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PRESCOTT
Commit 4d2e40b2 by Mustafa Tekpinar
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Added multiple mutations information.

parent e52c7a7b
Showing with 7 additions and 4613 deletions
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E26D:Y44R
E56N:A77F:H94V
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docs/_build/html/_sources/analysis.rst.txt deleted 100644 → 0
Analyzing and Modifying the ESCOTT Output
==========================================
Raw ESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
We should note that most of the 'impactful' mutations are deleterious but
it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
Assuming that your fasta sequence has a name 'myProt' after '>' character, there will be three output files:
#. myProt_normPred_evolCombi.txt
myProt is the short name in the MSA file for your protein. The
'myProt_normPred_evolCombi.txt' file contains 20 rows (for 20 amino acids
in alphabetical order) and L columns, where L is the number of amino acids
in your protein of interest. Since this file is horizontal, it is easy to
read it in R or Python but difficult to find the mutations you are interested.
#. myProt_normPred_evolCombiTransposedRanksorted.csv
As the name implies, this is the transposed and reverse ranksorted version of the combined results.
It is easier to find the mutations you are interested in this file. It can be opened with any spreadsheet
program like MS Excel. Each row is an amino acid in the protein and 20 columns contain mutational effects
of the original amino acid. The values are between 0 and 1. While 0 indicates no effect, 1 indicates a
high impact.
#. myProt_normPred_evolCombi.png
This is the image file of the combined results. It selects 'turbo_r'
matplotlib color map by default. You can change it by adding '--colormap turbo_r'
for a more fancy look during the escott call. It --colormap argument accepts
all the color maps in matplotlib.
If your query sequence is longer than 500 amino acids, the program may produce
multiple png files, each one containing a 500 residue segment.
Note*: If you want to see epistatic and independent contributions as well,
you should add '--verbose true' argument while calling escott.
Selected Single Point or Multiple Point Mutation Calculations
-------------------------------------------------------------
Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent)
results in the same format, such as :
*. myProt_normPred_evolCombi.txt:
A2C -6.23
A2D -1.23
.
.
.
D286F -0.23
docs/_build/html/_sources/docker.rst.txt deleted 100644 → 0
Using ESCOTT via Docker
========================
Requirements
------------
You need to have docker installed on your machine. You can consult the
following page for this: https://docs.docker.com/get-docker/
I am assuming some basic familiarity with Linux/Unix/MacOS terminal
commands.
Let’s start our favorite terminal app.
You must create a folder called docker-tutorial and go to that empty
folder:
.. code:: bash
mkdir docker-tutorial
cd docker-tutorial
Getting the example input data
------------------------------
Let’s download the sample data provided in the PRESCOTT repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
In order to make sure that the docker is installed:
.. code:: bash
sudo docker -h
If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/prescott-docker:v1.5.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.
.. code:: bash
cd ../myexample/
When you check the data in that folder with ‘ls’ command, you are
supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.
Obtaining the entire single point mutation landscape
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
escott aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
the entire single point mutational landscape of BLAT protein in these
files.
If you want to utilize structural information (highly recommended) as well as
evolutionary information:
.. code:: bash
escott aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of PRESCOTT repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, let's do it without structural information:
.. code:: bash
escott aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
escott aliBLAT.fasta --pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
Each line of this file is a mutation and its predicted effect separated by a space.
In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. ESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
.. code:: bash
E26D:Y44R
E56N:A77F:H94V
The first line of the text file is impact of a double mutation and the second
line is the impact of the triple mutations. As you can see, the mutations are
separated by a colon(:) character.
The output file will be in a similar format. Each line will contain the multiple
mutation and its predicted effect, separated by a space.
Running several jobs using docker
---------------------------------
If you want to use docker in a more automated way for several proteins,
you can call docker within a bash script.
.. code:: bash
sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.5.0 escott aliBLAT.fasta --pdbfile blat-af2.pdb
Note: It is very important to have aliBLAT.fasta and blat-af2.pdb files in your local folder when you call docker like an executable.
Typically, I create a folder for each protein that contain the alignment and the structure. Then, I change the path to each folder with 'cd'
command inside bash script and execute the command above in each local folder.
docs/_build/html/_sources/index.rst.txt deleted 100644 → 0
.. PRESCOTT documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to PRESCOTT documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction.rst
docker.rst
analysis.rst
input-preparation.rst
singularity.rst
installation.rst
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/_build/html/_sources/input-preparation.rst.txt deleted 100644 → 0
Preparing Your Own Input
========================
Preparing Your Input MSA and PDB with Colabfold
-----------------------------------------------
You have a fasta file for your protein of interest and you want to understand
impact of (certain) mutations.
Before starting, please make sure that your fasta file does not contain a gap.
The quickest method to obtain both multiple sequence alignment and a protein
structure is to use Colabfold. Let's do this step by step:
1. Let's go the Colabfold web site:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Sign in using your gmail account.
2. Click on the 'Connect' button on the top right hand side.
3. Clean 'query_sequence' box and paste your sequence to the 'query_sequence' box.
For me, I selected adenylate kinase (AKE) as my example fasta sequence
(https://www.rcsb.org/fasta/entry/4AKE/display).
4. Change the 'jobname' to something that makes more sense to you.
5. Go to the menu bar of your 'AlphaFold2.ipynb' notebook, where 'File, Edit,
View, Insert, Runtime, Tools, Help' are listed. Click on the Runtime and
select 'Run all'.
6. This process make take from a few minutes to a few hours depending on your
protein size. It will give you an a3m file and up to 5 PDB models. Put these
files in a clean folder and change the directory to that folder in your
terminal.
7. Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the PRESCOTT docker image that I created.
8. Start the docker image with the following command:
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/prescott-docker:v1.5.0
9. Now, change the directory to myexample folder.
.. code:: bash
cd ../myexample/
ls -l
We are supposed to see our a3m and pdb files in this folder.
10. Let's use a small script from hhsuite to convert a3m file to fasta format.
.. code:: bash
reformat.pl a3m fas AKE.a3m AKE.fasta
11. Final step and we are there:
.. code:: bash
demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with
.. code:: bash
awk 'BEGIN{FS=" "}{if(NF>1) {printf(">%s\n", $1)}else{print $0}}' AKE_nogaps.fasta > AKE_nogaps_short_names.fasta
# Recheck this command if you can remove extra >
Congratulations! Now, you have all the input files required for PRESCOTT:
#. An input MSA: AKE_nogaps_short_names.fasta
#. An input PDB: myprotein.pdb
docs/_build/html/_sources/installation.rst.txt deleted 100644 → 0
Installation
------------
PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, here comes the
steps required to install it from the source.
Installing the dependencies:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PRESCOTT has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
* java
* naccess: http://www.bioinf.manchester.ac.uk/naccess/
After you installed JET2 define a parameter called JET2_PATH inside your .profile file.
You can open .profile as follows:
.. code:: bash
gedit ~/.profile
You should add a command like below to the end of that file, save and exit.
.. code:: bash
export JET2_PATH=/home/tekpinar/JET2/
Please, do not forget to replace /home/tekpinar/JET2 with your own file path.
Then, source the saved .profile so that the environment variable will be taken into account:
.. code:: bash
source ~/.profile
JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04
Prepare your environment and install the required packages:
.. code:: bash
sudo apt-get update --fix-missing && \
sudo apt-get install -y --no-install-recommends apt-utils && \
sudo apt-get install -y software-properties-common && \
sudo apt-get install -y autotools-dev && \
sudo apt-get install -y automake && \
sudo apt-get install -y build-essential && \
sudo apt-get install -y python3-dev && \
sudo apt-get install -y python3-pip && \
sudo apt-get install -y r-base r-base-core && \
sudo apt-get install -y muscle && \
sudo apt-get install -y default-jre && \
sudo apt-get install -y ncbi-blast+ && \
sudo apt-get install -y nano && \
sudo apt-get install -y less && \
sudo apt-get install -y wget && \
sudo apt-get install csh && \
sudo apt-get install -y hmmer && \
sudo apt-get install -y libboost-all-dev && \
sudo apt-get clean && \
sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
sudo apt-get install dssp
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && \
unzip -o master.zip && cd dssp-master/ && \
./autogen.sh && \
./configure && \
make && \
sudo make install && \
sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp && \
cd ../ && \
sudo rm -rf dssp-master/ && \
sudo rm -f master.zip
#HHSUITE installation
.. code:: bash
wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && \
mkdir hhsuite && \
mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ && \
cd hhsuite && \
tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz && \
rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
#Add it to your path permanently inside .bashrc or .profile or .bash_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
Open .profile file with gedit:
.. code:: bash
gedit ~/.profile
Now, add the following line to the end of the file.
.. code:: bash
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,
.. code:: bash
source ~/.profile
#
cd PRESCOTT
#Download PRESCOTT from http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT repository and go inside the PRESCOTT folder.!
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
If you would like the development version:
.. code:: bash
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
.. code:: bash
cd PRESCOTT
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside PRESCOTT/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of PRESCOTT, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
.. code:: bash
pip3 install -e . &&\
cd ../
#Installing the required R packages
.. code:: bash
sudo Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
#Installing secondary programs such as ev_couplings to obtain MSA files.
.. code:: bash
wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip && \
unzip -o master.zip && \
cd plmc-master && \
make all-openmp32 && \
sudo cp bin/plmc /usr/local/bin/ && \
cd ../ && \
rm -rf master.zip plmc-master
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*/
"use strict";
const _ready = (callback) => {
if (document.readyState !== "loading") {
callback();
} else {
document.addEventListener("DOMContentLoaded", callback);
}
};
/**
* 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 Documentation = {
init: () => {
Documentation.highlightSearchWords();
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 (${catalog.plural_expr})`
);
Documentation.LOCALE = catalog.locale;
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords: () => {
const highlight =
new URLSearchParams(window.location.search).get("highlight") || "";
const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
if (terms.length === 0) return; // nothing to do
// There should never be more than one element matching "div.body"
const divBody = document.querySelectorAll("div.body");
const body = divBody.length ? divBody[0] : document.querySelector("body");
window.setTimeout(() => {
terms.forEach((term) => _highlightText(body, term, "highlighted"));
}, 10);
const searchBox = document.getElementById("searchbox");
if (searchBox === null) return;
searchBox.appendChild(
document
.createRange()
.createContextualFragment(
'<p class="highlight-link">' +
'<a href="javascript:Documentation.hideSearchWords()">' +
Documentation.gettext("Hide Search Matches") +
"</a></p>"
)
);
},
/**
* helper function to hide the search marks again
*/
hideSearchWords: () => {
document
.querySelectorAll("#searchbox .highlight-link")
.forEach((el) => el.remove());
document
.querySelectorAll("span.highlighted")
.forEach((el) => el.classList.remove("highlighted"));
const url = new URL(window.location);
url.searchParams.delete("highlight");
window.history.replaceState({}, "", url);
},
/**
* helper function to focus on search bar
*/
focusSearchBar: () => {
document.querySelectorAll("input[name=q]")[0]?.focus();
},
/**
* Initialise the domain index toggle buttons
*/
initDomainIndexTable: () => {
const toggler = (el) => {
const idNumber = el.id.substr(7);
const toggledRows = document.querySelectorAll(`tr.cg-${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;
const blacklistedElements = new Set([
"TEXTAREA",
"INPUT",
"SELECT",
"BUTTON",
]);
document.addEventListener("keydown", (event) => {
if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
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;
case "Escape":
if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
Documentation.hideSearchWords();
event.preventDefault();
}
}
// 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);
docs/_build/html/_static/documentation_options.js deleted 100644 → 0
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.6.0',
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: false,
};
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docs/_build/html/_static/js/badge_only.js deleted 100644 → 0
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docs/_build/html/_static/js/html5shiv-printshiv.min.js deleted 100644 → 0
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docs/_build/html/_static/js/html5shiv.min.js deleted 100644 → 0
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docs/_build/html/_static/language_data.js deleted 100644 → 0
/*
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alli: 'al',
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aliti: 'al',
iviti: 'ive',
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logi: 'log'
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the ESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#raw-escott-scores-and-their-interpretation">Raw ESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
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<section id="analyzing-and-modifying-the-escott-output">
<h1>Analyzing and Modifying the ESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-escott-output" title="Permalink to this heading"></a></h1>
<section id="raw-escott-scores-and-their-interpretation">
<h2>Raw ESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-escott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.</p>
<p>We should note that most of the ‘impactful’ mutations are deleterious but
it is not always the case.</p>
</section>
<section id="entire-single-point-mutation-landscape-calculations">
<h2>Entire Single Point Mutation Landscape Calculations<a class="headerlink" href="#entire-single-point-mutation-landscape-calculations" title="Permalink to this heading"></a></h2>
<p>By default, ESCOTT will only output the combined (independent
and epistatic) scores*:</p>
<p>Assuming that your fasta sequence has a name ‘myProt’ after ‘&gt;’ character, there will be three output files:</p>
<ol class="arabic">
<li><p>myProt_normPred_evolCombi.txt</p>
<blockquote>
<div><p>myProt is the short name in the MSA file for your protein. The
‘myProt_normPred_evolCombi.txt’ file contains 20 rows (for 20 amino acids
in alphabetical order) and L columns, where L is the number of amino acids
in your protein of interest. Since this file is horizontal, it is easy to
read it in R or Python but difficult to find the mutations you are interested.</p>
</div></blockquote>
</li>
<li><p>myProt_normPred_evolCombiTransposedRanksorted.csv</p>
<blockquote>
<div><p>As the name implies, this is the transposed and reverse ranksorted version of the combined results.
