Hex */
+.highlight .mi { color: #990000 } /* Literal.Number.Integer */
+.highlight .mo { color: #990000 } /* Literal.Number.Oct */
+.highlight .sa { color: #4e9a06 } /* Literal.String.Affix */
+.highlight .sb { color: #4e9a06 } /* Literal.String.Backtick */
+.highlight .sc { color: #4e9a06 } /* Literal.String.Char */
+.highlight .dl { color: #4e9a06 } /* Literal.String.Delimiter */
+.highlight .sd { color: #8f5902; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4e9a06 } /* Literal.String.Double */
+.highlight .se { color: #4e9a06 } /* Literal.String.Escape */
+.highlight .sh { color: #4e9a06 } /* Literal.String.Heredoc */
+.highlight .si { color: #4e9a06 } /* Literal.String.Interpol */
+.highlight .sx { color: #4e9a06 } /* Literal.String.Other */
+.highlight .sr { color: #4e9a06 } /* Literal.String.Regex */
+.highlight .s1 { color: #4e9a06 } /* Literal.String.Single */
+.highlight .ss { color: #4e9a06 } /* Literal.String.Symbol */
+.highlight .bp { color: #3465a4 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #000000 } /* Name.Function.Magic */
+.highlight .vc { color: #000000 } /* Name.Variable.Class */
+.highlight .vg { color: #000000 } /* Name.Variable.Global */
+.highlight .vi { color: #000000 } /* Name.Variable.Instance */
+.highlight .vm { color: #000000 } /* Name.Variable.Magic */
+.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
\ No newline at end of file
diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js
new file mode 100644
index 0000000000000000000000000000000000000000..97d56a74d8207ec36a96a5e24f4a4b42dd51f6b2
--- /dev/null
+++ b/docs/build/html/_static/searchtools.js
@@ -0,0 +1,566 @@
+/*
+ * searchtools.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for the full-text search.
+ *
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+"use strict";
+
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
+ var Scorer = {
+ // Implement the following function to further tweak the score for each result
+ // The function takes a result array [docname, title, anchor, descr, score, filename]
+ // and returns the new score.
+ /*
+ score: result => {
+ const [docname, title, anchor, descr, score, filename] = result
+ return score
+ },
+ */
+
+ // query matches the full name of an object
+ objNameMatch: 11,
+ // or matches in the last dotted part of the object name
+ objPartialMatch: 6,
+ // Additive scores depending on the priority of the object
+ objPrio: {
+ 0: 15, // used to be importantResults
+ 1: 5, // used to be objectResults
+ 2: -5, // used to be unimportantResults
+ },
+ // Used when the priority is not in the mapping.
+ objPrioDefault: 0,
+
+ // query found in title
+ title: 15,
+ partialTitle: 7,
+ // query found in terms
+ term: 5,
+ partialTerm: 2,
+ };
+}
+
+const _removeChildren = (element) => {
+ while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+ string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, searchTerms) => {
+ const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+ const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
+ const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+ const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+ const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+
+ const [docName, title, anchor, descr, score, _filename] = item;
+
+ let listItem = document.createElement("li");
+ let requestUrl;
+ let linkUrl;
+ if (docBuilder === "dirhtml") {
+ // dirhtml builder
+ let dirname = docName + "/";
+ if (dirname.match(/\/index\/$/))
+ dirname = dirname.substring(0, dirname.length - 6);
+ else if (dirname === "index/") dirname = "";
+ requestUrl = docUrlRoot + dirname;
+ linkUrl = requestUrl;
+ } else {
+ // normal html builders
+ requestUrl = docUrlRoot + docName + docFileSuffix;
+ linkUrl = docName + docLinkSuffix;
+ }
+ let linkEl = listItem.appendChild(document.createElement("a"));
+ linkEl.href = linkUrl + anchor;
+ linkEl.dataset.score = score;
+ linkEl.innerHTML = title;
+ if (descr)
+ listItem.appendChild(document.createElement("span")).innerHTML =
