copy pasted grogu

.gitignore

@@ -0,0 +1,21 @@
+__pycache__
+
+# Build
+build
+dist
+**/*.egg-info
+
+# VSCode settings
+.vscode
+.conda
+.pytest_cache
+
+# Docs
+docs/make.bat
+docs/build
+docs/source/api/generated
+*generated
+
+
+# Debug
+tmp*

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/adrybakov/pre-commit-hooks
+  rev: 0.2.0
+  hooks:
+  - id: license-headers
+    args:
+      - --license-file
+      - L-HEADER
+      - --update-year
+      - --verbose
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+    args: ["--profile", "black", "--filter-files"]
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 24.4.2
+  hooks:
+  - id: black
+    language_version: python3.11
+- repo: local
+  hooks:
+    - id: pytest-check
+      name: pytest-check
+      entry: pytest
+      language: system
+      pass_filenames: false
+      always_run: true

L-HEADER

@@ -0,0 +1,19 @@
+Copyright (c) [2024] [Daniel Pozsar]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2024] [Daniel Pozsar]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1 @@
+# Relativistic magnetic interactions from non-orthogonal basis sets

docs/requirements.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_rtd_theme
+numpydoc
+doctest

docs/source/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/_build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 0f8ff1598a5b65221fc2ef8f29fdbeac
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/source/_build/html/_modules/grogu/useful.html