It is easier to find the mutations you are interested in this file. It can be opened with any spreadsheet
program like MS Excel. Each row is an amino acid in the protein and 20 columns contain mutational effects
of the original amino acid. The values are between 0 and 1. While 0 indicates no effect, 1 indicates a
high impact.</p>
</div></blockquote>
</li>
<li><p>myProt_normPred_evolCombi.png</p>
<blockquote>
<div><p>This is the image file of the combined results. It selects ‘turbo_r’
matplotlib color map by default. You can change it by adding ‘–colormap turbo_r’
for a more fancy look during the escott call. It –colormap argument accepts
all the color maps in matplotlib.
If your query sequence is longer than 500 amino acids, the program may produce
multiple png files, each one containing a 500 residue segment.</p>
</div></blockquote>
</li>
</ol>
<p>Note*: If you want to see epistatic and independent contributions as well,
you should add ‘–verbose true’ argument while calling escott.</p>
</section>
<section id="selected-single-point-or-multiple-point-mutation-calculations">
<h2>Selected Single Point or Multiple Point Mutation Calculations<a class="headerlink" href="#selected-single-point-or-multiple-point-mutation-calculations" title="Permalink to this heading"></a></h2>
<p>Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent)
results in the same format, such as :</p>
<dl class="simple">
<dt><a href="#id1"><span class="problematic" id="id2">*</span></a>. myProt_normPred_evolCombi.txt:</dt><dd><p>A2C -6.23
A2D -1.23
.
.
.
D286F -0.23</p>
</dd>
</dl>
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<section id="preparing-your-own-input">
<h1>Preparing Your Own Input<a class="headerlink" href="#preparing-your-own-input" title="Permalink to this heading"></a></h1>
<section id="preparing-your-input-msa-and-pdb-with-colabfold">
<h2>Preparing Your Input MSA and PDB with Colabfold<a class="headerlink" href="#preparing-your-input-msa-and-pdb-with-colabfold" title="Permalink to this heading"></a></h2>
<p>You have a fasta file for your protein of interest and you want to understand
impact of (certain) mutations.
Before starting, please make sure that your fasta file does not contain a gap.
The quickest method to obtain both multiple sequence alignment and a protein
structure is to use Colabfold. Let’s do this step by step:</p>
<ol class="arabic">
<li><p>Let’s go the Colabfold web site:</p>
<p><a class="reference external" href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a></p>
<p>Sign in using your gmail account.</p>
</li>
<li><p>Click on the ‘Connect’ button on the top right hand side.</p></li>
<li><p>Clean ‘query_sequence’ box and paste your sequence to the ‘query_sequence’ box.
For me, I selected adenylate kinase (AKE) as my example fasta sequence
(<a class="reference external" href="https://www.rcsb.org/fasta/entry/4AKE/display">https://www.rcsb.org/fasta/entry/4AKE/display</a>).</p></li>
<li><p>Change the ‘jobname’ to something that makes more sense to you.</p></li>
<li><p>Go to the menu bar of your ‘AlphaFold2.ipynb’ notebook, where ‘File, Edit,
View, Insert, Runtime, Tools, Help’ are listed. Click on the Runtime and
select ‘Run all’.</p></li>
<li><p>This process make take from a few minutes to a few hours depending on your
protein size. It will give you an a3m file and up to 5 PDB models. Put these
files in a clean folder and change the directory to that folder in your
terminal.</p></li>
<li><p>Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the PRESCOTT docker image that I created.</p></li>
<li><p>Start the docker image with the following command:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span>
tekpinar/prescott-docker:v1.5.0
</pre></div>
</div>
</li>
<li><p>Now, change the directory to myexample folder.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ../myexample/
ls -l
</pre></div>
</div>
<p>We are supposed to see our a3m and pdb files in this folder.</p>
</li>
<li><p>Let’s use a small script from hhsuite to convert a3m file to fasta format.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>reformat.pl a3m fas AKE.a3m AKE.fasta
</pre></div>
</div>
</li>
<li><p>Final step and we are there:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
</pre></div>
</div>
</li>
</ol>
<p>There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>awk <span class="s1">&#39;BEGIN{FS=&quot; &quot;}{if(NF&gt;1) {printf(&quot;&gt;%s\n&quot;, $1)}else{print $0}}&#39;</span> AKE_nogaps.fasta &gt; AKE_nogaps_short_names.fasta
<span class="c1"># Recheck this command if you can remove extra &gt;</span>
</pre></div>
</div>
</div></blockquote>
<p>Congratulations! Now, you have all the input files required for PRESCOTT:</p>
<ol class="arabic simple">
<li><p>An input MSA: AKE_nogaps_short_names.fasta</p></li>
<li><p>An input PDB: myprotein.pdb</p></li>
</ol>
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\ No newline at end of file
docs/_build/latex/LICRcyr2utf8.xdy deleted 100644 → 0
;; -*- coding: utf-8; mode: Lisp; -*-
;; style file for xindy
;; filename: LICRcyr2utf8.xdy
;; description: style file for xindy which maps back LaTeX Internal
;; Character Representation of Cyrillic to utf-8
;; usage: for use with pdflatex produced .idx files.
;; Contributed by the Sphinx team, July 2018.
(merge-rule "\IeC {\'\CYRG }" "Ѓ" :string)
(merge-rule "\IeC {\'\CYRK }" "Ќ" :string)
(merge-rule "\IeC {\'\cyrg }" "ѓ" :string)
(merge-rule "\IeC {\'\cyrk }" "ќ" :string)
(merge-rule "\IeC {\CYRA }" "А" :string)
(merge-rule "\IeC {\CYRB }" "Б" :string)
(merge-rule "\IeC {\CYRC }" "Ц" :string)
(merge-rule "\IeC {\CYRCH }" "Ч" :string)
(merge-rule "\IeC {\CYRD }" "Д" :string)
(merge-rule "\IeC {\CYRDJE }" "Ђ" :string)
(merge-rule "\IeC {\CYRDZE }" "Ѕ" :string)
(merge-rule "\IeC {\CYRDZHE }" "Џ" :string)
(merge-rule "\IeC {\CYRE }" "Е" :string)
(merge-rule "\IeC {\CYREREV }" "Э" :string)
(merge-rule "\IeC {\CYRERY }" "Ы" :string)
(merge-rule "\IeC {\CYRF }" "Ф" :string)
(merge-rule "\IeC {\CYRG }" "Г" :string)
(merge-rule "\IeC {\CYRGUP }" "Ґ" :string)
(merge-rule "\IeC {\CYRH }" "Х" :string)
(merge-rule "\IeC {\CYRHRDSN }" "Ъ" :string)
(merge-rule "\IeC {\CYRI }" "И" :string)
(merge-rule "\IeC {\CYRIE }" "Є" :string)
(merge-rule "\IeC {\CYRII }" "І" :string)
(merge-rule "\IeC {\CYRISHRT }" "Й" :string)
(merge-rule "\IeC {\CYRJE }" "Ј" :string)
(merge-rule "\IeC {\CYRK }" "К" :string)
(merge-rule "\IeC {\CYRL }" "Л" :string)
(merge-rule "\IeC {\CYRLJE }" "Љ" :string)
(merge-rule "\IeC {\CYRM }" "М" :string)
(merge-rule "\IeC {\CYRN }" "Н" :string)
(merge-rule "\IeC {\CYRNJE }" "Њ" :string)
(merge-rule "\IeC {\CYRO }" "О" :string)
(merge-rule "\IeC {\CYRP }" "П" :string)
(merge-rule "\IeC {\CYRR }" "Р" :string)
(merge-rule "\IeC {\CYRS }" "С" :string)
(merge-rule "\IeC {\CYRSFTSN }" "Ь" :string)
(merge-rule "\IeC {\CYRSH }" "Ш" :string)
(merge-rule "\IeC {\CYRSHCH }" "Щ" :string)
(merge-rule "\IeC {\CYRT }" "Т" :string)
(merge-rule "\IeC {\CYRTSHE }" "Ћ" :string)
(merge-rule "\IeC {\CYRU }" "У" :string)
(merge-rule "\IeC {\CYRUSHRT }" "Ў" :string)
(merge-rule "\IeC {\CYRV }" "В" :string)
(merge-rule "\IeC {\CYRYA }" "Я" :string)
(merge-rule "\IeC {\CYRYI }" "Ї" :string)
(merge-rule "\IeC {\CYRYO }" "Ё" :string)
(merge-rule "\IeC {\CYRYU }" "Ю" :string)
(merge-rule "\IeC {\CYRZ }" "З" :string)
(merge-rule "\IeC {\CYRZH }" "Ж" :string)
(merge-rule "\IeC {\cyra }" "а" :string)
(merge-rule "\IeC {\cyrb }" "б" :string)
(merge-rule "\IeC {\cyrc }" "ц" :string)
(merge-rule "\IeC {\cyrch }" "ч" :string)
(merge-rule "\IeC {\cyrd }" "д" :string)
(merge-rule "\IeC {\cyrdje }" "ђ" :string)
(merge-rule "\IeC {\cyrdze }" "ѕ" :string)
(merge-rule "\IeC {\cyrdzhe }" "џ" :string)
(merge-rule "\IeC {\cyre }" "е" :string)
(merge-rule "\IeC {\cyrerev }" "э" :string)
(merge-rule "\IeC {\cyrery }" "ы" :string)
(merge-rule "\IeC {\cyrf }" "ф" :string)
(merge-rule "\IeC {\cyrg }" "г" :string)
(merge-rule "\IeC {\cyrgup }" "ґ" :string)
(merge-rule "\IeC {\cyrh }" "х" :string)
(merge-rule "\IeC {\cyrhrdsn }" "ъ" :string)
(merge-rule "\IeC {\cyri }" "и" :string)
(merge-rule "\IeC {\cyrie }" "є" :string)
(merge-rule "\IeC {\cyrii }" "і" :string)
(merge-rule "\IeC {\cyrishrt }" "й" :string)
(merge-rule "\IeC {\cyrje }" "ј" :string)
(merge-rule "\IeC {\cyrk }" "к" :string)
(merge-rule "\IeC {\cyrl }" "л" :string)
(merge-rule "\IeC {\cyrlje }" "љ" :string)
(merge-rule "\IeC {\cyrm }" "м" :string)
(merge-rule "\IeC {\cyrn }" "н" :string)
(merge-rule "\IeC {\cyrnje }" "њ" :string)
(merge-rule "\IeC {\cyro }" "о" :string)
(merge-rule "\IeC {\cyrp }" "п" :string)
(merge-rule "\IeC {\cyrr }" "р" :string)
(merge-rule "\IeC {\cyrs }" "с" :string)
(merge-rule "\IeC {\cyrsftsn }" "ь" :string)
(merge-rule "\IeC {\cyrsh }" "ш" :string)
(merge-rule "\IeC {\cyrshch }" "щ" :string)
(merge-rule "\IeC {\cyrt }" "т" :string)
(merge-rule "\IeC {\cyrtshe }" "ћ" :string)
(merge-rule "\IeC {\cyru }" "у" :string)
(merge-rule "\IeC {\cyrushrt }" "ў" :string)
(merge-rule "\IeC {\cyrv }" "в" :string)
(merge-rule "\IeC {\cyrya }" "я" :string)
(merge-rule "\IeC {\cyryi }" "ї" :string)
(merge-rule "\IeC {\cyryo }" "ё" :string)
(merge-rule "\IeC {\cyryu }" "ю" :string)
(merge-rule "\IeC {\cyrz }" "з" :string)
(merge-rule "\IeC {\cyrzh }" "ж" :string)
docs/_build/latex/Makefile deleted 100644 → 0
# Makefile for Sphinx LaTeX output
ALLDOCS = $(basename $(wildcard *.tex))
ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
ALLXDV =
ALLPS = $(addsuffix .ps,$(ALLDOCS))
# Prefix for archive names
ARCHIVEPREFIX =
# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
export LATEXOPTS ?=
# Additional latexmk options
LATEXMKOPTS ?=
# format: pdf or dvi (used only by archive targets)
FMT = pdf
LATEX = latexmk -dvi
PDFLATEX = latexmk -pdf -dvi- -ps-
%.dvi: %.tex FORCE_MAKE
$(LATEX) $(LATEXMKOPTS) '$<'
%.ps: %.dvi
dvips '$<'
%.pdf: %.tex FORCE_MAKE
$(PDFLATEX) $(LATEXMKOPTS) '$<'
all: $(ALLPDF)
all-dvi: $(ALLDVI)
all-ps: $(ALLPS)
all-pdf: $(ALLPDF)
zip: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
tar: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
gz: tar
gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
bz2: tar
bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
xz: tar
xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
clean:
rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
.PHONY: FORCE_MAKE
\ No newline at end of file
docs/_build/latex/_static/_sphinx_javascript_frameworks_compat.js deleted 100644 → 0
/* Compatability shim for jQuery and underscores.js.