+ " (" + descr + ")";
+ else if (showSearchSummary)
+ fetch(requestUrl)
+ .then((responseData) => responseData.text())
+ .then((data) => {
+ if (data)
+ listItem.appendChild(
+ Search.makeSearchSummary(data, searchTerms)
+ );
+ });
+ Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+ Search.stopPulse();
+ Search.title.innerText = _("Search Results");
+ if (!resultCount)
+ Search.status.innerText = Documentation.gettext(
+ "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+ );
+ else
+ Search.status.innerText = _(
+ `Search finished, found ${resultCount} page(s) matching the search query.`
+ );
+};
+const _displayNextItem = (
+ results,
+ resultCount,
+ searchTerms
+) => {
+ // results left, load the summary and display it
+ // this is intended to be dynamic (don't sub resultsCount)
+ if (results.length) {
+ _displayItem(results.pop(), searchTerms);
+ setTimeout(
+ () => _displayNextItem(results, resultCount, searchTerms),
+ 5
+ );
+ }
+ // search finished, update title and status message
+ else _finishSearch(resultCount);
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+ var splitQuery = (query) => query
+ .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+ .filter(term => term) // remove remaining empty strings
+}
+
+/**
+ * Search Module
+ */
+const Search = {
+ _index: null,
+ _queued_query: null,
+ _pulse_status: -1,
+
+ htmlToText: (htmlString) => {
+ const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
+ htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+ const docContent = htmlElement.querySelector('[role="main"]');
+ if (docContent !== undefined) return docContent.textContent;
+ console.warn(
+ "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+ );
+ return "";
+ },
+
+ init: () => {
+ const query = new URLSearchParams(window.location.search).get("q");
+ document
+ .querySelectorAll('input[name="q"]')
+ .forEach((el) => (el.value = query));
+ if (query) Search.performSearch(query);
+ },
+
+ loadIndex: (url) =>
+ (document.body.appendChild(document.createElement("script")).src = url),
+
+ setIndex: (index) => {
+ Search._index = index;
+ if (Search._queued_query !== null) {
+ const query = Search._queued_query;
+ Search._queued_query = null;
+ Search.query(query);
+ }
+ },
+
+ hasIndex: () => Search._index !== null,
+
+ deferQuery: (query) => (Search._queued_query = query),
+
+ stopPulse: () => (Search._pulse_status = -1),
+
+ startPulse: () => {
+ if (Search._pulse_status >= 0) return;
+
+ const pulse = () => {
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ Search.dots.innerText = ".".repeat(Search._pulse_status);
+ if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+ };
+ pulse();
+ },
+
+ /**
+ * perform a search for something (or wait until index is loaded)
+ */
+ performSearch: (query) => {
+ // create the required interface elements
+ const searchText = document.createElement("h2");
+ searchText.textContent = _("Searching");
+ const searchSummary = document.createElement("p");
+ searchSummary.classList.add("search-summary");
+ searchSummary.innerText = "";
+ const searchList = document.createElement("ul");
+ searchList.classList.add("search");
+
+ const out = document.getElementById("search-results");
+ Search.title = out.appendChild(searchText);
+ Search.dots = Search.title.appendChild(document.createElement("span"));
+ Search.status = out.appendChild(searchSummary);
+ Search.output = out.appendChild(searchList);
+
+ const searchProgress = document.getElementById("search-progress");
+ // Some themes don't use the search progress node
+ if (searchProgress) {
+ searchProgress.innerText = _("Preparing search...");
+ }
+ Search.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (Search.hasIndex()) Search.query(query);
+ else Search.deferQuery(query);
+ },
+
+ /**
+ * execute search (requires search index to be loaded)
+ */
+ query: (query) => {
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const titles = Search._index.titles;
+ const allTitles = Search._index.alltitles;
+ const indexEntries = Search._index.indexentries;