@@ -0,0 +1,282 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>grogu.useful &mdash; Grogu 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">grogu.useful</li>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>Source code for grogu.useful</h1><div class="highlight"><pre>
+<span></span><span class="c1"># Copyright (c) [2024] [Daniel Pozsar]</span>
+<span class="c1">#</span>
+<span class="c1"># Permission is hereby granted, free of charge, to any person obtaining a copy</span>
+<span class="c1"># of this software and associated documentation files (the &quot;Software&quot;), to deal</span>
+<span class="c1"># in the Software without restriction, including without limitation the rights</span>
+<span class="c1"># to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
+<span class="c1"># copies of the Software, and to permit persons to whom the Software is</span>
+<span class="c1"># furnished to do so, subject to the following conditions:</span>
+<span class="c1">#</span>
+<span class="c1"># The above copyright notice and this permission notice shall be included in all</span>
+<span class="c1"># copies or substantial portions of the Software.</span>
+<span class="c1">#</span>
+<span class="c1"># THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
+<span class="c1"># IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
+<span class="c1"># FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
+<span class="c1"># AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
+<span class="c1"># LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
+<span class="c1"># OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
+<span class="c1"># SOFTWARE.</span>
+
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">from</span> <span class="nn">scipy.special</span> <span class="kn">import</span> <span class="n">roots_legendre</span>
+<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">permutations</span><span class="p">,</span> <span class="n">product</span>
+
+
+<span class="c1"># define some useful functions</span>
+<div class="viewcode-block" id="hsk">
+<a class="viewcode-back" href="../../grogu.html#grogu.useful.hsk">[docs]</a>
+<span class="k">def</span> <span class="nf">hsk</span><span class="p">(</span><span class="n">dh</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    One way to speed up Hk and Sk generation</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">k</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span>  <span class="c1"># this two conversion lines</span>
+    <span class="n">k</span><span class="o">.</span><span class="n">shape</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,)</span>  <span class="c1"># are from the sisl source</span>
+
+    <span class="c1"># this generates the list of phases</span>
+    <span class="n">phases</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="n">j</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">dh</span><span class="o">.</span><span class="n">rcell</span><span class="p">,</span> <span class="n">k</span><span class="p">),</span> <span class="n">dh</span><span class="o">.</span><span class="n">cell</span><span class="p">),</span> <span class="n">dh</span><span class="o">.</span><span class="n">sc</span><span class="o">.</span><span class="n">sc_off</span><span class="o">.</span><span class="n">T</span><span class="p">))</span>
+
+    <span class="n">HKU</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">einsum</span><span class="p">(</span><span class="s2">&quot;abc,c-&gt;ab&quot;</span><span class="p">,</span> <span class="n">dh</span><span class="o">.</span><span class="n">hup</span><span class="p">,</span> <span class="n">phases</span><span class="p">)</span>
+    <span class="n">HKD</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">einsum</span><span class="p">(</span><span class="s2">&quot;abc,c-&gt;ab&quot;</span><span class="p">,</span> <span class="n">dh</span><span class="o">.</span><span class="n">hdo</span><span class="p">,</span> <span class="n">phases</span><span class="p">)</span>
+    <span class="n">SK</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">einsum</span><span class="p">(</span><span class="s2">&quot;abc,c-&gt;ab&quot;</span><span class="p">,</span> <span class="n">dh</span><span class="o">.</span><span class="n">sov</span><span class="p">,</span> <span class="n">phases</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">HKU</span><span class="p">,</span> <span class="n">HKD</span><span class="p">,</span> <span class="n">SK</span></div>
+
+
+
+<div class="viewcode-block" id="make_contour">
+<a class="viewcode-back" href="../../grogu.html#grogu.useful.make_contour">[docs]</a>
+<span class="k">def</span> <span class="nf">make_contour</span><span class="p">(</span><span class="n">emin</span><span class="o">=-</span><span class="mi">20</span><span class="p">,</span> <span class="n">emax</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">enum</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="mi">150</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A more sophisticated contour generator</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">x</span><span class="p">,</span> <span class="n">wl</span> <span class="o">=</span> <span class="n">roots_legendre</span><span class="p">(</span><span class="n">enum</span><span class="p">)</span>
+    <span class="n">R</span> <span class="o">=</span> <span class="p">(</span><span class="n">emax</span> <span class="o">-</span> <span class="n">emin</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
+    <span class="n">z0</span> <span class="o">=</span> <span class="p">(</span><span class="n">emax</span> <span class="o">+</span> <span class="n">emin</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
+    <span class="n">y1</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">p</span><span class="p">)</span>
+    <span class="n">y2</span> <span class="o">=</span> <span class="mi">0</span>
+
+    <span class="n">y</span> <span class="o">=</span> <span class="p">(</span><span class="n">y2</span> <span class="o">-</span> <span class="n">y1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">x</span> <span class="o">+</span> <span class="p">(</span><span class="n">y2</span> <span class="o">+</span> <span class="n">y1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
+    <span class="n">phi</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">y</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="n">p</span>
+    <span class="n">ze</span> <span class="o">=</span> <span class="n">z0</span> <span class="o">+</span> <span class="n">R</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="mi">1</span><span class="n">j</span> <span class="o">*</span> <span class="n">phi</span><span class="p">)</span>
+    <span class="n">we</span> <span class="o">=</span> <span class="o">-</span><span class="p">(</span><span class="n">y2</span> <span class="o">-</span> <span class="n">y1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">y</span><span class="p">)</span> <span class="o">/</span> <span class="n">p</span> <span class="o">*</span> <span class="mi">1</span><span class="n">j</span> <span class="o">*</span> <span class="p">(</span><span class="n">ze</span> <span class="o">-</span> <span class="n">z0</span><span class="p">)</span> <span class="o">*</span> <span class="n">wl</span>
+
+    <span class="k">class</span> <span class="nc">ccont</span><span class="p">:</span>
+        <span class="c1"># just an empty container class</span>
+        <span class="k">pass</span>
+
+    <span class="n">cont</span> <span class="o">=</span> <span class="n">ccont</span><span class="p">()</span>