*
* Copyright Sphinx contributors
* Released under the two clause BSD licence
*/
/**
* small helper function to urldecode strings
*
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
if (!x) {
return x
}
return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.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": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
docs/_build/latex/latexmkjarc deleted 100644 → 0
$latex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' -kanji=utf8 %O %S';
$dvipdf = 'dvipdfmx %O -o %D %S';
$makeindex = 'internal mendex %S %B %D';
sub mendex {
my ($source, $basename, $destination) = @_;
my $dictfile = $basename . ".dic";
unlink($destination);
system("mendex", "-U", "-f", "-d", $dictfile, "-s", "python.ist", $source);
if ($? > 0) {
print("mendex exited with error code $? (ignored)\n");
}
if (!-e $destination) {
# create an empty .ind file if nothing
open(FH, ">" . $destination);
close(FH);
}
return 0;
}
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
return system( "mendex -J -f -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}
\ No newline at end of file
docs/_build/latex/latexmkrc deleted 100644 → 0
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}
\ No newline at end of file
docs/_build/latex/make.bat deleted 100644 → 0
@ECHO OFF
REM Command file for Sphinx documentation
pushd %~dp0
set PDFLATEX=latexmk -pdf -dvi- -ps-
set "LATEXOPTS= "
if "%1" == "" goto all-pdf
if "%1" == "all-pdf" (
:all-pdf
for %%i in (*.tex) do (
%PDFLATEX% %LATEXMKOPTS% %%i
)
goto end
)
if "%1" == "all-pdf-ja" (
goto all-pdf
)
if "%1" == "clean" (
del /q /s *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz *.fls *.fdb_latexmk
goto end
)
:end
popd
\ No newline at end of file
docs/_build/latex/prescott.aux deleted 100644 → 0
\relax
\providecommand\hyper@newdestlabel[2]{}
\providecommand\babel@aux[2]{}
\@nameuse{bbl@beforestart}
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand\HyField@AuxAddToFields[1]{}
\providecommand\HyField@AuxAddToCoFields[2]{}
\babel@aux{english}{}
\newlabel{index::doc}{{}{1}{}{section*.2}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\newlabel{introduction:introduction}{{1}{1}{Introduction}{chapter.1}{}}
\newlabel{introduction::doc}{{1}{1}{Introduction}{chapter.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}\protected@file@percent }
\newlabel{introduction:what-is-prescott}{{1.1}{1}{What is PRESCOTT?}{section.1.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}\protected@file@percent }
\newlabel{introduction:input-data-requirements}{{1.2}{1}{Input Data Requirements}{section.1.2}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}\protected@file@percent }
\newlabel{introduction:input-data-requirements-for-escott}{{1.2.1}{1}{Input Data Requirements for escott}{subsection.1.2.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}\protected@file@percent }
\newlabel{introduction:input-data-requirements-for-prescott}{{1.2.2}{2}{Input Data Requirements for prescott}{subsection.1.2.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}\protected@file@percent }
\newlabel{introduction:usage}{{1.3}{2}{Usage}{section.1.3}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}\protected@file@percent }
\newlabel{introduction:running-the-escott-program}{{1.3.1}{2}{Running the escott program}{subsection.1.3.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}\protected@file@percent }
\newlabel{introduction:running-the-prescott-program}{{1.3.2}{2}{Running the prescott program}{subsection.1.3.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}\protected@file@percent }
\newlabel{introduction:installation}{{1.4}{3}{Installation}{section.1.4}{}}
\@writefile{toc}{\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}\protected@file@percent }
\newlabel{introduction:citation}{{1.5}{3}{Citation}{section.1.5}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}\protected@file@percent }
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
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\newlabel{docker::doc}{{2}{5}{Using ESCOTT via Docker}{chapter.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}\protected@file@percent }
\newlabel{docker:requirements}{{2.1}{5}{Requirements}{section.2.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}\protected@file@percent }
\newlabel{docker:getting-the-example-input-data}{{2.2}{5}{Getting the example input data}{section.2.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}\protected@file@percent }
\newlabel{docker:single-point-mutation-calculations}{{2.3}{6}{Single point mutation calculations}{section.2.3}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}\protected@file@percent }
\newlabel{docker:obtaining-the-entire-single-point-mutation-landscape}{{2.3.1}{6}{Obtaining the entire single point mutation landscape}{subsection.2.3.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}\protected@file@percent }
\newlabel{docker:predicting-the-effect-of-a-subset-of-single-point-mutations}{{2.3.2}{6}{Predicting the effect of a subset of single point mutations}{subsection.2.3.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}\protected@file@percent }
\newlabel{docker:multiple-point-mutation-calculations}{{2.4}{7}{Multiple point mutation calculations}{section.2.4}{}}
\@writefile{toc}{\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}\protected@file@percent }
\newlabel{docker:running-several-jobs-using-docker}{{2.5}{7}{Running several jobs using docker}{section.2.5}{}}
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\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
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\newlabel{analysis::doc}{{3}{9}{Analyzing and Modifying the ESCOTT Output}{chapter.3}{}}
\@writefile{toc}{\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}\protected@file@percent }
\newlabel{analysis:raw-escott-scores-and-their-interpretation}{{3.1}{9}{Raw ESCOTT Scores and Their Interpretation}{section.3.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}\protected@file@percent }
\newlabel{analysis:entire-single-point-mutation-landscape-calculations}{{3.2}{9}{Entire Single Point Mutation Landscape Calculations}{section.3.2}{}}
\@writefile{toc}{\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}\protected@file@percent }
\newlabel{analysis:selected-single-point-or-multiple-point-mutation-calculations}{{3.3}{10}{Selected Single Point or Multiple Point Mutation Calculations}{section.3.3}{}}
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\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
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\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
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\newlabel{singularity::doc}{{5}{13}{Using ESCOTT via Singularity}{chapter.5}{}}
\@writefile{toc}{\contentsline {chapter}{\numberline {6}Installation}{15}{chapter.6}\protected@file@percent }
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docs/_build/latex/prescott.ilg deleted 100644 → 0
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docs/_build/latex/prescott.toc deleted 100644 → 0
\babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
\contentsline {chapter}{\numberline {3}Analyzing and Modifying the ESCOTT Output}{9}{chapter.3}%
\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}%
\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}%
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
\contentsline {chapter}{\numberline {5}Using ESCOTT via Singularity}{13}{chapter.5}%
\contentsline {chapter}{\numberline {6}Installation}{15}{chapter.6}%
\contentsline {section}{\numberline {6.1}Installing the dependencies:}{15}{section.6.1}%
\contentsline {section}{\numberline {6.2}Preparation of the environment and installation of PRESCOTT}{15}{section.6.2}%
\contentsline {section}{\numberline {6.3}Configuring default.conf file}{17}{section.6.3}%
\contentsline {chapter}{\numberline {7}Indices and tables}{19}{chapter.7}%
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(merge-rule "\IeC {\textDelta }" "Δ" :string)
(merge-rule "\IeC {\textEpsilon }" "Ε" :string)
(merge-rule "\IeC {\textZeta }" "Ζ" :string)
(merge-rule "\IeC {\textEta }" "Η" :string)
(merge-rule "\IeC {\textTheta }" "Θ" :string)
(merge-rule "\IeC {\textIota }" "Ι" :string)
(merge-rule "\IeC {\textKappa }" "Κ" :string)
(merge-rule "\IeC {\textLambda }" "Λ" :string)
(merge-rule "\IeC {\textMu }" "Μ" :string)
(merge-rule "\IeC {\textNu }" "Ν" :string)
(merge-rule "\IeC {\textTheta }" "Θ" :string)
(merge-rule "\IeC {\textIota }" "Ι" :string)
(merge-rule "\IeC {\textKappa }" "Κ" :string)
(merge-rule "\IeC {\textLambda }" "Λ" :string)
(merge-rule "\IeC {\textMu }" "Μ" :string)
(merge-rule "\IeC {\textNu }" "Ν" :string)
(merge-rule "\IeC {\textXi }" "Ξ" :string)
(merge-rule "\IeC {\textOmicron }" "Ο" :string)
(merge-rule "\IeC {\textPi }" "Π" :string)
(merge-rule "\IeC {\textRho }" "Ρ" :string)
(merge-rule "\IeC {\textSigma }" "Σ" :string)
(merge-rule "\IeC {\textTau }" "Τ" :string)
(merge-rule "\IeC {\textUpsilon }" "Υ" :string)
(merge-rule "\IeC {\textPhi }" "Φ" :string)
(merge-rule "\IeC {\textChi }" "Χ" :string)
(merge-rule "\IeC {\textPsi }" "Ψ" :string)
(merge-rule "\IeC {\textOmega }" "Ω" :string)
(merge-rule "\IeC {\textohm }" "Ω" :string)
;; This xindy module provides some basic support for "see"
(require "makeindex.xdy")
;; This creates one-letter headings and works fine with utf-8 letters.
;; For Cyrillic with pdflatex works thanks to LICRcyr2utf8.xdy
(require "latin-lettergroups.xdy")
;; currently we don't (know how to easily) separate "Numbers" from
;; "Symbols" with xindy as is the case with makeindex.
(markup-index :open "\begin{sphinxtheindex}
\let\lettergroup\sphinxstyleindexlettergroup
\let\lettergroupDefault\sphinxstyleindexlettergroupDefault
\let\spxpagem\sphinxstyleindexpagemain
\let\spxentry\sphinxstyleindexentry
\let\spxextra\sphinxstyleindexextra
"
:close "
\end{sphinxtheindex}
"
:tree)
docs/_build/latex/sphinxhighlight.sty deleted 100644 → 0
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\ProvidesPackage{sphinxhighlight}[2016/05/29 stylesheet for highlighting with pygments]
% Its contents depend on pygments_style configuration variable.