+
+ // stem the search terms and add them to the correct list
+ const stemmer = new Stemmer();
+ const searchTerms = new Set();
+ const excludedTerms = new Set();
+ const highlightTerms = new Set();
+ const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+ splitQuery(query.trim()).forEach((queryTerm) => {
+ const queryTermLower = queryTerm.toLowerCase();
+
+ // maybe skip this "word"
+ // stopwords array is from language_data.js
+ if (
+ stopwords.indexOf(queryTermLower) !== -1 ||
+ queryTerm.match(/^\d+$/)
+ )
+ return;
+
+ // stem the word
+ let word = stemmer.stemWord(queryTermLower);
+ // select the correct list
+ if (word[0] === "-") excludedTerms.add(word.substr(1));
+ else {
+ searchTerms.add(word);
+ highlightTerms.add(queryTermLower);
+ }
+ });
+
+ if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js
+ localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+ }
+
+ // console.debug("SEARCH: searching for:");
+ // console.info("required: ", [...searchTerms]);
+ // console.info("excluded: ", [...excludedTerms]);
+
+ // array of [docname, title, anchor, descr, score, filename]
+ let results = [];
+ _removeChildren(document.getElementById("search-progress"));
+
+ const queryLower = query.toLowerCase();
+ for (const [title, foundTitles] of Object.entries(allTitles)) {
+ if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+ for (const [file, id] of foundTitles) {
+ let score = Math.round(100 * queryLower.length / title.length)
+ results.push([
+ docNames[file],
+ titles[file] !== title ? `${titles[file]} > ${title}` : title,
+ id !== null ? "#" + id : "",
+ null,
+ score,
+ filenames[file],
+ ]);
+ }
+ }
+ }
+
+ // search for explicit entries in index directives
+ for (const [entry, foundEntries] of Object.entries(indexEntries)) {
+ if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
+ for (const [file, id] of foundEntries) {
+ let score = Math.round(100 * queryLower.length / entry.length)
+ results.push([
+ docNames[file],
+ titles[file],
+ id ? "#" + id : "",
+ null,
+ score,
+ filenames[file],
+ ]);
+ }
+ }
+ }
+
+ // lookup as object
+ objectTerms.forEach((term) =>
+ results.push(...Search.performObjectSearch(term, objectTerms))
+ );
+
+ // lookup as search terms in fulltext
+ results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+
+ // let the scorer override scores with a custom scoring function
+ if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
+
+ // now sort the results by score (in opposite order of appearance, since the
+ // display function below uses pop() to retrieve items) and then
+ // alphabetically
+ results.sort((a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
+ // same score: sort alphabetically
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+ }
+ return leftScore > rightScore ? 1 : -1;
+ });
+
+ // remove duplicate search results
+ // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+ let seen = new Set();
+ results = results.reverse().reduce((acc, result) => {
+ let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+ if (!seen.has(resultStr)) {
+ acc.push(result);
+ seen.add(resultStr);
+ }
+ return acc;
+ }, []);
+
+ results = results.reverse();
+
+ // for debugging
+ //Search.lastresults = results.slice(); // a copy
+ // console.info("search results:", Search.lastresults);
+
+ // print the results
+ _displayNextItem(results, results.length, searchTerms);
+ },
+
+ /**
+ * search for object names
+ */
+ performObjectSearch: (object, objectTerms) => {
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const objects = Search._index.objects;
+ const objNames = Search._index.objnames;
+ const titles = Search._index.titles;
+
+ const results = [];
+
+ const objectSearchCallback = (prefix, match) => {
+ const name = match[4]
+ const fullname = (prefix ? prefix + "." : "") + name;
+ const fullnameLower = fullname.toLowerCase();
+ if (fullnameLower.indexOf(object) < 0) return;
+
+ let score = 0;
+ const parts = fullnameLower.split(".");
+
+ // check for different match types: exact matches of full name or