+    <span class="n">cont</span><span class="o">.</span><span class="n">R</span> <span class="o">=</span> <span class="n">R</span>
+    <span class="n">cont</span><span class="o">.</span><span class="n">z0</span> <span class="o">=</span> <span class="n">z0</span>
+    <span class="n">cont</span><span class="o">.</span><span class="n">ze</span> <span class="o">=</span> <span class="n">ze</span>
+    <span class="n">cont</span><span class="o">.</span><span class="n">we</span> <span class="o">=</span> <span class="n">we</span>
+    <span class="n">cont</span><span class="o">.</span><span class="n">enum</span> <span class="o">=</span> <span class="n">enum</span>
+
+    <span class="k">return</span> <span class="n">cont</span></div>
+
+
+
+<div class="viewcode-block" id="make_kset">
+<a class="viewcode-back" href="../../grogu.html#grogu.useful.make_kset">[docs]</a>
+<span class="k">def</span> <span class="nf">make_kset</span><span class="p">(</span><span class="n">dirs</span><span class="o">=</span><span class="s2">&quot;xyz&quot;</span><span class="p">,</span> <span class="n">NUMK</span><span class="o">=</span><span class="mi">20</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Simple k-grid generator. Depending on the value of the dirs</span>
+<span class="sd">    argument k sampling in 1,2 or 3 dimensions is generated.</span>
+<span class="sd">    If dirs argument does not contain either of x,y or z</span>
+<span class="sd">    a kset of a single k-pont at the origin is returend.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">sum</span><span class="p">([</span><span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">])):</span>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]])</span>
+
+    <span class="n">kran</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">dirs</span><span class="p">)</span> <span class="o">*</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">NUMK</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">False</span><span class="p">)]</span>
+    <span class="n">mg</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</span><span class="p">(</span><span class="o">*</span><span class="n">kran</span><span class="p">)</span>
+    <span class="n">dirsdict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dirs</span><span class="p">):</span>
+        <span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="n">mg</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">:</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">):</span>
+            <span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> <span class="o">*</span> <span class="n">dirsdict</span><span class="p">[</span><span class="n">dirs</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+    <span class="n">kset</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span>
+
+    <span class="k">return</span> <span class="n">kset</span></div>
+
+
+
+<div class="viewcode-block" id="make_atran">
+<a class="viewcode-back" href="../../grogu.html#grogu.useful.make_atran">[docs]</a>
+<span class="k">def</span> <span class="nf">make_atran</span><span class="p">(</span><span class="n">nauc</span><span class="p">,</span> <span class="n">dirs</span><span class="o">=</span><span class="s2">&quot;xyz&quot;</span><span class="p">,</span> <span class="n">dist</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Simple pair generator. Depending on the value of the dirs</span>
+<span class="sd">    argument sampling in 1,2 or 3 dimensions is generated.</span>
+<span class="sd">    If dirs argument does not contain either of x,y or z</span>
+<span class="sd">    a single pair is returend.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">sum</span><span class="p">([</span><span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">])):</span>
+        <span class="k">return</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
+
+    <span class="n">dran</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">dirs</span><span class="p">)</span> <span class="o">*</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="o">-</span><span class="n">dist</span><span class="p">,</span> <span class="n">dist</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)]</span>
+    <span class="n">mg</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</span><span class="p">(</span><span class="o">*</span><span class="n">dran</span><span class="p">)</span>
+    <span class="n">dirsdict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dirs</span><span class="p">):</span>
+        <span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="n">mg</span><span class="p">[</span><span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">:</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">):</span>
+            <span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> <span class="o">*</span> <span class="n">dirsdict</span><span class="p">[</span><span class="n">dirs</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+
+    <span class="n">ucran</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">dirsdict</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="s2">&quot;xyz&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">T</span>
+    <span class="n">atran</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">product</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">nauc</span><span class="p">),</span> <span class="n">repeat</span><span class="o">=</span><span class="mi">2</span><span class="p">)):</span>
+        <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">ucran</span><span class="p">:</span>
+            <span class="k">if</span> <span class="p">(</span><span class="nb">abs</span><span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">+</span> <span class="nb">sum</span><span class="p">(</span><span class="nb">abs</span><span class="p">(</span><span class="n">u</span><span class="p">)))</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">atran</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">u</span><span class="p">)))</span>
+
+    <span class="k">return</span> <span class="n">atran</span></div>
+
+
+
+<div class="viewcode-block" id="add">
+<a class="viewcode-back" href="../../grogu.html#grogu.useful.add">[docs]</a>
+<span class="k">def</span> <span class="nf">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;The sum of two numbers for testing.</span>
+
+<span class="sd">    This function adds to numbers together. I only created this for testing documentation and examples.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    x : float</span>
+<span class="sd">        First number</span>
+<span class="sd">    y : float</span>
+<span class="sd">        Second number added to `x`</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    sum : int</span>
+<span class="sd">        The sum of the inputs</span>
+
+<span class="sd">    See Also</span>
+<span class="sd">    --------</span>
+<span class="sd">    numpy.add : Adds more than two numbers.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    We can create some latex notes here [1]_ :</span>
+
+<span class="sd">    .. math:: a + b = c</span>
+
+<span class="sd">    References</span>
+<span class="sd">    ----------</span>
+<span class="sd">    .. [1] https://numpydoc.readthedocs.io/en/latest/format.html</span>
+
+
+<span class="sd">    Examples</span>
+<span class="sd">    --------</span>
+<span class="sd">    &gt;&gt;&gt; add(1, 2)</span>
+<span class="sd">    3</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span></div>
+
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Grogu.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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docs/source/_build/html/_modules/index.html