\makeatletter
\def\PYG@reset{\let\PYG@it=\relax \let\PYG@bf=\relax%
\let\PYG@ul=\relax \let\PYG@tc=\relax%
\let\PYG@bc=\relax \let\PYG@ff=\relax}
\def\PYG@tok#1{\csname PYG@tok@#1\endcsname}
\def\PYG@toks#1+{\ifx\relax#1\empty\else%
\PYG@tok{#1}\expandafter\PYG@toks\fi}
\def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{%
\PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}}
\def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}}
\@namedef{PYG@tok@w}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
\@namedef{PYG@tok@c}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
\@namedef{PYG@tok@cp}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@cs}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}\def\PYG@bc##1{{\setlength{\fboxsep}{0pt}\colorbox[rgb]{1.00,0.94,0.94}{\strut ##1}}}}
\@namedef{PYG@tok@k}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@kp}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@kt}{\def\PYG@tc##1{\textcolor[rgb]{0.56,0.13,0.00}{##1}}}
\@namedef{PYG@tok@o}{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\@namedef{PYG@tok@ow}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@nb}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@nf}{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}}
\@namedef{PYG@tok@nc}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}}
\@namedef{PYG@tok@nn}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}}
\@namedef{PYG@tok@ne}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@nv}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
\@namedef{PYG@tok@no}{\def\PYG@tc##1{\textcolor[rgb]{0.38,0.68,0.84}{##1}}}
\@namedef{PYG@tok@nl}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.13,0.44}{##1}}}
\@namedef{PYG@tok@ni}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.84,0.33,0.22}{##1}}}
\@namedef{PYG@tok@na}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@nt}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.45}{##1}}}
\@namedef{PYG@tok@nd}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.33,0.33,0.33}{##1}}}
\@namedef{PYG@tok@s}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@sd}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@si}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.44,0.63,0.82}{##1}}}
\@namedef{PYG@tok@se}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@sr}{\def\PYG@tc##1{\textcolor[rgb]{0.14,0.33,0.53}{##1}}}
\@namedef{PYG@tok@ss}{\def\PYG@tc##1{\textcolor[rgb]{0.32,0.47,0.09}{##1}}}
\@namedef{PYG@tok@sx}{\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}}
\@namedef{PYG@tok@m}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@gh}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
\@namedef{PYG@tok@gu}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
\@namedef{PYG@tok@gd}{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
\@namedef{PYG@tok@gi}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
\@namedef{PYG@tok@gr}{\def\PYG@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
\@namedef{PYG@tok@ge}{\let\PYG@it=\textit}
\@namedef{PYG@tok@gs}{\let\PYG@bf=\textbf}
\@namedef{PYG@tok@gp}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}}
\@namedef{PYG@tok@go}{\def\PYG@tc##1{\textcolor[rgb]{0.20,0.20,0.20}{##1}}}
\@namedef{PYG@tok@gt}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
\@namedef{PYG@tok@err}{\def\PYG@bc##1{{\setlength{\fboxsep}{\string -\fboxrule}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}}
\@namedef{PYG@tok@kc}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@kd}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@kn}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@kr}{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@bp}{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
\@namedef{PYG@tok@fm}{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}}
\@namedef{PYG@tok@vc}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
\@namedef{PYG@tok@vg}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
\@namedef{PYG@tok@vi}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
\@namedef{PYG@tok@vm}{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
\@namedef{PYG@tok@sa}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@sb}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@sc}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@dl}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@s2}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@sh}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@s1}{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
\@namedef{PYG@tok@mb}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@mf}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@mh}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@mi}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@il}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@mo}{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
\@namedef{PYG@tok@ch}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
\@namedef{PYG@tok@cm}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
\@namedef{PYG@tok@cpf}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
\@namedef{PYG@tok@c1}{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
\def\PYGZbs{\char`\\}
\def\PYGZus{\char`\_}
\def\PYGZob{\char`\{}
\def\PYGZcb{\char`\}}
\def\PYGZca{\char`\^}
\def\PYGZam{\char`\&}
\def\PYGZlt{\char`\<}
\def\PYGZgt{\char`\>}
\def\PYGZsh{\char`\#}
\def\PYGZpc{\char`\%}
\def\PYGZdl{\char`\$}
\def\PYGZhy{\char`\-}
\def\PYGZsq{\char`\'}
\def\PYGZdq{\char`\"}
\def\PYGZti{\char`\~}
% for compatibility with earlier versions
\def\PYGZat{@}
\def\PYGZlb{[}
\def\PYGZrb{]}
\makeatother
\renewcommand\PYGZsq{\textquotesingle}
docs/_build/latex/sphinxhowto.cls deleted 100644 → 0
%
% sphinxhowto.cls for Sphinx (https://www.sphinx-doc.org/)
%
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\ProvidesClass{sphinxhowto}[2019/12/01 v2.3.0 Document class (Sphinx howto)]
% 'oneside' option overriding the 'twoside' default
\newif\if@oneside
\DeclareOption{oneside}{\@onesidetrue}
% Pass remaining document options to the parent class.
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}}
\ProcessOptions\relax
% Default to two-side document
\if@oneside
% nothing to do (oneside is the default)
\else
\PassOptionsToClass{twoside}{\sphinxdocclass}
\fi
\LoadClass{\sphinxdocclass}
% Set some sane defaults for section numbering depth and TOC depth. You can
% reset these counters in your preamble.
%
\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}% i.e. section and subsection
% Adapt \and command to the flushright context of \sphinxmaketitle, to
% avoid ragged line endings if author names do not fit all on one single line
\DeclareRobustCommand{\and}{%
\end{tabular}\kern-\tabcolsep
\allowbreak
\hskip\dimexpr1em+\tabcolsep\@plus.17fil\begin{tabular}[t]{c}%
}%
% If it is desired that each author name be on its own line, use in preamble:
%\DeclareRobustCommand{\and}{%
% \end{tabular}\kern-\tabcolsep\\\begin{tabular}[t]{c}%
%}%
% Change the title page to look a bit better, and fit in with the fncychap
% ``Bjarne'' style a bit better.
%
\newcommand{\sphinxmaketitle}{%
\noindent\rule{\linewidth}{1pt}\par
\begingroup % for PDF information dictionary
\def\endgraf{ }\def\and{\& }%
\pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup
\hypersetup{pdfauthor={\@author}, pdftitle={\@title}}%
\endgroup
\begin{flushright}
\sphinxlogo
\py@HeaderFamily
{\Huge \@title }\par
{\itshape\large \py@release \releaseinfo}\par
\vspace{25pt}
{\Large
\begin{tabular}[t]{c}
\@author
\end{tabular}\kern-\tabcolsep}\par
\vspace{25pt}
\@date \par
\py@authoraddress \par
\end{flushright}
\@thanks
\setcounter{footnote}{0}
\let\thanks\relax\let\maketitle\relax
%\gdef\@thanks{}\gdef\@author{}\gdef\@title{}
}
\newcommand{\sphinxtableofcontents}{%
\begingroup
\parskip \z@skip
\sphinxtableofcontentshook
\tableofcontents
\endgroup
\noindent\rule{\linewidth}{1pt}\par
\vspace{12pt}%
}
\newcommand\sphinxtableofcontentshook{}
\pagenumbering{arabic}
% Fix the bibliography environment to add an entry to the Table of
% Contents.
% For an article document class this environment is a section,
% so no page break before it.
%
\newenvironment{sphinxthebibliography}[1]{%
% \phantomsection % not needed here since TeXLive 2010's hyperref
\begin{thebibliography}{#1}%
\addcontentsline{toc}{section}{\ifdefined\refname\refname\else\ifdefined\bibname\bibname\fi\fi}}{\end{thebibliography}}
% Same for the indices.
% The memoir class already does this, so we don't duplicate it in that case.
%
\@ifclassloaded{memoir}
{\newenvironment{sphinxtheindex}{\begin{theindex}}{\end{theindex}}}
{\newenvironment{sphinxtheindex}{%
\phantomsection % needed because no chapter, section, ... is created by theindex
\begin{theindex}%
\addcontentsline{toc}{section}{\indexname}}{\end{theindex}}}
docs/_build/latex/sphinxlatexadmonitions.sty deleted 100644 → 0
%% NOTICES AND ADMONITIONS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexadmonitions.sty}[2021/01/27 admonitions]
% Provides support for this output mark-up from Sphinx latex writer:
%
% - sphinxadmonition (environment)
% This is a dispatch supporting
%
% - note, hint, important, tip (via sphinxlightbox)
% - warning, caution, attention, danger, error (via sphinxheavybox)
%
% Each sphinx<notice name> environment can be redefined by user.
% The defaults are customizable via various colour and dimension
% settings, cf sphinx docs (latex customization).
%
% Requires:
\RequirePackage{framed}% used by sphinxheavybox
%
% Dependencies (they do not need to be defined at time of loading):
% - of course the various colour and dimension options handled via sphinx.sty
% - \sphinxstrong (for sphinxlightbox and sphinxheavybox)
% - dimension register \spx@image@maxheight from sphinxlatexgraphics.sty
% - \savenotes/\spewnotes from sphinxpackagefootnote (for sphinxheavybox)
% Provides: (also in sphinxlatexliterals.sty)
\providecommand*\sphinxvspacefixafterfrenchlists{%
\ifvmode\ifdim\lastskip<\z@ \vskip\parskip\fi\else\par\fi
}
% Some are quite plain
% the spx@notice@bordercolor etc are set in the sphinxadmonition environment
\newenvironment{sphinxlightbox}{%
\par
\noindent{\color{spx@notice@bordercolor}%
\rule{\linewidth}{\spx@notice@border}}\par\nobreak
{\parskip\z@skip\noindent}%
}
{%
% counteract previous possible negative skip (French lists!):
% (we can't cancel that any earlier \vskip introduced a potential pagebreak)
\sphinxvspacefixafterfrenchlists
\nobreak\vbox{\noindent\kern\@totalleftmargin
{\color{spx@notice@bordercolor}%
\rule[\dimexpr.4\baselineskip-\spx@notice@border\relax]
{\linewidth}{\spx@notice@border}}\hss}\allowbreak
}% end of sphinxlightbox environment definition
% may be renewenvironment'd by user for complete customization
\newenvironment{sphinxnote}[1]
{\begin{sphinxlightbox}\sphinxstrong{#1} }{\end{sphinxlightbox}}
\newenvironment{sphinxhint}[1]
{\begin{sphinxlightbox}\sphinxstrong{#1} }{\end{sphinxlightbox}}
\newenvironment{sphinximportant}[1]
{\begin{sphinxlightbox}\sphinxstrong{#1} }{\end{sphinxlightbox}}
\newenvironment{sphinxtip}[1]
{\begin{sphinxlightbox}\sphinxstrong{#1} }{\end{sphinxlightbox}}
% or just use the package options
% these are needed for common handling by notice environment of lightbox
% and heavybox but they are currently not used by lightbox environment
% and there is consequently no corresponding package option
\definecolor{sphinxnoteBgColor}{rgb}{1,1,1}
\definecolor{sphinxhintBgColor}{rgb}{1,1,1}
\definecolor{sphinximportantBgColor}{rgb}{1,1,1}
\definecolor{sphinxtipBgColor}{rgb}{1,1,1}
% Others get more distinction
% Code adapted from framed.sty's "snugshade" environment.
% Nesting works (inner frames do not allow page breaks).
\newenvironment{sphinxheavybox}{\par
\setlength{\FrameRule}{\spx@notice@border}%
\setlength{\FrameSep}{\dimexpr.6\baselineskip-\FrameRule\relax}
\advance\spx@image@maxheight
-\dimexpr2\FrameRule
+2\FrameSep
+\baselineskip\relax % will happen again if nested, needed indeed!
% configure framed.sty's parameters to obtain same vertical spacing
% as for "light" boxes. We need for this to manually insert parskip glue and
% revert a skip done by framed before the frame.
\ltx@ifundefined{OuterFrameSep}{}{\OuterFrameSep\z@skip}%
\vspace{\FrameHeightAdjust}
% copied/adapted from framed.sty's snugshade
\def\FrameCommand##1{\hskip\@totalleftmargin
\fboxsep\FrameSep \fboxrule\FrameRule
\fcolorbox{spx@notice@bordercolor}{spx@notice@bgcolor}{##1}%
\hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
\savenotes
% use a minipage if we are already inside a framed environment
\ifspx@inframed
\noindent\begin{minipage}{\linewidth}
\else
% handle case where notice is first thing in a list item (or is quoted)
\if@inlabel
\noindent\par\vspace{-\baselineskip}
\else
\vspace{\parskip}
\fi
\fi
\MakeFramed {\spx@inframedtrue
\advance\hsize-\width \@totalleftmargin\z@ \linewidth\hsize
% minipage initialization copied from LaTeX source code.
\@pboxswfalse
\let\@listdepth\@mplistdepth \@mplistdepth\z@
\@minipagerestore
\@setminipage }%
}
{%
\par\unskip
\@minipagefalse
\endMakeFramed
\ifspx@inframed\end{minipage}\fi
% set footnotes at bottom of page
\spewnotes
% arrange for similar spacing below frame as for "light" boxes.