+ // "last name" (i.e. last dotted part)
+ if (fullnameLower === object || parts.slice(-1)[0] === object)
+ score += Scorer.objNameMatch;
+ else if (parts.slice(-1)[0].indexOf(object) > -1)
+ score += Scorer.objPartialMatch; // matches in last name
+
+ const objName = objNames[match[1]][2];
+ const title = titles[match[0]];
+
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ const otherTerms = new Set(objectTerms);
+ otherTerms.delete(object);
+ if (otherTerms.size > 0) {
+ const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+ if (
+ [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+ )
+ return;
+ }
+
+ let anchor = match[3];
+ if (anchor === "") anchor = fullname;
+ else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+ const descr = objName + _(", in ") + title;
+
+ // add custom score for some objects according to scorer
+ if (Scorer.objPrio.hasOwnProperty(match[2]))
+ score += Scorer.objPrio[match[2]];
+ else score += Scorer.objPrioDefault;
+
+ results.push([
+ docNames[match[0]],
+ fullname,
+ "#" + anchor,
+ descr,
+ score,
+ filenames[match[0]],
+ ]);
+ };
+ Object.keys(objects).forEach((prefix) =>
+ objects[prefix].forEach((array) =>
+ objectSearchCallback(prefix, array)
+ )
+ );
+ return results;
+ },
+
+ /**
+ * search for full-text terms in the index
+ */
+ performTermsSearch: (searchTerms, excludedTerms) => {
+ // prepare search
+ const terms = Search._index.terms;
+ const titleTerms = Search._index.titleterms;
+ const filenames = Search._index.filenames;
+ const docNames = Search._index.docnames;
+ const titles = Search._index.titles;
+
+ const scoreMap = new Map();
+ const fileMap = new Map();
+
+ // perform the search on the required terms
+ searchTerms.forEach((word) => {
+ const files = [];
+ const arr = [
+ { files: terms[word], score: Scorer.term },
+ { files: titleTerms[word], score: Scorer.title },
+ ];
+ // add support for partial matches
+ if (word.length > 2) {
+ const escapedWord = _escapeRegExp(word);
+ Object.keys(terms).forEach((term) => {
+ if (term.match(escapedWord) && !terms[word])
+ arr.push({ files: terms[term], score: Scorer.partialTerm });
+ });
+ Object.keys(titleTerms).forEach((term) => {
+ if (term.match(escapedWord) && !titleTerms[word])
+ arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
+ });
+ }
+
+ // no match but word was a required one
+ if (arr.every((record) => record.files === undefined)) return;
+
+ // found search word in contents
+ arr.forEach((record) => {
+ if (record.files === undefined) return;
+
+ let recordFiles = record.files;
+ if (recordFiles.length === undefined) recordFiles = [recordFiles];
+ files.push(...recordFiles);
+
+ // set score for the word in each file
+ recordFiles.forEach((file) => {
+ if (!scoreMap.has(file)) scoreMap.set(file, {});
+ scoreMap.get(file)[word] = record.score;
+ });
+ });
+
+ // create the mapping
+ files.forEach((file) => {
+ if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
+ fileMap.get(file).push(word);
+ else fileMap.set(file, [word]);
+ });
+ });
+
+ // now check if the files don't contain excluded terms
+ const results = [];
+ for (const [file, wordList] of fileMap) {
+ // check if all requirements are matched
+
+ // as search terms with length < 3 are discarded
+ const filteredTermCount = [...searchTerms].filter(
+ (term) => term.length > 2
+ ).length;
+ if (
+ wordList.length !== searchTerms.size &&
+ wordList.length !== filteredTermCount
+ )
+ continue;
+
+ // ensure that none of the excluded terms is in the search result
+ if (
+ [...excludedTerms].some(
+ (term) =>
+ terms[term] === file ||
+ titleTerms[term] === file ||
+ (terms[term] || []).includes(file) ||
+ (titleTerms[term] || []).includes(file)
+ )
+ )
+ break;
+
+ // select one (max) score for the file.
+ const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+ // add result to the result list
+ results.push([
+ docNames[file],
+ titles[file],
+ "",
+ null,
+ score,
+ filenames[file],
+ ]);
+ }
+ return results;
+ },
+
+ /**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words.