@@ -0,0 +1,101 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; Grogu 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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+
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+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            Grogu
+          </a>
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+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
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+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">src</a></li>
+</ul>
+
+        </div>
+      </div>
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+
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+      <li class="breadcrumb-item active">Overview: module code</li>
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+      </li>
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+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="grogu/useful.html">grogu.useful</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Grogu.</p>
+  </div>
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+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
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docs/source/_build/html/_sources/grogu.rst.txt

@@ -0,0 +1,37 @@
+grogu package
+=============
+
+Submodules
+----------
+
+grogu.example module
+--------------------
+
+.. automodule:: grogu.example
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+grogu.jij module
+----------------
+
+.. automodule:: grogu.jij
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+grogu.useful module
+-------------------
+
+.. automodule:: grogu.useful
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: grogu
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/_build/html/_sources/index.rst.txt

@@ -0,0 +1,25 @@
+.. asd documentation master file, created by
+   sphinx-quickstart on Thu Oct 10 17:10:03 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+asd documentation
+=================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/_build/html/_sources/modules.rst.txt

@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   grogu

docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js

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+ *
+ * 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;
+
+/**
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+ * 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')
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+    var parts = s.substr(s.indexOf('?') + 1).split('&');
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+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
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+        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;
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+        }
+        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;
+}