\vskip .4\baselineskip
}% end of sphinxheavybox environment definition
% may be renewenvironment'd by user for complete customization
\newenvironment{sphinxwarning}[1]
{\begin{sphinxheavybox}\sphinxstrong{#1} }{\end{sphinxheavybox}}
\newenvironment{sphinxcaution}[1]
{\begin{sphinxheavybox}\sphinxstrong{#1} }{\end{sphinxheavybox}}
\newenvironment{sphinxattention}[1]
{\begin{sphinxheavybox}\sphinxstrong{#1} }{\end{sphinxheavybox}}
\newenvironment{sphinxdanger}[1]
{\begin{sphinxheavybox}\sphinxstrong{#1} }{\end{sphinxheavybox}}
\newenvironment{sphinxerror}[1]
{\begin{sphinxheavybox}\sphinxstrong{#1} }{\end{sphinxheavybox}}
% or just use package options
% the \colorlet of xcolor (if at all loaded) is overkill for our use case
\newcommand{\sphinxcolorlet}[2]
{\expandafter\let\csname\@backslashchar color@#1\expandafter\endcsname
\csname\@backslashchar color@#2\endcsname }
% the main dispatch for all types of notices
\newenvironment{sphinxadmonition}[2]{% #1=type, #2=heading
% can't use #1 directly in definition of end part
\def\spx@noticetype {#1}%
% set parameters of heavybox/lightbox
\sphinxcolorlet{spx@notice@bordercolor}{sphinx#1BorderColor}%
\sphinxcolorlet{spx@notice@bgcolor}{sphinx#1BgColor}%
\spx@notice@border \dimexpr\csname spx@opt@#1border\endcsname\relax
% start specific environment, passing the heading as argument
\begin{sphinx#1}{#2}}
% workaround some LaTeX "feature" of \end command
{\edef\spx@temp{\noexpand\end{sphinx\spx@noticetype}}\spx@temp}
\endinput
docs/_build/latex/sphinxlatexcontainers.sty deleted 100644 → 0
%% CONTAINER DIRECTIVES
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexcontainers.sty}[2021/05/03 containers]
% The purpose of this file is to provide a dummy environment sphinxclass which
% will be inserted for each class in each container directive. The class name
% will be passed as the argument to the environment.
%
% For a class foo, the user can define customised handling of that class by
% defining the sphinxclassfoo LaTeX environment.
\newenvironment{sphinxuseclass}[1]{%
\def\sphinxClassFunctionName{sphinxclass#1}%
\ltx@ifundefined{\sphinxClassFunctionName}%
{}% undefined so do nothing
{\expandafter\begin\expandafter{\sphinxClassFunctionName}}%
}{%
\ltx@ifundefined{\sphinxClassFunctionName}%
{}% we did nothing so we keep doing nothing
{\expandafter\end\expandafter{\sphinxClassFunctionName}}%
}%
docs/_build/latex/sphinxlatexgraphics.sty deleted 100644 → 0
%% GRAPHICS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexgraphics.sty}[2021/01/27 graphics]
% Provides support for this output mark-up from Sphinx latex writer:
%
% - macros:
%
% - \sphinxfigcaption
% - \sphinxincludegraphics
%
% - environments:
%
% - sphinxfigure-in-table
%
% May change:
%
% - \sphinxcaption (at begin document)
%
% Also provides:
%
% - \sphinxsafeincludegraphics (default of \sphinxincludegraphics since 2.0)
% - \spx@image@maxheight dimension (used by sphinxlatexadmonitions.sty)
% - \spx@image@box scratch box register (also used by sphinxlatexliterals.sty)
%
% Requires:
% \RequirePackage{graphicx}% done in sphinx.sty
\RequirePackage{amstext}% needed for \firstchoice@true(false)
% \sphinxincludegraphics resizes images larger than the TeX \linewidth (which
% is adjusted in indented environments), or taller than a certain maximal
% height (usually \textheight and this is reduced in the environments which use
% framed.sty to avoid infinite loop if image too tall).
%
% In case height or width options are present the rescaling is done
% (since 2.0), in a way keeping the width:height ratio either native from
% image or from the width and height options if both were present.
%
\newdimen\spx@image@maxheight
\AtBeginDocument{\spx@image@maxheight\textheight}
% box scratch register
\newbox\spx@image@box
\newcommand*{\sphinxsafeincludegraphics}[2][]{%
% #1 contains possibly width=, height=, but no scale= since 1.8.4
\setbox\spx@image@box\hbox{\includegraphics[#1,draft]{#2}}%
\in@false % use some handy boolean flag
\ifdim \wd\spx@image@box>\linewidth
\in@true % flag to remember to adjust options and set box dimensions
% compute height which results from rescaling width to \linewidth
% and keep current aspect ratio. multiply-divide in \numexpr uses
% temporarily doubled precision, hence no overflow. (of course we
% assume \ht is not a few sp's below \maxdimen...(about 16384pt).
\edef\spx@image@rescaledheight % with sp units
{\the\numexpr\ht\spx@image@box
*\linewidth/\wd\spx@image@box sp}%
\ifdim\spx@image@rescaledheight>\spx@image@maxheight
% the rescaled height will be too big, so it is height which decides
% the rescaling factor
\def\spx@image@requiredheight{\spx@image@maxheight}% dimen register
\edef\spx@image@requiredwidth % with sp units
{\the\numexpr\wd\spx@image@box
*\spx@image@maxheight/\ht\spx@image@box sp}%
% TODO: decide if this commented-out block could be needed due to
% rounding in numexpr operations going up
% \ifdim\spx@image@requiredwidth>\linewidth
% \def\spx@image@requiredwidth{\linewidth}% dimen register
% \fi
\else
\def\spx@image@requiredwidth{\linewidth}% dimen register
\let\spx@image@requiredheight\spx@image@rescaledheight% sp units
\fi
\else
% width is ok, let's check height
\ifdim\ht\spx@image@box>\spx@image@maxheight
\in@true
\edef\spx@image@requiredwidth % with sp units
{\the\numexpr\wd\spx@image@box
*\spx@image@maxheight/\ht\spx@image@box sp}%
\def\spx@image@requiredheight{\spx@image@maxheight}% dimen register
\fi
\fi % end of check of width and height
\ifin@
\setbox\spx@image@box
\hbox{\includegraphics
[%#1,% contained only width and/or height and overruled anyhow
width=\spx@image@requiredwidth,height=\spx@image@requiredheight]%
{#2}}%
% \includegraphics does not set box dimensions to the exactly
% requested ones, see https://github.com/latex3/latex2e/issues/112
\wd\spx@image@box\spx@image@requiredwidth
\ht\spx@image@box\spx@image@requiredheight
\leavevmode\box\spx@image@box
\else
% here we do not modify the options, no need to adjust width and height
% on output, they will be computed exactly as with "draft" option
\setbox\spx@image@box\box\voidb@x % clear memory
\includegraphics[#1]{#2}%
\fi
}%
% Use the "safe" one by default (2.0)
\def\sphinxincludegraphics{\sphinxsafeincludegraphics}
%% FIGURE IN TABLE
%
\newenvironment{sphinxfigure-in-table}[1][\linewidth]{%
\def\@captype{figure}%
\sphinxsetvskipsforfigintablecaption
\begin{minipage}{#1}%
}{\end{minipage}}
% tabulary expands twice contents, we need to prevent double counter stepping
\newcommand*\sphinxfigcaption
{\ifx\equation$%$% this is trick to identify tabulary first pass
\firstchoice@false\else\firstchoice@true\fi
\spx@originalcaption }
\newcommand*\sphinxsetvskipsforfigintablecaption
{\abovecaptionskip\smallskipamount
\belowcaptionskip\smallskipamount}
\endinput
docs/_build/latex/sphinxlatexindbibtoc.sty deleted 100644 → 0
%% INDEX, BIBLIOGRAPHY, APPENDIX, TABLE OF CONTENTS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexindbibtoc.sty}[2021/01/27 index, bib., toc]
% Provides support for this output mark-up from Sphinx latex writer:
%
% - environments: (backup defaults or get redefined)
%
% - sphinxtheindex (direct mark-up or via python.ist or sphinx.xdy)
% - sphinxthebibliography
%
% - macros: (defines defaults)
%
% - \sphinxmaketitle
% - \sphinxtableofcontents
% - \sphinxnonalphabeticalgroupname
% - \sphinxsymbolsname
% - \sphinxnumbersname
% - \sphinxcite
%
% Requires:
\RequirePackage{makeidx}
% fix the double index and bibliography on the table of contents
% in jsclasses (Japanese standard document classes)
\ifx\@jsc@uplatextrue\@undefined\else
\renewenvironment{sphinxtheindex}
{\cleardoublepage\phantomsection
\begin{theindex}}
{\end{theindex}}
\renewenvironment{sphinxthebibliography}[1]
{\cleardoublepage% \phantomsection % not needed here since TeXLive 2010's hyperref
\begin{thebibliography}{#1}}
{\end{thebibliography}}
\fi
% disable \@chappos in Appendix in pTeX
\ifx\kanjiskip\@undefined\else
\let\py@OldAppendix=\appendix
\renewcommand{\appendix}{
\py@OldAppendix
\gdef\@chappos{}
}
\fi
% make commands known to non-Sphinx document classes
\providecommand*{\sphinxmaketitle}{\maketitle}
\providecommand*{\sphinxtableofcontents}{\tableofcontents}
\ltx@ifundefined{sphinxthebibliography}
{\newenvironment
{sphinxthebibliography}{\begin{thebibliography}}{\end{thebibliography}}%
}
{}% else clause of \ltx@ifundefined
\ltx@ifundefined{sphinxtheindex}
{\newenvironment{sphinxtheindex}{\begin{theindex}}{\end{theindex}}}%
{}% else clause of \ltx@ifundefined
% for usage with xindy: this string gets internationalized in preamble
\newcommand*{\sphinxnonalphabeticalgroupname}{}
% redefined in preamble, headings for makeindex produced index
\newcommand*{\sphinxsymbolsname}{}
\newcommand*{\sphinxnumbersname}{}
\protected\def\sphinxcite{\cite}
\endinput
docs/_build/latex/sphinxlatexlists.sty deleted 100644 → 0
%% ALPHANUMERIC LIST ITEMS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexlists.sty}[2021/12/20 lists]
% Provides support for this output mark-up from Sphinx latex writer:
% - \sphinxsetlistlabels
% - \sphinxlineitem
% and for the maxlistdepth key of sphinxsetup
% Dependencies: the \spx@opt@maxlistdepth from sphinx.sty
% We need some helpers macros
\newtoks\spx@lineitemlabel
\long\def\sphinx@gobto@sphinxlineitem#1\sphinxlineitem{}
% TeX/LaTeX has no (easy to use) built-in "peek-ahead" mechanism, but
% we would like to know if next token is another \sphinxlineitem (this
% can happen in glossary entries with multiple terms for same definition)
% so we simply grab next token (assuming it is not {tokens} originally)
\newcommand\sphinxlineitem[2]{%
% safe test of whether #2 is \sphinxlineitem
\sphinx@gobto@sphinxlineitem#2\@gobbletwo\sphinxlineitem\unless
\iftrue
% case with sphinxlineitem immediately followed by another \sphinxlineitem:
% accumulate successive terms until actual definition or sub-list is found
\spx@lineitemlabel\expandafter{\the\spx@lineitemlabel\strut#1\\}%
\else
% now issue the \item command with possibly multi-line contents
% these weird incantations with \kern are related to how LaTeX
% handles \item generally
\item[\kern\labelwidth\kern-\itemindent\kern-\leftmargin
{\parbox[t]{\dimexpr\linewidth+\leftmargin\relax}{%
\raggedright
\the\spx@lineitemlabel% accumulated terms before this one, CR separated
\strut#1}}% due to LaTeX internals no \par token allowed here,
% but the \parbox will insert one tacitly at end
\kern-\labelsep]%
\spx@lineitemlabel{}%
% this causes the label to be typeset (filling up the line), clearing up
% things in case a nested list follows.
\leavevmode
\fi #2%
}%
\newcommand\sphinxsetlistlabels[5]
{% #1 = style, #2 = enum, #3 = enumnext, #4 = prefix, #5 = suffix
% #2 and #3 are counters used by enumerate environment e.g. enumi, enumii.
% #1 is a macro such as \arabic or \alph
% prefix and suffix are strings (by default empty and a dot).
\@namedef{the#2}{#1{#2}}%
\@namedef{label#2}{#4\@nameuse{the#2}#5}%
\@namedef{p@#3}{\@nameuse{p@#2}#4\@nameuse{the#2}#5}%
}%
%% MAXLISTDEPTH
%
% remove LaTeX's cap on nesting depth if 'maxlistdepth' key used.
% This is a hack, which works with the standard classes: it assumes \@toodeep
% is always used in "true" branches: "\if ... \@toodeep \else .. \fi."