+ */
+ makeSearchSummary: (htmlText, keywords) => {
+ const text = Search.htmlToText(htmlText);
+ if (text === "") return null;
+
+ const textLower = text.toLowerCase();
+ const actualStartPosition = [...keywords]
+ .map((k) => textLower.indexOf(k.toLowerCase()))
+ .filter((i) => i > -1)
+ .slice(-1)[0];
+ const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+ const top = startWithContext === 0 ? "" : "...";
+ const tail = startWithContext + 240 < text.length ? "..." : "";
+
+ let summary = document.createElement("p");
+ summary.classList.add("context");
+ summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+ return summary;
+ },
+};
+
+_ready(Search.init);
diff --git a/docs/build/html/_static/sphinx_highlight.js b/docs/build/html/_static/sphinx_highlight.js
new file mode 100644
index 0000000000000000000000000000000000000000..aae669d7ea6b1dc6edcb5c651f5d095f7a2dc6e6
--- /dev/null
+++ b/docs/build/html/_static/sphinx_highlight.js
@@ -0,0 +1,144 @@
+/* Highlighting utilities for Sphinx HTML documentation. */
+"use strict";
+
+const SPHINX_HIGHLIGHT_ENABLED = true
+
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+ if (node.nodeType === Node.TEXT_NODE) {
+ const val = node.nodeValue;
+ const parent = node.parentNode;
+ const pos = val.toLowerCase().indexOf(text);
+ if (
+ pos >= 0 &&
+ !parent.classList.contains(className) &&
+ !parent.classList.contains("nohighlight")
+ ) {
+ let span;
+
+ const closestNode = parent.closest("body, svg, foreignObject");
+ const isInSVG = closestNode && closestNode.matches("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.classList.add(className);
+ }
+
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ parent.insertBefore(
+ span,
+ parent.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling
+ )
+ );
+ node.nodeValue = val.substr(0, pos);
+
+ if (isInSVG) {
+ const rect = document.createElementNS(
+ "http://www.w3.org/2000/svg",
+ "rect"
+ );
+ const bbox = parent.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute("class", className);
+ addItems.push({ parent: parent, target: rect });
+ }
+ }
+ } else if (node.matches && !node.matches("button, select, textarea")) {
+ node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+ }
+};
+const _highlightText = (thisNode, text, className) => {
+ let addItems = [];
+ _highlight(thisNode, addItems, text, className);
+ addItems.forEach((obj) =>
+ obj.parent.insertAdjacentElement("beforebegin", obj.target)
+ );
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const SphinxHighlight = {
+
+ /**
+ * highlight the search words provided in localstorage in the text
+ */
+ highlightSearchWords: () => {
+ if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight
+
+ // get and clear terms from localstorage
+ const url = new URL(window.location);
+ const highlight =
+ localStorage.getItem("sphinx_highlight_terms")
+ || url.searchParams.get("highlight")
+ || "";
+ localStorage.removeItem("sphinx_highlight_terms")
+ url.searchParams.delete("highlight");
+ window.history.replaceState({}, "", url);
+
+ // get individual terms from highlight string
+ const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+ if (terms.length === 0) return; // nothing to do
+
+ // There should never be more than one element matching "div.body"
+ const divBody = document.querySelectorAll("div.body");
+ const body = divBody.length ? divBody[0] : document.querySelector("body");
+ window.setTimeout(() => {
+ terms.forEach((term) => _highlightText(body, term, "highlighted"));
+ }, 10);
+
+ const searchBox = document.getElementById("searchbox");
+ if (searchBox === null) return;
+ searchBox.appendChild(
+ document
+ .createRange()
+ .createContextualFragment(
+ '<p class="highlight-link">' +
+ '<a href="javascript:SphinxHighlight.hideSearchWords()">' +
+ _("Hide Search Matches") +
+ "</a></p>"
+ )
+ );
+ },
+
+ /**
+ * helper function to hide the search marks again
+ */
+ hideSearchWords: () => {
+ document
+ .querySelectorAll("#searchbox .highlight-link")
+ .forEach((el) => el.remove());
+ document
+ .querySelectorAll("span.highlighted")
+ .forEach((el) => el.classList.remove("highlighted"));
+ localStorage.removeItem("sphinx_highlight_terms")
+ },
+
+ initEscapeListener: () => {
+ // only install a listener if it is really needed
+ if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return;
+