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+ */
+
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+
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+    clear: left;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
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+    width: 100%;
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+}
+
+div.related h3 {
+    display: none;
+}
+
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+    margin: 0;
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+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
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+    margin-left: auto;
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+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+    width: 100%;
+}
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable ul {
+    margin-top: 0;
+    margin-bottom: 0;
+    list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+    padding-left: 0em;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+div.modindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+    padding: 2px;
+    border-collapse: collapse;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+div.body {
+    min-width: 360px;
+    max-width: 800px;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -webkit-hyphens: auto;
+    hyphens: auto;
+}
+
+a.headerlink {
+    visibility: hidden;
+}
+
+a:visited {
+    color: #551A8B;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+img.align-default, figure.align-default, .figure.align-default {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-default {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar,
+aside.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+    clear: right;
+    overflow-x: auto;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+nav.contents,
+aside.topic,
+div.admonition, div.topic, blockquote {
+    clear: left;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- content of sidebars/topics/admonitions -------------------------------- */
+
+div.sidebar > :last-child,
+aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
+div.topic > :last-child,
+div.admonition > :last-child {
+    margin-bottom: 0;
+}
+
+div.sidebar::after,
+aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
+div.topic::after,
+div.admonition::after,
+blockquote::after {
+    display: block;
+    content: '';
+    clear: both;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table.align-default {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+
+th > :first-child,
+td > :first-child {
+    margin-top: 0px;
+}
+
+th > :last-child,
+td > :last-child {
+    margin-bottom: 0px;
+}
+
+/* -- figures --------------------------------------------------------------- */
+
+div.figure, figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption, figcaption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
+}
+
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.field-name {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist {
+    margin: 1em 0;
+}
+
+table.hlist td {
+    vertical-align: top;
+}
+
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+	font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+.sig-name {
+	font-size: 1.1em;
+}
+
+code.descname {
+    font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+    background-color: transparent;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.sig-paren {
+    font-size: larger;
+}
+
+.sig-param.n {
+	font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+	font-family: unset;
+}
+
+.sig.c   .k, .sig.c   .kt,
+.sig.cpp .k, .sig.cpp .kt {
+	color: #0033B3;
+}
+
+.sig.c   .m,
+.sig.cpp .m {
+	color: #1750EB;
+}
+
+.sig.c   .s, .sig.c   .sc,
+.sig.cpp .s, .sig.cpp .sc {
+	color: #067D17;
+}
+
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+    list-style: decimal;
+}
+
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
+ol.upperalpha {
+    list-style: upper-alpha;
+}
+
+ol.lowerroman {
+    list-style: lower-roman;
+}
+
+ol.upperroman {
+    list-style: upper-roman;
+}
+
+:not(li) > ol > li:first-child > :first-child,
+:not(li) > ul > li:first-child > :first-child {
+    margin-top: 0px;
+}
+
+:not(li) > ol > li:last-child > :last-child,
+:not(li) > ul > li:last-child > :last-child {
+    margin-bottom: 0px;
+}
+
+ol.simple ol p,
+ol.simple ul p,
+ul.simple ol p,
+ul.simple ul p {
+    margin-top: 0;
+}
+
+ol.simple > li:not(:first-child) > p,
+ul.simple > li:not(:first-child) > p {
+    margin-top: 0;
+}
+
+ol.simple p,
+ul.simple p {
+    margin-bottom: 0;
+}
+
+aside.footnote > span,
+div.citation > span {
+    float: left;
+}
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
+    margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: grid;
+    grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+    font-weight: bold;
+    word-break: break-word;
+    padding-left: 0.5em;
+    padding-right: 5px;
+}
+
+dl.field-list > dd {
+    padding-left: 0.5em;
+    margin-top: 0em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd > :first-child {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+dl > dd:last-child,
+dl > dd:last-child > :last-child {
+    margin-bottom: 0;
+}
+
+dt:target, span.highlighted {
+    background-color: #fbe54e;
+}
+
+rect.highlighted {
+    fill: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+    font-family: sans-serif;
+}
+
+.accelerator {
+    text-decoration: underline;
+}
+
+.classifier {
+    font-style: oblique;
+}
+
+.classifier:before {
+    font-style: normal;
+    margin: 0 0.5em;
+    content: ":";
+    display: inline-block;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+pre, div[class*="highlight-"] {
+    clear: both;
+}
+
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+    white-space: nowrap;
+}
+
+div[class*="highlight-"] {
+    margin: 1em 0;
+}
+
+td.linenos pre {
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    display: block;
+}
+
+table.highlighttable tbody {
+    display: block;
+}
+
+table.highlighttable tr {
+    display: flex;
+}
+
+table.highlighttable td {
+    margin: 0;
+    padding: 0;
+}
+
+table.highlighttable td.linenos {
+    padding-right: 0.5em;
+}
+
+table.highlighttable td.code {
+    flex: 1;
+    overflow: hidden;
+}
+
+.highlight .hll {
+    display: block;
+}
+
+div.highlight pre,
+table.highlighttable pre {
+    margin: 0;
+}
+
+div.code-block-caption + div {
+    margin-top: 0;
+}
+
+div.code-block-caption {
+    margin-top: 1em;
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+table.highlighttable td.linenos,
+span.linenos,
+div.highlight span.gp {  /* gp: Generic.Prompt */
+  user-select: none;
+  -webkit-user-select: text; /* Safari fallback only */
+  -webkit-user-select: none; /* Chrome/Safari */
+  -moz-user-select: none; /* Firefox */
+  -ms-user-select: none; /* IE10+ */
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    margin: 1em 0;
+}
+
+code.xref, a code {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+    background-color: transparent;
+}
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+span.eqno a.headerlink {
+    position: absolute;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}

docs/source/_build/html/_static/css/badge_only.css

@@ -0,0 +1 @@
+.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before,.icon-book:before{content:"\f02d"}.fa-caret-down:before,.icon-caret-down:before{content:"\f0d7"}.fa-caret-up:before,.icon-caret-up:before{content:"\f0d8"}.fa-caret-left:before,.icon-caret-left:before{content:"\f0d9"}.fa-caret-right:before,.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60}.rst-versions .rst-current-version:after{clear:both;content:"";display:block}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions .rst-other-versions .rtd-current-item{font-weight:700}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}#flyout-search-form{padding:6px}