% will force use the "false" branch (if there is one)
\def\spx@toodeep@hack{\fi\iffalse}
% do nothing if 'maxlistdepth' key not used or if package enumitem loaded.
\ifnum\spx@opt@maxlistdepth=\z@\expandafter\@gobbletwo\fi
\AtBeginDocument{%
\@ifpackageloaded{enumitem}{\remove@to@nnil}{}%
\let\spx@toodeepORI\@toodeep
\def\@toodeep{%
\ifnum\@listdepth<\spx@opt@maxlistdepth\relax
\expandafter\spx@toodeep@hack
\else
\expandafter\spx@toodeepORI
\fi}%
% define all missing \@list... macros
\count@\@ne
\loop
\ltx@ifundefined{@list\romannumeral\the\count@}
{\iffalse}{\iftrue\advance\count@\@ne}%
\repeat
\loop
\ifnum\count@>\spx@opt@maxlistdepth\relax\else
\expandafter\let
\csname @list\romannumeral\the\count@\expandafter\endcsname
\csname @list\romannumeral\the\numexpr\count@-\@ne\endcsname
% workaround 2.6--3.2d babel-french issue (fixed in 3.2e; no change needed)
\ltx@ifundefined{leftmargin\romannumeral\the\count@}
{\expandafter\let
\csname leftmargin\romannumeral\the\count@\expandafter\endcsname
\csname leftmargin\romannumeral\the\numexpr\count@-\@ne\endcsname}{}%
\advance\count@\@ne
\repeat
% define all missing enum... counters and \labelenum... macros and \p@enum..
\count@\@ne
\loop
\ltx@ifundefined{c@enum\romannumeral\the\count@}
{\iffalse}{\iftrue\advance\count@\@ne}%
\repeat
\loop
\ifnum\count@>\spx@opt@maxlistdepth\relax\else
\newcounter{enum\romannumeral\the\count@}%
\expandafter\def
\csname labelenum\romannumeral\the\count@\expandafter\endcsname
\expandafter
{\csname theenum\romannumeral\the\numexpr\count@\endcsname.}%
\expandafter\def
\csname p@enum\romannumeral\the\count@\expandafter\endcsname
\expandafter
{\csname p@enum\romannumeral\the\numexpr\count@-\@ne\expandafter
\endcsname\csname theenum\romannumeral\the\numexpr\count@-\@ne\endcsname.}%
\advance\count@\@ne
\repeat
% define all missing labelitem... macros
\count@\@ne
\loop
\ltx@ifundefined{labelitem\romannumeral\the\count@}
{\iffalse}{\iftrue\advance\count@\@ne}%
\repeat
\loop
\ifnum\count@>\spx@opt@maxlistdepth\relax\else
\expandafter\let
\csname labelitem\romannumeral\the\count@\expandafter\endcsname
\csname labelitem\romannumeral\the\numexpr\count@-\@ne\endcsname
\advance\count@\@ne
\repeat
\PackageInfo{sphinx}{maximal list depth extended to \spx@opt@maxlistdepth}%
\@gobble\@nnil
}
\endinput
docs/_build/latex/sphinxlatexnumfig.sty deleted 100644 → 0
%% NUMBERING OF FIGURES, TABLES, AND LITERAL BLOCKS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexnumfig.sty}[2021/01/27 numbering]
% Requires: remreset (old LaTeX only)
% relates to numfig and numfig_secnum_depth configuration variables
% LaTeX 2018-04-01 and later provides \@removefromreset
\ltx@ifundefined{@removefromreset}
{\RequirePackage{remreset}}
{}% avoid warning
% Everything is delayed to \begin{document} to allow hyperref patches into
% \newcounter to solve duplicate label problems for internal hyperlinks to
% code listings (literalblock counter). User or extension re-definitions of
% \theliteralblock, et al., thus have also to be delayed. (changed at 3.5.0)
\AtBeginDocument{%
\ltx@ifundefined{c@chapter}
{\newcounter{literalblock}}%
{\newcounter{literalblock}[chapter]%
\def\theliteralblock{\ifnum\c@chapter>\z@\arabic{chapter}.\fi
\arabic{literalblock}}%
}%
\ifspx@opt@nonumfigreset
\ltx@ifundefined{c@chapter}{}{%
\@removefromreset{figure}{chapter}%
\@removefromreset{table}{chapter}%
\@removefromreset{literalblock}{chapter}%
\ifspx@opt@mathnumfig
\@removefromreset{equation}{chapter}%
\fi
}%
\def\thefigure{\arabic{figure}}%
\def\thetable {\arabic{table}}%
\def\theliteralblock{\arabic{literalblock}}%
\ifspx@opt@mathnumfig
\def\theequation{\arabic{equation}}%
\fi
\else
\let\spx@preAthefigure\@empty
\let\spx@preBthefigure\@empty
% \ifspx@opt@usespart % <-- LaTeX writer could pass such a 'usespart' boolean
% % as sphinx.sty package option
% If document uses \part, (triggered in Sphinx by latex_toplevel_sectioning)
% LaTeX core per default does not reset chapter or section
% counters at each part.
% But if we modify this, we need to redefine \thechapter, \thesection to
% include the part number and this will cause problems in table of contents
% because of too wide numbering. Simplest is to do nothing.
% \fi
\ifnum\spx@opt@numfigreset>0
\ltx@ifundefined{c@chapter}
{}
{\g@addto@macro\spx@preAthefigure{\ifnum\c@chapter>\z@\arabic{chapter}.}%
\g@addto@macro\spx@preBthefigure{\fi}}%
\fi
\ifnum\spx@opt@numfigreset>1
\@addtoreset{figure}{section}%
\@addtoreset{table}{section}%
\@addtoreset{literalblock}{section}%
\ifspx@opt@mathnumfig
\@addtoreset{equation}{section}%
\fi%
\g@addto@macro\spx@preAthefigure{\ifnum\c@section>\z@\arabic{section}.}%
\g@addto@macro\spx@preBthefigure{\fi}%
\fi
\ifnum\spx@opt@numfigreset>2
\@addtoreset{figure}{subsection}%
\@addtoreset{table}{subsection}%
\@addtoreset{literalblock}{subsection}%
\ifspx@opt@mathnumfig
\@addtoreset{equation}{subsection}%
\fi%
\g@addto@macro\spx@preAthefigure{\ifnum\c@subsection>\z@\arabic{subsection}.}%
\g@addto@macro\spx@preBthefigure{\fi}%
\fi
\ifnum\spx@opt@numfigreset>3
\@addtoreset{figure}{subsubsection}%
\@addtoreset{table}{subsubsection}%
\@addtoreset{literalblock}{subsubsection}%
\ifspx@opt@mathnumfig
\@addtoreset{equation}{subsubsection}%
\fi%
\g@addto@macro\spx@preAthefigure{\ifnum\c@subsubsection>\z@\arabic{subsubsection}.}%
\g@addto@macro\spx@preBthefigure{\fi}%
\fi
\ifnum\spx@opt@numfigreset>4
\@addtoreset{figure}{paragraph}%
\@addtoreset{table}{paragraph}%
\@addtoreset{literalblock}{paragraph}%
\ifspx@opt@mathnumfig
\@addtoreset{equation}{paragraph}%
\fi%
\g@addto@macro\spx@preAthefigure{\ifnum\c@subparagraph>\z@\arabic{subparagraph}.}%
\g@addto@macro\spx@preBthefigure{\fi}%
\fi
\ifnum\spx@opt@numfigreset>5
\@addtoreset{figure}{subparagraph}%
\@addtoreset{table}{subparagraph}%
\@addtoreset{literalblock}{subparagraph}%
\ifspx@opt@mathnumfig
\@addtoreset{equation}{subparagraph}%
\fi%
\g@addto@macro\spx@preAthefigure{\ifnum\c@subsubparagraph>\z@\arabic{subsubparagraph}.}%
\g@addto@macro\spx@preBthefigure{\fi}%
\fi
\expandafter\g@addto@macro
\expandafter\spx@preAthefigure\expandafter{\spx@preBthefigure}%
\let\thefigure\spx@preAthefigure
\let\thetable\spx@preAthefigure
\let\theliteralblock\spx@preAthefigure
\g@addto@macro\thefigure{\arabic{figure}}%
\g@addto@macro\thetable{\arabic{table}}%
\g@addto@macro\theliteralblock{\arabic{literalblock}}%
\ifspx@opt@mathnumfig
\let\theequation\spx@preAthefigure
\g@addto@macro\theequation{\arabic{equation}}%
\fi
\fi
}% end of big \AtBeginDocument
\endinput
docs/_build/latex/sphinxlatexobjects.sty deleted 100644 → 0
%% MODULE RELEASE DATA AND OBJECT DESCRIPTIONS
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexobjects.sty}[2022/01/13 documentation environments]
% Provides support for this output mark-up from Sphinx latex writer:
%
% - environments
%
% - fulllineitems
% - productionlist
% - optionlist
% - DUlineblock (also "lineblock")
%
% - macros
%
% - \DUrole
% - various legacy support macros related to author and release
% data of documented objects and modules.
% \moduleauthor{name}{email}
\newcommand{\moduleauthor}[2]{}
% \sectionauthor{name}{email}
\newcommand{\sectionauthor}[2]{}
% Allow the release number to be specified independently of the
% \date{}. This allows the date to reflect the document's date and
% release to specify the release that is documented.
%
\newcommand{\py@release}{\releasename\space\version}
\newcommand{\version}{}% part of \py@release, used by title page and headers
% \releaseinfo is used on titlepage (sphinxmanual.cls, sphinxhowto.cls)
\newcommand{\releaseinfo}{}
\newcommand{\setreleaseinfo}[1]{\renewcommand{\releaseinfo}{#1}}
% this is inserted via template and #1=release config variable
\newcommand{\release}[1]{\renewcommand{\version}{#1}}
% this is defined by template to 'releasename' latex_elements key
\newcommand{\releasename}{}
% Fix issue in case release and releasename deliberately left blank
\newcommand{\sphinxheadercomma}{, }% used in fancyhdr header definition
\newcommand{\sphinxifemptyorblank}[1]{%
% test after one expansion of macro #1 if contents is empty or spaces
\if&\expandafter\@firstofone\detokenize\expandafter{#1}&%
\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi}%
\AtBeginDocument {%
\sphinxifemptyorblank{\releasename}
{\sphinxifemptyorblank{\version}{\let\sphinxheadercomma\empty}{}}
{}%
}%
% Allow specification of the author's address separately from the
% author's name. This can be used to format them differently, which
% is a good thing.
%
\newcommand{\py@authoraddress}{}
\newcommand{\authoraddress}[1]{\renewcommand{\py@authoraddress}{#1}}
% {fulllineitems} is the main environment for object descriptions.
%
% With 4.0.0 \pysigline (and \pysiglinewithargsret), used in a fulllineitems
% environment the #1 will already be of the width which is computed here, i.e.
% the available width on line, so the \makebox becomes a bit superfluous
\newcommand{\py@itemnewline}[1]{% macro used as \makelabel in fulllineitems
% Memo: this presupposes \itemindent is 0pt
\kern\labelsep % because \@labels core latex box does \hskip-\labelsep
\makebox[\dimexpr\linewidth+\labelwidth\relax][l]{#1}%
\kern-\labelsep % because at end of \@labels box there is \hskip\labelsep
}
\newenvironment{fulllineitems}{%
\begin{list}{}{\labelwidth \leftmargin
\rightmargin \z@ \topsep -\parskip \partopsep \parskip
\itemsep -\parsep
\let\makelabel=\py@itemnewline}%
}{\end{list}}
% Signatures, possibly multi-line
%
% For legacy reasons Sphinx uses LaTeX \list and \item's for signatures
% This is delicate:
% - the actual item label is not typeset immediately by \item but later as part
% of the \everypar which will be triggered by either next paragraph or a manual
% \leavevmode, or if nothing in-between by the next \item,
% - \begingroup <set-up>\item[foo] <setup>\endgroup leads to errors,
% - vertical space depends on \parskip and \itemsep values in somewhat
% subtle manners.