+ document.addEventListener("keydown", (event) => {
+ // bail for input elements
+ if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+ // bail with special keys
+ if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return;
+ if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) {
+ SphinxHighlight.hideSearchWords();
+ event.preventDefault();
+ }
+ });
+ },
+};
+
+_ready(SphinxHighlight.highlightSearchWords);
+_ready(SphinxHighlight.initEscapeListener);
diff --git a/docs/build/html/api.html b/docs/build/html/api.html
new file mode 100644
index 0000000000000000000000000000000000000000..70fc682d908edde44e739035c7a7aaa6843036ce
--- /dev/null
+++ b/docs/build/html/api.html
@@ -0,0 +1,97 @@
+
+<!DOCTYPE html>
+
+<html lang="en">
+ <head>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+
+ <title><no title> — DART-WRF 2023.2.17 documentation</title>
+ <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+ <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+ <script src="_static/doctools.js"></script>
+ <script src="_static/sphinx_highlight.js"></script>
+ <link rel="index" title="Index" href="genindex.html" />
+ <link rel="search" title="Search" href="search.html" />
+
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head><body>
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+
+
+ <div class="body" role="main">
+
+
+
+ </div>
+
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index2.html">DART-WRF</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index2.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
+ <form class="search" action="search.html" method="get">
+ <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+ <input type="submit" value="Go" />
+ </form>
+ </div>
+</div>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+
+
+
+
+
+
+
+
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2023, Lukas Kugler.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 6.1.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+
+ |
+ <a href="_sources/api.rst.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/docs/build/html/example.html b/docs/build/html/example.html
new file mode 100644
index 0000000000000000000000000000000000000000..1497caae0a274c73b3a501632cffd7615549c5cb
--- /dev/null
+++ b/docs/build/html/example.html
@@ -0,0 +1,192 @@
+
+<!DOCTYPE html>
+
+<html lang="en">
+ <head>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+
+ <title><no title> — DART-WRF 2023.2.17 documentation</title>
+ <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+ <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
+ <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+ <script src="_static/doctools.js"></script>
+ <script src="_static/sphinx_highlight.js"></script>
+ <link rel="index" title="Index" href="genindex.html" />
+ <link rel="search" title="Search" href="search.html" />
+
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head><body>
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+
+
+ <div class="body" role="main">
+
+ <p>## Workflow
+#### Configure your experiment
+Define simulation specific variables in [<cite>config/cfg.py</cite>](<a class="reference external" href="https://github.com/lkugler/DART-WRF/blob/master/config/cfg.py">https://github.com/lkugler/DART-WRF/blob/master/config/cfg.py</a>).
+Define paths for python, ncks, etc. in [<cite>config/clusters.py</cite>](<a class="reference external" href="https://github.com/lkugler/DART-WRF/blob/master/config/clusters.py">https://github.com/lkugler/DART-WRF/blob/master/config/clusters.py</a>).
+Dependencies are <cite>numpy, pandas, scipy, xarray, netCDF4</cite>. Install non-standard packages with <cite>pip install docopt slurmpy –user</cite>.
+Workflow is defined using meta-routines (functions) like <cite>run_ENS</cite> which are defined in <cite>scheduler.py</cite>.</p>
+<p>#### Prepare initial conditions (from input_sounding)
+1) Define starting time:
+<cite>begin = dt.datetime(2008, 7, 30, 6)</cite>
+2) WRF needs directories with certain files:
+<cite>id = prepare_WRFrundir(begin)</cite>
+3) Create 3D initial conditions from input_sounding etc.:
+<cite>id = run_ideal(depends_on=id)</cite></p>
+<p>### Run free forecast
+Let’s say you want to run a free forecast starting at 6z, which you want to use as prior for an assimilation at 9z. Then you need can use the above defined 3 steps to create initial conditions.