docs/source/_build/html/_static/doctools.js

@@ -0,0 +1,149 @@
+/*
+ * Base JavaScript utilities for all Sphinx HTML documentation.
+ */
+"use strict";
+
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+  "TEXTAREA",
+  "INPUT",
+  "SELECT",
+  "BUTTON",
+]);
+
+const _ready = (callback) => {
+  if (document.readyState !== "loading") {
+    callback();
+  } else {
+    document.addEventListener("DOMContentLoaded", callback);
+  }
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const Documentation = {
+  init: () => {
+    Documentation.initDomainIndexTable();
+    Documentation.initOnKeyListeners();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS: {},
+  PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
+  LOCALE: "unknown",
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext: (string) => {
+    const translated = Documentation.TRANSLATIONS[string];
+    switch (typeof translated) {
+      case "undefined":
+        return string; // no translation
+      case "string":
+        return translated; // translation exists
+      default:
+        return translated[0]; // (singular, plural) translation tuple exists
+    }
+  },
+
+  ngettext: (singular, plural, n) => {
+    const translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated !== "undefined")
+      return translated[Documentation.PLURAL_EXPR(n)];
+    return n === 1 ? singular : plural;
+  },
+
+  addTranslations: (catalog) => {
+    Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+    Documentation.PLURAL_EXPR = new Function(
+      "n",
+      `return (${catalog.plural_expr})`
+    );
+    Documentation.LOCALE = catalog.locale;
+  },
+
+  /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar: () => {
+    document.querySelectorAll("input[name=q]")[0]?.focus();
+  },
+
+  /**
+   * Initialise the domain index toggle buttons
+   */
+  initDomainIndexTable: () => {
+    const toggler = (el) => {
+      const idNumber = el.id.substr(7);
+      const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+      if (el.src.substr(-9) === "minus.png") {
+        el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+        toggledRows.forEach((el) => (el.style.display = "none"));
+      } else {
+        el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+        toggledRows.forEach((el) => (el.style.display = ""));
+      }
+    };
+
+    const togglerElements = document.querySelectorAll("img.toggler");
+    togglerElements.forEach((el) =>
+      el.addEventListener("click", (event) => toggler(event.currentTarget))
+    );
+    togglerElements.forEach((el) => (el.style.display = ""));
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+  },
+
+  initOnKeyListeners: () => {
+    // only install a listener if it is really needed
+    if (
+      !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+      !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+    )
+      return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.altKey || event.ctrlKey || event.metaKey) return;
+
+      if (!event.shiftKey) {
+        switch (event.key) {
+          case "ArrowLeft":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const prevLink = document.querySelector('link[rel="prev"]');
+            if (prevLink && prevLink.href) {
+              window.location.href = prevLink.href;
+              event.preventDefault();
+            }
+            break;
+          case "ArrowRight":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const nextLink = document.querySelector('link[rel="next"]');
+            if (nextLink && nextLink.href) {
+              window.location.href = nextLink.href;
+              event.preventDefault();
+            }
+            break;
+        }
+      }
+
+      // some keyboard layouts may need Shift to get /
+      switch (event.key) {
+        case "/":
+          if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+          Documentation.focusSearchBar();
+          event.preventDefault();
+      }
+    });
+  },
+};
+
+// quick alias for translations
+const _ = Documentation.gettext;
+
+_ready(Documentation.init);

docs/source/_build/html/_static/documentation_options.js

@@ -0,0 +1,13 @@
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '0.0.1',
+    LANGUAGE: 'en',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'html',
+    FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
+};

docs/source/_build/html/_static/js/badge_only.js

@@ -0,0 +1 @@
+!function(e){var t={};function r(n){if(t[n])return t[n].exports;var o=t[n]={i:n,l:!1,exports:{}};return e[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}r.m=e,r.c=t,r.d=function(e,t,n){r.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:n})},r.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return r.d(t,"a",t),t},r.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},r.p="",r(r.s=4)}({4:function(e,t,r){}});