%
% Since the 2022/01/13 version things are simpler as \parskip is simply set
% to zero during execution of \pysigline/\pysiglinewithargsret
%
% Parameter for separation via \itemsep of multiple signatures with common desc
\newlength\sphinxsignaturesep
\setlength\sphinxsignaturesep{\smallskipamount}
% latex.py outputs mark-up like this:
% \pysigstartsignatures <signatures> \pysigstopsignatures <actual desc>
\newcommand{\pysigstartsignatures}{%
% store current \parskip and \itemsep
\edef\pysig@restore@itemsep@and@parskip{%
\itemsep\the\itemsep\relax
\parskip\the\parskip\relax
}%
% set them to control the spacing between signatures sharing common desc
\parskip\z@skip
\itemsep\sphinxsignaturesep
}
\newcommand{\pysigstopsignatures}{%
% 1) encourage a pagebreak in an attempt to try to avoid last
% signature ending up separated from description (due to voodoo next)
\penalty-100
% 2) some voodoo to separate last signature from description in a manner
% robust with respect to the latter being itself a LaTeX list object
\leavevmode\par\kern-\baselineskip\item[\strut]
%
\leavevmode
% it is important \leavevmode was issued before the \parskip reset, and
% it is also needed for the case of an object desc itself a LaTeX \list
% now restore \itemsep and \parskip
\pysig@restore@itemsep@and@parskip
}
%
% Use a \parbox to accomodate long argument list in signatures
% LaTeX did not imagine that an \item label could need multi-line rendering
\newlength{\py@argswidth}
\newcommand{\py@sigparams}[2]{%
% The \py@argswidth has been computed in \pysiglinewithargsret to make the
% argument list use full available width
\parbox[t]{\py@argswidth}{\raggedright #1\sphinxcode{)}#2\strut}%
% final strut is to help get correct vertical separation
}
\newcommand{\pysigline}[1]{%
% as \py@argswidth is available, we use it but no "args" here
% the \relax\relax is because \py@argswidth is a "skip" variable
% this will make the label occupy the full available linewidth
\py@argswidth=\dimexpr\linewidth+\labelwidth\relax\relax
\item[{\parbox[t]{\py@argswidth}{\raggedright #1\strut}}]
\pysigadjustitemsep
}
\newcommand{\pysiglinewithargsret}[3]{%
% as #1 may contain a footnote using \label we need to make \label
% a no-op here to avoid LaTeX complaining about duplicates
\let\spx@label\label\let\label\@gobble
\settowidth{\py@argswidth}{#1\sphinxcode{(}}%
\let\label\spx@label
\py@argswidth=\dimexpr\linewidth+\labelwidth-\py@argswidth\relax\relax
\item[{#1\sphinxcode{(}\py@sigparams{#2}{#3}\strut}]
\pysigadjustitemsep
}
\newcommand{\pysigadjustitemsep}{%
% adjust \itemsep to control the separation with the next signature
% sharing common description
\ifsphinxsigismultiline
% inside a multiline signature, no extra vertical spacing
% ("multiline" here does not refer to possibly long
% list of arguments, but to a cpp domain feature)
\itemsep\z@skip
\else
\itemsep\sphinxsignaturesep
\fi
}
\newif\ifsphinxsigismultiline
\newcommand{\pysigstartmultiline}{\sphinxsigismultilinetrue}%
\newcommand{\pysigstopmultiline}{\sphinxsigismultilinefalse\itemsep\sphinxsignaturesep}%
% Production lists
%
\newenvironment{productionlist}{%
% \def\sphinxoptional##1{{\Large[}##1{\Large]}}
\def\production##1##2{\\\sphinxcode{\sphinxupquote{##1}}&::=&\sphinxcode{\sphinxupquote{##2}}}%
\def\productioncont##1{\\& &\sphinxcode{\sphinxupquote{##1}}}%
\parindent=2em
\indent
\setlength{\LTpre}{0pt}%
\setlength{\LTpost}{0pt}%
\begin{longtable}[l]{lcl}
}{%
\end{longtable}
}
% Definition lists; requested by AMK for HOWTO documents. Probably useful
% elsewhere as well, so keep in in the general style support.
%
\newenvironment{definitions}{%
\begin{description}%
\def\term##1{\item[{##1}]\mbox{}\\*[0mm]}%
}{%
\end{description}%
}
%% FROM DOCTUTILS LATEX WRITER
%
% The following is stuff copied from docutils' latex writer.
%
\newcommand{\optionlistlabel}[1]{\normalfont\bfseries #1 \hfill}% \bf deprecated
\newenvironment{optionlist}[1]
{\begin{list}{}
{\setlength{\labelwidth}{#1}
\setlength{\rightmargin}{1cm}
\setlength{\leftmargin}{\rightmargin}
\addtolength{\leftmargin}{\labelwidth}
\addtolength{\leftmargin}{\labelsep}
\renewcommand{\makelabel}{\optionlistlabel}}
}{\end{list}}
\newlength{\lineblockindentation}
\setlength{\lineblockindentation}{2.5em}
\newenvironment{lineblock}[1]
{\begin{list}{}
{\setlength{\partopsep}{\parskip}
\addtolength{\partopsep}{\baselineskip}
\topsep0pt\itemsep0.15\baselineskip\parsep0pt
\leftmargin#1\relax}
\raggedright}
{\end{list}}
% From docutils.writers.latex2e
% inline markup (custom roles)
% \DUrole{#1}{#2} tries \DUrole#1{#2}
\providecommand*{\DUrole}[2]{%
\ifcsname DUrole\detokenize{#1}\endcsname
\csname DUrole\detokenize{#1}\endcsname{#2}%
\else% backwards compatibility: try \docutilsrole#1{#2}
\ifcsname docutilsrole\detokenize{#1}\endcsname
\csname docutilsrole\detokenize{#1}\endcsname{#2}%
\else
#2%
\fi
\fi
}
\providecommand*{\DUprovidelength}[2]{%
\ifdefined#1\else\newlength{#1}\setlength{#1}{#2}\fi
}
\DUprovidelength{\DUlineblockindent}{2.5em}
\ifdefined\DUlineblock\else
\newenvironment{DUlineblock}[1]{%
\list{}{\setlength{\partopsep}{\parskip}
\addtolength{\partopsep}{\baselineskip}
\setlength{\topsep}{0pt}
\setlength{\itemsep}{0.15\baselineskip}
\setlength{\parsep}{0pt}
\setlength{\leftmargin}{#1}}
\raggedright
}
{\endlist}
\fi
\endinput
docs/_build/latex/sphinxlatexshadowbox.sty deleted 100644 → 0
%% TOPIC AND CONTENTS BOXES
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexshadowbox.sty}[2021/01/27 sphinxShadowBox]
% Provides support for this output mark-up from Sphinx latex writer:
%
% - sphinxShadowBox (environment)
%
% Dependencies (they do not need to be defined at time of loading):
%
% - of course the various colour and dimension options handled via sphinx.sty
% - dimension register \spx@image@maxheight from sphinxlatexgraphics.sty
% - \savenotes/\spewnotes from sphinxpackagefootnote
% - \ifspx@inframed defined in sphinx.sty
%
% Requires:
\RequirePackage{framed}
% Again based on use of "framed.sty", this allows breakable framed boxes.
\long\def\spx@ShadowFBox#1{%
\leavevmode\begingroup
% first we frame the box #1
\setbox\@tempboxa
\hbox{\vrule\@width\sphinxshadowrule
\vbox{\hrule\@height\sphinxshadowrule
\kern\sphinxshadowsep
\hbox{\kern\sphinxshadowsep #1\kern\sphinxshadowsep}%
\kern\sphinxshadowsep
\hrule\@height\sphinxshadowrule}%
\vrule\@width\sphinxshadowrule}%
% Now we add the shadow, like \shadowbox from fancybox.sty would do
\dimen@\dimexpr.5\sphinxshadowrule+\sphinxshadowsize\relax
\hbox{\vbox{\offinterlineskip
\hbox{\copy\@tempboxa\kern-.5\sphinxshadowrule
% add shadow on right side
\lower\sphinxshadowsize
\hbox{\vrule\@height\ht\@tempboxa \@width\dimen@}%
}%
\kern-\dimen@ % shift back vertically to bottom of frame
% and add shadow at bottom
\moveright\sphinxshadowsize
\vbox{\hrule\@width\wd\@tempboxa \@height\dimen@}%
}%
% move left by the size of right shadow so shadow adds no width
\kern-\sphinxshadowsize
}%
\endgroup
}
% use framed.sty to allow page breaks in frame+shadow
% works well inside Lists and Quote-like environments
% produced by ``topic'' directive (or local contents)
% could nest if LaTeX writer authorized it
\newenvironment{sphinxShadowBox}
{\def\FrameCommand {\spx@ShadowFBox }%
\advance\spx@image@maxheight
-\dimexpr2\sphinxshadowrule
+2\sphinxshadowsep
+\sphinxshadowsize
+\baselineskip\relax
% configure framed.sty not to add extra vertical spacing
\ltx@ifundefined{OuterFrameSep}{}{\OuterFrameSep\z@skip}%
% the \trivlist will add the vertical spacing on top and bottom which is
% typical of center environment as used in Sphinx <= 1.4.1
% the \noindent has the effet of an extra blank line on top, to
% imitate closely the layout from Sphinx <= 1.4.1; the \FrameHeightAdjust
% will put top part of frame on this baseline.
\def\FrameHeightAdjust {\baselineskip}%
% use package footnote to handle footnotes
\savenotes
\trivlist\item\noindent
% use a minipage if we are already inside a framed environment
\ifspx@inframed\begin{minipage}{\linewidth}\fi
\MakeFramed {\spx@inframedtrue
% framed.sty puts into "\width" the added width (=2shadowsep+2shadowrule)
% adjust \hsize to what the contents must use
\advance\hsize-\width
% adjust LaTeX parameters to behave properly in indented/quoted contexts
\FrameRestore
% typeset the contents as in a minipage (Sphinx <= 1.4.1 used a minipage and
% itemize/enumerate are therein typeset more tightly, we want to keep
% that). We copy-paste from LaTeX source code but don't do a real minipage.
\@pboxswfalse
\let\@listdepth\@mplistdepth \@mplistdepth\z@
\@minipagerestore
\@setminipage
}%
}%
{% insert the "endminipage" code
\par\unskip
\@minipagefalse
\endMakeFramed
\ifspx@inframed\end{minipage}\fi
\endtrivlist
% output the stored footnotes
\spewnotes
}
\endinput
docs/_build/latex/sphinxlatexstyleheadings.sty deleted 100644 → 0
%% TITLES
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexstyleheadings.sty}[2021/01/27 headings]
\RequirePackage[nobottomtitles*]{titlesec}
\@ifpackagelater{titlesec}{2016/03/15}%
{\@ifpackagelater{titlesec}{2016/03/21}%
{}%
{\newif\ifsphinx@ttlpatch@ok
\IfFileExists{etoolbox.sty}{%
\RequirePackage{etoolbox}%
\patchcmd{\ttlh@hang}{\parindent\z@}{\parindent\z@\leavevmode}%
{\sphinx@ttlpatch@oktrue}{}%
\ifsphinx@ttlpatch@ok
\patchcmd{\ttlh@hang}{\noindent}{}{}{\sphinx@ttlpatch@okfalse}%
\fi
}{}%
\ifsphinx@ttlpatch@ok
\typeout{^^J Package Sphinx Info: ^^J
**** titlesec 2.10.1 successfully patched for bugfix ****^^J}%
\else
\AtEndDocument{\PackageWarningNoLine{sphinx}{^^J%
******** titlesec 2.10.1 has a bug, (section numbers disappear) ......|^^J%
******** and Sphinx could not patch it, perhaps because your local ...|^^J%
******** copy is already fixed without a changed release date. .......|^^J%
******** If not, you must update titlesec! ...........................|}}%
\fi
}%
}{}
% Augment the sectioning commands used to get our own font family in place,
% and reset some internal data items (\titleformat from titlesec package)
\titleformat{\section}{\Large\py@HeaderFamily}%
{\py@TitleColor\thesection}{0.5em}{\py@TitleColor}
\titleformat{\subsection}{\large\py@HeaderFamily}%
{\py@TitleColor\thesubsection}{0.5em}{\py@TitleColor}
\titleformat{\subsubsection}{\py@HeaderFamily}%
{\py@TitleColor\thesubsubsection}{0.5em}{\py@TitleColor}
% By default paragraphs (and subsubsections) will not be numbered because
% sphinxmanual.cls and sphinxhowto.cls set secnumdepth to 2
\titleformat{\paragraph}{\py@HeaderFamily}%
{\py@TitleColor\theparagraph}{0.5em}{\py@TitleColor}
\titleformat{\subparagraph}{\py@HeaderFamily}%
{\py@TitleColor\thesubparagraph}{0.5em}{\py@TitleColor}
% Since Sphinx 1.5, users should use HeaderFamily key to 'sphinxsetup' rather
% than defining their own \py@HeaderFamily command (which is still possible).