+Then you can run an ensemble forecast using:
+<a href="#id1"><span class="problematic" id="id2">``</span></a>`
+id = run_ENS(begin=begin, # start integration from here</p>
+<blockquote>
+<div><p>end=end, # integrate until here
+input_is_restart=False,
+output_restart_interval=(end-begin).total_seconds()/60,
+depends_on=id)</p>
+</div></blockquote>
+<p><a href="#id3"><span class="problematic" id="id4">``</span></a>`
+where <cite>begin</cite> & <cite>end</cite> are <cite>dt.datetime</cite> objects.</p>
+<p>### Assimilation experiment
+#### Assimilate
+To assimilate observations at dt.datetime <cite>time</cite> use this command:</p>
+<p><cite>id = assimilate(time, prior_init_time, prior_valid_time, prior_path_exp, depends_on=id)</cite></p>
+<p>#### Update initial conditions from Data Assimilation
+In order to continue after assimilation you need the posterior = prior (1) + increments (2)</p>
+<ol class="arabic simple">
+<li><p>Set prior with this function:</p></li>
+</ol>
+<p><cite>id = prepare_IC_from_prior(prior_path_exp, prior_init_time, prior_valid_time, depends_on=id)</cite></p>
+<p>where path is <cite>str</cite>, times are <cite>dt.datetime</cite>.</p>
+<ol class="arabic simple" start="2">
+<li><p>To update the model state with assimilation increments, you need to update the WRF restart files by running</p></li>
+</ol>
+<p><cite>id = update_IC_from_DA(time, depends_on=id)</cite></p>
+<p>After this, the wrfrst files are updated with assimilation increments (filter_restart) and copied to the WRF’s run directories so you can continue to run the ENS after assimilation using</p>
+<p><a href="#id5"><span class="problematic" id="id6">``</span></a>`
+id = run_ENS(begin=time, # start integration from here</p>
+<blockquote>
+<div><p>end=time + timedelta_integrate, # integrate until here
+restart_path=cluster.archivedir+prior_init_time.strftime(‘/%Y-%m-%d_%H:%M/’),
+output_restart_interval=timedelta_btw_assim.total_seconds()/60,
+depends_on=id)</p>
+</div></blockquote>
+<p><a href="#id7"><span class="problematic" id="id8">``</span></a>`
+where times are <cite>dt.datetime</cite>; <cite>timedelta</cite> variables are <cite>dt.timedelta</cite>.</p>
+<p>### Examples
+[<cite>scheduler.py</cite>](<a class="reference external" href="https://github.com/lkugler/DART-WRF/blob/master/scheduler.py">https://github.com/lkugler/DART-WRF/blob/master/scheduler.py</a>)
+[<cite>generate_free.py</cite>](<a class="reference external" href="https://github.com/lkugler/DART-WRF/blob/master/generate_free.py">https://github.com/lkugler/DART-WRF/blob/master/generate_free.py</a>)</p>
+<p>## Finally</p>
+<p>### SLURM submissions
+<cite>scheduler.py</cite> submits jobs into the SLURM queue with dependencies, so that SLURM starts the jobs itself as soon as resources are available. Most jobs need only one node, but model integration is done in a SLURM job array across e.g. 10 nodes:
+<a href="#id9"><span class="problematic" id="id10">``</span></a>`
+$ squeue -u <cite>whoami</cite> –sort=i</p>
+<blockquote>
+<div><blockquote>
+<div><blockquote>
+<div><p>JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)</p>
+</div></blockquote>
+<p>1710274 mem_0384 prepwrfr lkugler PD 0:00 1 (Priority)
+1710275 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+1710276 mem_0384 Assim-42 lkugler PD 0:00 1 (Dependency)
+1710277 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+1710278 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
+1710279 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)</p>
+</div></blockquote>
+<dl class="simple">
+<dt>1710280_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)</dt><dd><p>1710281 mem_0384 pRTTOV-6 lkugler PD 0:00 1 (Dependency)
+1710282 mem_0384 Assim-3a lkugler PD 0:00 1 (Dependency)
+1710283 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
+1710284 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
+1710285 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)</p>
+</dd>
+<dt>1710286_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)</dt><dd><p>1710287 mem_0384 pRTTOV-7 lkugler PD 0:00 1 (Dependency)</p>
+</dd>
+</dl>
+</div></blockquote>
+<p><a href="#id11"><span class="problematic" id="id12">``</span></a><a href="#id13"><span class="problematic" id="id14">`</span></a></p>
+<p>### Easily switch between clusters
+Define cluster specific variables in <a href="#id15"><span class="problematic" id="id16">`</span></a>config/clusters.py <a href="#id17"><span class="problematic" id="id18">`</span></a>:
+<a href="#id19"><span class="problematic" id="id20">``</span></a><a href="#id21"><span class="problematic" id="id22">`</span></a>python</p>
+<p>clusterA = ClusterConfig()
+clusterA.name = ‘vsc’