% Memo: \py@HeaderFamily is also used by \maketitle as defined in
% sphinxmanual.cls/sphinxhowto.cls
\newcommand{\py@HeaderFamily}{\spx@opt@HeaderFamily}
% This sets up the fancy chapter headings that make the documents look
% at least a little better than the usual LaTeX output.
\@ifpackagewith{fncychap}{Bjarne}{
\ChNameVar {\raggedleft\normalsize \py@HeaderFamily}
\ChNumVar {\raggedleft\Large \py@HeaderFamily}
\ChTitleVar{\raggedleft\Large \py@HeaderFamily}
% This creates (numbered) chapter heads without the leading \vspace*{}:
\def\@makechapterhead#1{%
{\parindent \z@ \raggedright \normalfont
\ifnum \c@secnumdepth >\m@ne
\if@mainmatter
\DOCH
\fi
\fi
\interlinepenalty\@M
\if@mainmatter
\DOTI{#1}%
\else%
\DOTIS{#1}%
\fi
}}
}{}% <-- "false" clause of \@ifpackagewith
% fix fncychap's bug which uses prematurely the \textwidth value
\@ifpackagewith{fncychap}{Bjornstrup}
{\AtBeginDocument{\mylen\textwidth\advance\mylen-2\myhi}}%
{}% <-- "false" clause of \@ifpackagewith
\endinput
docs/_build/latex/sphinxlatexstylepage.sty deleted 100644 → 0
%% PAGE STYLING
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexstylepage.sty}[2021/01/27 page styling]
% Separate paragraphs by space by default.
\IfFileExists{parskip-2001-04-09.sty}% since September 2018 TeXLive update
% new parskip.sty, but let it rollback to old one.
% hopefully TeX installation not broken and LaTeX kernel not too old
{\RequirePackage{parskip}[=v1]}
% standard one from 1989. Admittedly \section of article/book gives possibly
% anomalous spacing, but we can't require September 2018 release for some time.
{\RequirePackage{parskip}}
% Style parameters and macros used by most documents here
\raggedbottom
\sloppy
\hbadness = 5000 % don't print trivial gripes
% Require package fancyhdr except under memoir class
\@ifclassloaded{memoir}{}{\RequirePackage{fancyhdr}}
% Use \pagestyle{normal} as the primary pagestyle for text.
% Redefine the 'normal' header/footer style when using "fancyhdr" package:
\@ifpackageloaded{fancyhdr}{%
\ltx@ifundefined{c@chapter}
{% no \chapter, "howto" (non-Japanese) docclass
\fancypagestyle{plain}{
\fancyhf{}
\fancyfoot[C]{{\py@HeaderFamily\thepage}}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
% Same as 'plain', this way we can use it in template
% FIXME: shouldn't this have a running header with Name and Release like 'manual'?
\fancypagestyle{normal}{
\fancyhf{}
\fancyfoot[C]{{\py@HeaderFamily\thepage}}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
}%
{% classes with \chapter command
\fancypagestyle{normal}{
\fancyhf{}
\fancyfoot[RO]{{\py@HeaderFamily\thepage}}
\fancyfoot[LO]{{\py@HeaderFamily\nouppercase{\rightmark}}}
\fancyhead[RO]{{\py@HeaderFamily \@title\sphinxheadercomma\py@release}}
\if@twoside
\fancyfoot[LE]{{\py@HeaderFamily\thepage}}
\fancyfoot[RE]{{\py@HeaderFamily\nouppercase{\leftmark}}}
\fancyhead[LE]{{\py@HeaderFamily \@title\sphinxheadercomma\py@release}}
\fi
\renewcommand{\headrulewidth}{0.4pt}
\renewcommand{\footrulewidth}{0.4pt}
% define chaptermark with \@chappos when \@chappos is available for Japanese
\ltx@ifundefined{@chappos}{}
{\def\chaptermark##1{\markboth{\@chapapp\space\thechapter\space\@chappos\space ##1}{}}}
}
% Update the plain style so we get the page number & footer line,
% but not a chapter or section title. This is to keep the first
% page of a chapter `clean.'
\fancypagestyle{plain}{
\fancyhf{}
\fancyfoot[RO]{{\py@HeaderFamily\thepage}}
\if@twoside\fancyfoot[LE]{{\py@HeaderFamily\thepage}}\fi
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0.4pt}
}
}
}
{% no fancyhdr: memoir class
% Provide default for 'normal' style simply as an alias of 'plain' style
% This way we can use \pagestyle{normal} in LaTeX template
\def\ps@normal{\ps@plain}
% Users of memoir class are invited to redefine 'normal' style in preamble
}
\endinput
docs/_build/latex/sphinxlatexstyletext.sty deleted 100644 → 0
%% TEXT STYLING
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexstyletext.sty}[2021/12/06 text styling]
% Basically everything here consists of macros which are part of the latex
% markup produced by the Sphinx latex writer
% Some custom font markup commands.
\protected\def\sphinxstrong#1{\textbf{#1}}
\protected\def\sphinxcode#1{\texttt{#1}}
\protected\def\sphinxbfcode#1{\textbf{\sphinxcode{#1}}}
\protected\def\sphinxemail#1{\textsf{#1}}
\protected\def\sphinxtablecontinued#1{\textsf{#1}}
\protected\def\sphinxtitleref#1{\emph{#1}}
\protected\def\sphinxmenuselection#1{\emph{#1}}
\protected\def\sphinxguilabel#1{\emph{#1}}
\protected\def\sphinxkeyboard#1{\sphinxcode{#1}}
\protected\def\sphinxaccelerator#1{\underline{#1}}
\protected\def\sphinxcrossref#1{\emph{#1}}
\protected\def\sphinxtermref#1{\emph{#1}}
% \optional is used for ``[, arg]``, i.e. desc_optional nodes.
\long\protected\def\sphinxoptional#1{%
{\textnormal{\Large[}}{#1}\hspace{0.5mm}{\textnormal{\Large]}}}
% additional customizable styling
\def\sphinxstyleindexentry #1{\texttt{#1}}
\def\sphinxstyleindexextra #1{ (\emph{#1})}
\def\sphinxstyleindexpageref #1{, \pageref{#1}}
\def\sphinxstyleindexpagemain#1{\textbf{#1}}
\def\spxentry{\@backslashchar spxentry}% let to \sphinxstyleindexentry in index
\def\spxextra{\@backslashchar spxextra}% let to \sphinxstyleindexextra in index
\def\sphinxstyleindexlettergroup #1%
{{\Large\sffamily#1}\nopagebreak\vspace{1mm}}
\def\sphinxstyleindexlettergroupDefault #1%
{{\Large\sffamily\sphinxnonalphabeticalgroupname}\nopagebreak\vspace{1mm}}
\protected\def\sphinxstyletopictitle #1{\textbf{#1}\par\medskip}
\let\sphinxstylesidebartitle\sphinxstyletopictitle
\protected\def\sphinxstyleothertitle #1{\textbf{#1}}
\protected\def\sphinxstylesidebarsubtitle #1{~\\\textbf{#1} \smallskip}
% \text.. commands do not allow multiple paragraphs
\protected\def\sphinxstyletheadfamily {\sffamily}
\protected\def\sphinxstyleemphasis #1{\emph{#1}}
\protected\def\sphinxstyleliteralemphasis#1{\emph{\sphinxcode{#1}}}
\protected\def\sphinxstylestrong #1{\textbf{#1}}
\protected\def\sphinxstyleliteralstrong#1{\sphinxbfcode{#1}}
\protected\def\sphinxstyleabbreviation #1{\textsc{#1}}
\protected\def\sphinxstyleliteralintitle#1{\sphinxcode{#1}}
\newcommand*\sphinxstylecodecontinued[1]{\footnotesize(#1)}%
\newcommand*\sphinxstylecodecontinues[1]{\footnotesize(#1)}%
% figure legend comes after caption and may contain arbitrary body elements
\newenvironment{sphinxlegend}{\par\small}{\par}
% reduce hyperref "Token not allowed in a PDF string" warnings on PDF builds
\AtBeginDocument{\pdfstringdefDisableCommands{%
% all "protected" macros possibly ending up in section titles should be here
% TODO: examine if \sphinxhref, \sphinxurl, \sphinnolinkurl should be handled
\let\sphinxstyleemphasis \@firstofone
\let\sphinxstyleliteralemphasis \@firstofone
\let\sphinxstylestrong \@firstofone
\let\sphinxstyleliteralstrong \@firstofone
\let\sphinxstyleabbreviation \@firstofone
\let\sphinxstyleliteralintitle \@firstofone
\let\sphinxupquote \@firstofone
\let\sphinxstrong \@firstofone
\let\sphinxcode \@firstofone
\let\sphinxbfcode \@firstofone
\let\sphinxemail \@firstofone
\let\sphinxcrossref \@firstofone
\let\sphinxtermref \@firstofone
\let\sphinxhyphen\sphinxhyphenforbookmarks
}}
% Special characters
%
% The \kern\z@ is to prevent en-dash and em-dash TeX ligatures.
% A linebreak can occur after the dash in regular text (this is
% normal behaviour of "-" in TeX, it is not related to \kern\z@).
%
% Parsed-literals and inline literals also use the \sphinxhyphen
% but linebreaks there are prevented due to monospace font family.
% (xelatex needs a special addition, cf. sphinxlatexliterals.sty)
%
% Inside code-blocks, dashes are escaped via another macro, from
% Pygments latex output (search for \PYGZhy in sphinxlatexliterals.sty),
% and are configured to allow linebreaks despite the monospace font.
% (the #1 swallows the {} from \sphinxhyphen{} mark-up)
\protected\def\sphinxhyphen#1{-\kern\z@}
\protected\def\sphinxhyphennobreak#1{\mbox{-}}
% The {} from texescape mark-up is kept, else -- gives en-dash in PDF bookmark
\def\sphinxhyphenforbookmarks{-}
% For curly braces inside \index macro
\def\sphinxleftcurlybrace{\{}
\def\sphinxrightcurlybrace{\}}
% Declare Unicode characters used by linux tree command to pdflatex utf8/utf8x
\def\spx@bd#1#2{%
\leavevmode
\begingroup
\ifx\spx@bd@height \@undefined\def\spx@bd@height{\baselineskip}\fi
\ifx\spx@bd@width \@undefined\setbox0\hbox{0}\def\spx@bd@width{\wd0 }\fi
\ifx\spx@bd@thickness\@undefined\def\spx@bd@thickness{.6\p@}\fi
\ifx\spx@bd@lower \@undefined\def\spx@bd@lower{\dp\strutbox}\fi
\lower\spx@bd@lower#1{#2}%
\endgroup
}%
\@namedef{sphinx@u2500}% BOX DRAWINGS LIGHT HORIZONTAL
{\spx@bd{\vbox to\spx@bd@height}
{\vss\hrule\@height\spx@bd@thickness
\@width\spx@bd@width\vss}}%
\@namedef{sphinx@u2502}% BOX DRAWINGS LIGHT VERTICAL
{\spx@bd{\hb@xt@\spx@bd@width}
{\hss\vrule\@height\spx@bd@height
\@width \spx@bd@thickness\hss}}%
\@namedef{sphinx@u2514}% BOX DRAWINGS LIGHT UP AND RIGHT
{\spx@bd{\hb@xt@\spx@bd@width}
{\hss\raise.5\spx@bd@height
\hb@xt@\z@{\hss\vrule\@height.5\spx@bd@height
\@width \spx@bd@thickness\hss}%
\vbox to\spx@bd@height{\vss\hrule\@height\spx@bd@thickness
\@width.5\spx@bd@width\vss}}}%
\@namedef{sphinx@u251C}% BOX DRAWINGS LIGHT VERTICAL AND RIGHT
{\spx@bd{\hb@xt@\spx@bd@width}
{\hss
\hb@xt@\z@{\hss\vrule\@height\spx@bd@height
\@width \spx@bd@thickness\hss}%
\vbox to\spx@bd@height{\vss\hrule\@height\spx@bd@thickness
\@width.5\spx@bd@width\vss}}}%
\protected\def\sphinxunichar#1{\@nameuse{sphinx@u#1}}%
% Tell TeX about pathological hyphenation cases:
\hyphenation{Base-HTTP-Re-quest-Hand-ler}
\endinput
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