+clusterA.userdir = ‘/home/pathA/myuser/’
+…
+clusterB = ClusterConfig()
+clusterB.name = ‘jet’
+clusterB.userdir = ‘/home/pathB/myuser/’
+<a href="#id23"><span class="problematic" id="id24">``</span></a><a href="#id25"><span class="problematic" id="id26">`</span></a></p>
+
+
+ </div>
+
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+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
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+
+<!DOCTYPE html>
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+<html lang="en">
+ <head>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Index — DART-WRF 2023.2.17 documentation</title>
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diff --git a/docs/build/html/index.html b/docs/build/html/index.html
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--- /dev/null
+++ b/docs/build/html/index.html
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+
+<!DOCTYPE html>
+
+<html lang="en">
+ <head>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+
+ <title>Welcome to the DART-WRF documentation! — DART-WRF 2023.2.17 documentation</title>
+ <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+ <link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
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+
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+
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+ <div class="bodywrapper">
+
+
+ <div class="body" role="main">
+
+ <section id="welcome-to-the-dart-wrf-documentation">
+<h1>Welcome to the DART-WRF documentation!<a class="headerlink" href="#welcome-to-the-dart-wrf-documentation" title="Permalink to this heading">¶</a></h1>
+<p>DART-WRF is a Python package to run an Ensemble Data Assimilation system with the software packages DART and WRF.</p>
+<ul class="simple">
+<li><p>Why should I use it?
+- It’s pythonic: see what it does at first glance, modular, flexible
+- It handles dependencies using SLURM without ‘<cite>sleep</cite> loops in the bash script’.</p></li>
+</ul>
+<p>Functions return a SLURM ID which can be used to trigger the start of another function (interface by [brentp/slurmpy](<a class="reference external" href="https://github.com/brentp/slurmpy">https://github.com/brentp/slurmpy</a>)).</p>
+<ul class="simple">
+<li><p>How does it work?
+- There are two kinds of code/scripts: One that is run immediately and one that is run later on.
+- The first one instructs the cluster (SLURM) to do the things you tell it - in the right order - using the right input.
+- The latter kind of code actually does the things. Its code is not executed right away, but when there are resources assigned to you by SLURM.</p></li>
+<li><p>Can I use it for real weather?
+- Yes, but you need to [convert your observations into DART format.](<a class="reference external" href="https://docs.dart.ucar.edu">https://docs.dart.ucar.edu</a>)</p></li>
+</ul>
+<section id="contents">
+<h2>Contents<a class="headerlink" href="#contents" title="Permalink to this heading">¶</a></h2>
+<div class="toctree-wrapper compound">
+</div>
+</section>
+</section>
+
+
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+
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diff --git a/docs/build/html/index2.html b/docs/build/html/index2.html
new file mode 100644
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--- /dev/null
+++ b/docs/build/html/index2.html
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+
+<!DOCTYPE html>
+
+<html lang="en">
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
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+<div class="toctree-wrapper compound">
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+</section>
+<section id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading">¶</a></h1>
+<ul class="simple">
+<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
+<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
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diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
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diff --git a/docs/build/html/search.html b/docs/build/html/search.html
new file mode 100644
index 0000000000000000000000000000000000000000..075b53210fd7f8493b41c43341df5424d824740d
--- /dev/null
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+
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diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
new file mode 100644
index 0000000000000000000000000000000000000000..6880cbd39db7deaad02713032ff71cdd311fce75
--- /dev/null
+++ b/docs/build/html/searchindex.js
@@ -0,0 +1 @@
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