docs/source/_build/html/_static/js/versions.js

@@ -0,0 +1,224 @@
+const themeFlyoutDisplay = "hidden";
+const themeVersionSelector = "True";
+const themeLanguageSelector = "True";
+
+if (themeFlyoutDisplay === "attached") {
+  function renderLanguages(config) {
+    if (!config.projects.translations.length) {
+      return "";
+    }
+
+    const languagesHTML = `
+      <dl>
+        <dt>Languages</dt>
+        ${config.projects.translations
+          .map(
+            (translation) => `
+        <dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
+          <a href="${translation.urls.documentation}">${translation.language.code}</a>
+        </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return languagesHTML;
+  }
+
+  function renderVersions(config) {
+    if (!config.versions.active.length) {
+      return "";
+    }
+    const versionsHTML = `
+      <dl>
+        <dt>Versions</dt>
+        ${config.versions.active
+          .map(
+            (version) => `
+        <dd ${version.slug === config.versions.current.slug ? 'class="rtd-current-item"' : ""}>
+          <a href="${version.urls.documentation}">${version.slug}</a>
+        </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return versionsHTML;
+  }
+
+  function renderDownloads(config) {
+    if (!Object.keys(config.versions.current.downloads).length) {
+      return "";
+    }
+    const downloadsNameDisplay = {
+      pdf: "PDF",
+      epub: "Epub",
+      htmlzip: "HTML",
+    };
+
+    const downloadsHTML = `
+      <dl>
+        <dt>Downloads</dt>
+        ${Object.entries(config.versions.current.downloads)
+          .map(
+            ([name, url]) => `
+          <dd>
+            <a href="${url}">${downloadsNameDisplay[name]}</a>
+          </dd>
+        `,
+          )
+          .join("\n")}
+      </dl>
+    `;
+    return downloadsHTML;
+  }
+
+  document.addEventListener("readthedocs-addons-data-ready", function (event) {
+    const config = event.detail.data();
+
+    const flyout = `
+      <div class="rst-versions" data-toggle="rst-versions" role="note">
+        <span class="rst-current-version" data-toggle="rst-current-version">
+          <span class="fa fa-book"> Read the Docs</span>
+          v: ${config.versions.current.slug}
+          <span class="fa fa-caret-down"></span>
+        </span>
+        <div class="rst-other-versions">
+          <div class="injected">
+            ${renderLanguages(config)}
+            ${renderVersions(config)}
+            ${renderDownloads(config)}
+            <dl>
+              <dt>On Read the Docs</dt>
+              <dd>
+                <a href="${config.projects.current.urls.home}">Project Home</a>
+              </dd>
+              <dd>
+                <a href="${config.projects.current.urls.builds}">Builds</a>
+              </dd>
+              <dd>
+                <a href="${config.projects.current.urls.downloads}">Downloads</a>
+              </dd>
+            </dl>
+            <dl>
+              <dt>Search</dt>
+              <dd>
+                <form id="flyout-search-form">
+                  <input
+                    class="wy-form"
+                    type="text"
+                    name="q"
+                    aria-label="Search docs"
+                    placeholder="Search docs"
+                    />
+                </form>
+              </dd>
+            </dl>
+            <hr />
+            <small>
+              <span>Hosted by <a href="https://about.readthedocs.org/?utm_source=&utm_content=flyout">Read the Docs</a></span>
+            </small>
+          </div>
+        </div>
+    `;
+
+    // Inject the generated flyout into the body HTML element.
+    document.body.insertAdjacentHTML("beforeend", flyout);
+
+    // Trigger the Read the Docs Addons Search modal when clicking on the "Search docs" input from inside the flyout.
+    document
+      .querySelector("#flyout-search-form")
+      .addEventListener("focusin", () => {
+        const event = new CustomEvent("readthedocs-search-show");
+        document.dispatchEvent(event);
+      });
+  })
+}
+
+if (themeLanguageSelector || themeVersionSelector) {
+  function onSelectorSwitch(event) {
+    const option = event.target.selectedIndex;
+    const item = event.target.options[option];
+    window.location.href = item.dataset.url;
+  }
+
+  document.addEventListener("readthedocs-addons-data-ready", function (event) {
+    const config = event.detail.data();
+
+    const versionSwitch = document.querySelector(
+      "div.switch-menus > div.version-switch",
+    );
+    if (themeVersionSelector) {
+      let versions = config.versions.active;
+      if (config.versions.current.hidden || config.versions.current.type === "external") {
+        versions.unshift(config.versions.current);
+      }
+      const versionSelect = `
+    <select>
+      ${versions
+        .map(
+          (version) => `
+        <option
+  value="${version.slug}"
+  ${config.versions.current.slug === version.slug ? 'selected="selected"' : ""}
+              data-url="${version.urls.documentation}">
+              ${version.slug}
+          </option>`,
+        )
+        .join("\n")}
+    </select>
+  `;
+
+      versionSwitch.innerHTML = versionSelect;
+      versionSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+    }
+
+    const languageSwitch = document.querySelector(
+      "div.switch-menus > div.language-switch",
+    );
+
+    if (themeLanguageSelector) {
+      if (config.projects.translations.length) {
+        // Add the current language to the options on the selector
+        let languages = config.projects.translations.concat(
+          config.projects.current,
+        );
+        languages = languages.sort((a, b) =>
+          a.language.name.localeCompare(b.language.name),
+        );
+
+        const languageSelect = `
+      <select>
+        ${languages
+          .map(
+            (language) => `
+              <option
+                  value="${language.language.code}"
+                  ${config.projects.current.slug === language.slug ? 'selected="selected"' : ""}
+                  data-url="${language.urls.documentation}">
+                  ${language.language.name}
+              </option>`,
+          )
+          .join("\n")}
+       </select>
+    `;
+
+        languageSwitch.innerHTML = languageSelect;
+        languageSwitch.firstElementChild.addEventListener("change", onSelectorSwitch);
+      }
+      else {
+        languageSwitch.remove();
+      }
+    }
+  });
+}
+
+document.addEventListener("readthedocs-addons-data-ready", function (event) {
+  // Trigger the Read the Docs Addons Search modal when clicking on "Search docs" input from the topnav.
+  document
+    .querySelector("[role='search'] input")
+    .addEventListener("focusin", () => {
+      const event = new CustomEvent("readthedocs-search-show");
+      document.dispatchEvent(event);
+    });
+});

docs/source/_build/html/_static/language_data.js

@@ -0,0 +1,191 @@
+/*
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ */
+
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
+
+
+/* Non-minified version is copied as a separate JS file, if available */
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}

docs/source/_build/html/_static/pygments.css

@@ -0,0 +1,75 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #f8f8f8; }
+.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #008000; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #9C6500 } /* Comment.Preproc */
+.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
+.highlight .gr { color: #E40000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #008400 } /* Generic.Inserted */
+.highlight .go { color: #717171 } /* Generic.Output */
+.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #008000 } /* Keyword.Pseudo */
+.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #B00040 } /* Keyword.Type */
+.highlight .m { color: #666666 } /* Literal.Number */
+.highlight .s { color: #BA2121 } /* Literal.String */
+.highlight .na { color: #687822 } /* Name.Attribute */
+.highlight .nb { color: #008000 } /* Name.Builtin */
+.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
+.highlight .no { color: #880000 } /* Name.Constant */
+.highlight .nd { color: #AA22FF } /* Name.Decorator */
+.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */
+.highlight .nf { color: #0000FF } /* Name.Function */
+.highlight .nl { color: #767600 } /* Name.Label */
+.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #19177C } /* Name.Variable */
+.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mb { color: #666666 } /* Literal.Number.Bin */
+.highlight .mf { color: #666666 } /* Literal.Number.Float */
+.highlight .mh { color: #666666 } /* Literal.Number.Hex */
+.highlight .mi { color: #666666 } /* Literal.Number.Integer */
+.highlight .mo { color: #666666 } /* Literal.Number.Oct */
+.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
+.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
+.highlight .sc { color: #BA2121 } /* Literal.String.Char */
+.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
+.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
+.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
+.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */
+.highlight .sx { color: #008000 } /* Literal.String.Other */
+.highlight .sr { color: #A45A77 } /* Literal.String.Regex */
+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
+.highlight .ss { color: #19177C } /* Literal.String.Symbol */
+.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #0000FF } /* Name.Function.Magic */
+.highlight .vc { color: #19177C } /* Name.Variable.Class */
+.highlight .vg { color: #19177C } /* Name.Variable.Global */
+.highlight .vi { color: #19177C } /* Name.Variable.Instance */
+.highlight .vm { color: #19177C } /* Name.Variable.Magic */
+.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */

docs/source/_build/html/_static/searchtools.js

@@ -0,0 +1,632 @@
+/*
+ * Sphinx JavaScript utilities for the full-text search.
+ */
+"use strict";
+
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [docname, title, anchor, descr, score, filename]
+    // and returns the new score.
+    /*
+    score: result => {
+      const [docname, title, anchor, descr, score, filename, kind] = result
+      return score
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {
+      0: 15, // used to be importantResults
+      1: 5, // used to be objectResults
+      2: -5, // used to be unimportantResults
+    },
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    partialTitle: 7,
+    // query found in terms
+    term: 5,
+    partialTerm: 2,
+  };
+}
+
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+    static get index() { return  "index"; }
+    static get object() { return "object"; }
+    static get text() { return "text"; }
+    static get title() { return "title"; }
+}
+
+const _removeChildren = (element) => {
+  while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+  string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, searchTerms, highlightTerms) => {
+  const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+  const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+  const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+  const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
+
+  const [docName, title, anchor, descr, score, _filename, kind] = item;
+
+  let listItem = document.createElement("li");
+  // Add a class representing the item's type:
+  // can be used by a theme's CSS selector for styling
+  // See SearchResultKind for the class names.
+  listItem.classList.add(`kind-${kind}`);
+  let requestUrl;
+  let linkUrl;
+  if (docBuilder === "dirhtml") {
+    // dirhtml builder
+    let dirname = docName + "/";
+    if (dirname.match(/\/index\/$/))
+      dirname = dirname.substring(0, dirname.length - 6);
+    else if (dirname === "index/") dirname = "";
+    requestUrl = contentRoot + dirname;
+    linkUrl = requestUrl;
+  } else {
+    // normal html builders
+    requestUrl = contentRoot + docName + docFileSuffix;
+    linkUrl = docName + docLinkSuffix;
+  }
+  let linkEl = listItem.appendChild(document.createElement("a"));
+  linkEl.href = linkUrl + anchor;
+  linkEl.dataset.score = score;
+  linkEl.innerHTML = title;
+  if (descr) {
+    listItem.appendChild(document.createElement("span")).innerHTML =
+      " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
+  else if (showSearchSummary)
+    fetch(requestUrl)
+      .then((responseData) => responseData.text())
+      .then((data) => {
+        if (data)
+          listItem.appendChild(
+            Search.makeSearchSummary(data, searchTerms, anchor)
+          );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+      });
+  Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+  Search.stopPulse();
+  Search.title.innerText = _("Search Results");
+  if (!resultCount)
+    Search.status.innerText = Documentation.gettext(
+      "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+    );
+  else
+    Search.status.innerText = Documentation.ngettext(
+      "Search finished, found one page matching the search query.",
+      "Search finished, found ${resultCount} pages matching the search query.",
+      resultCount,
+    ).replace('${resultCount}', resultCount);
+};
+const _displayNextItem = (
+  results,
+  resultCount,
+  searchTerms,
+  highlightTerms,
+) => {
+  // results left, load the summary and display it
+  // this is intended to be dynamic (don't sub resultsCount)
+  if (results.length) {
+    _displayItem(results.pop(), searchTerms, highlightTerms);
+    setTimeout(
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
+      5
+    );
+  }
+  // search finished, update title and status message
+  else _finishSearch(resultCount);
+};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+  var splitQuery = (query) => query
+      .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+      .filter(term => term)  // remove remaining empty strings
+}
+
+/**
+ * Search Module
+ */
+const Search = {
+  _index: null,
+  _queued_query: null,
+  _pulse_status: -1,
+
+  htmlToText: (htmlString, anchor) => {
+    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
+    for (const removalQuery of [".headerlink", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
+    const docContent = htmlElement.querySelector('[role="main"]');
+    if (docContent) return docContent.textContent;
+
+    console.warn(
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
+    );
+    return "";
+  },
+
+  init: () => {
+    const query = new URLSearchParams(window.location.search).get("q");
+    document
+      .querySelectorAll('input[name="q"]')
+      .forEach((el) => (el.value = query));
+    if (query) Search.performSearch(query);
+  },
+
+  loadIndex: (url) =>
+    (document.body.appendChild(document.createElement("script")).src = url),
+
+  setIndex: (index) => {
+    Search._index = index;
+    if (Search._queued_query !== null) {
+      const query = Search._queued_query;
+      Search._queued_query = null;
+      Search.query(query);
+    }
+  },
+
+  hasIndex: () => Search._index !== null,
+
+  deferQuery: (query) => (Search._queued_query = query),
+
+  stopPulse: () => (Search._pulse_status = -1),
+
+  startPulse: () => {
+    if (Search._pulse_status >= 0) return;
+
+    const pulse = () => {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      Search.dots.innerText = ".".repeat(Search._pulse_status);
+      if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch: (query) => {
+    // create the required interface elements
+    const searchText = document.createElement("h2");
+    searchText.textContent = _("Searching");
+    const searchSummary = document.createElement("p");
+    searchSummary.classList.add("search-summary");
+    searchSummary.innerText = "";
+    const searchList = document.createElement("ul");
+    searchList.setAttribute("role", "list");
+    searchList.classList.add("search");
+
+    const out = document.getElementById("search-results");
+    Search.title = out.appendChild(searchText);
+    Search.dots = Search.title.appendChild(document.createElement("span"));
+    Search.status = out.appendChild(searchSummary);
+    Search.output = out.appendChild(searchList);
+
+    const searchProgress = document.getElementById("search-progress");
+    // Some themes don't use the search progress node
+    if (searchProgress) {
+      searchProgress.innerText = _("Preparing search...");
+    }
+    Search.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (Search.hasIndex()) Search.query(query);
+    else Search.deferQuery(query);
+  },
+
+  _parseQuery: (query) => {
+    // stem the search terms and add them to the correct list
+    const stemmer = new Stemmer();
+    const searchTerms = new Set();
+    const excludedTerms = new Set();
+    const highlightTerms = new Set();
+    const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+    splitQuery(query.trim()).forEach((queryTerm) => {
+      const queryTermLower = queryTerm.toLowerCase();
+
+      // maybe skip this "word"
+      // stopwords array is from language_data.js
+      if (
+        stopwords.indexOf(queryTermLower) !== -1 ||
+        queryTerm.match(/^\d+$/)
+      )
+        return;
+
+      // stem the word
+      let word = stemmer.stemWord(queryTermLower);
+      // select the correct list
+      if (word[0] === "-") excludedTerms.add(word.substr(1));
+      else {
+        searchTerms.add(word);
+        highlightTerms.add(queryTermLower);
+      }
+    });
+
+    if (SPHINX_HIGHLIGHT_ENABLED) {  // set in sphinx_highlight.js
+      localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+    }
+
+    // console.debug("SEARCH: searching for:");
+    // console.info("required: ", [...searchTerms]);
+    // console.info("excluded: ", [...excludedTerms]);
+
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
+    _removeChildren(document.getElementById("search-progress"));
+
+    const queryLower = query.toLowerCase().trim();
+    for (const [title, foundTitles] of Object.entries(allTitles)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
+        for (const [file, id] of foundTitles) {
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
+          normalResults.push([
+            docNames[file],
+            titles[file] !== title ? `${titles[file]} > ${title}` : title,
+            id !== null ? "#" + id : "",
+            null,
+            score + boost,
+            filenames[file],
+            SearchResultKind.title,
+          ]);
+        }
+      }
+    }
+
+    // search for explicit entries in index directives
+    for (const [entry, foundEntries] of Object.entries(indexEntries)) {
+      if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
+            docNames[file],
+            titles[file],
+            id ? "#" + id : "",
+            null,
+            score,
+            filenames[file],
+            SearchResultKind.index,
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
+        }
+      }
+    }
+
+    // lookup as object
+    objectTerms.forEach((term) =>
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
+    );
+
+    // lookup as search terms in fulltext
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
+
+    // remove duplicate search results
+    // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+    let seen = new Set();
+    results = results.reverse().reduce((acc, result) => {
+      let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+      if (!seen.has(resultStr)) {
+        acc.push(result);
+        seen.add(resultStr);
+      }
+      return acc;
+    }, []);
+
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    // console.info("search results:", Search.lastresults);
+
+    // print the results
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch: (object, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const objects = Search._index.objects;
+    const objNames = Search._index.objnames;
+    const titles = Search._index.titles;
+
+    const results = [];
+
+    const objectSearchCallback = (prefix, match) => {
+      const name = match[4]
+      const fullname = (prefix ? prefix + "." : "") + name;
+      const fullnameLower = fullname.toLowerCase();
+      if (fullnameLower.indexOf(object) < 0) return;
+
+      let score = 0;
+      const parts = fullnameLower.split(".");
+
+      // check for different match types: exact matches of full name or
+      // "last name" (i.e. last dotted part)
+      if (fullnameLower === object || parts.slice(-1)[0] === object)
+        score += Scorer.objNameMatch;
+      else if (parts.slice(-1)[0].indexOf(object) > -1)
+        score += Scorer.objPartialMatch; // matches in last name
+
+      const objName = objNames[match[1]][2];
+      const title = titles[match[0]];
+
+      // If more than one term searched for, we require other words to be
+      // found in the name/title/description
+      const otherTerms = new Set(objectTerms);
+      otherTerms.delete(object);
+      if (otherTerms.size > 0) {
+        const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+        if (
+          [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+        )
+          return;
+      }
+
+      let anchor = match[3];
+      if (anchor === "") anchor = fullname;
+      else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+      const descr = objName + _(", in ") + title;
+
+      // add custom score for some objects according to scorer
+      if (Scorer.objPrio.hasOwnProperty(match[2]))
+        score += Scorer.objPrio[match[2]];
+      else score += Scorer.objPrioDefault;
+
+      results.push([
+        docNames[match[0]],
+        fullname,
+        "#" + anchor,
+        descr,
+        score,
+        filenames[match[0]],
+        SearchResultKind.object,
+      ]);
+    };
+    Object.keys(objects).forEach((prefix) =>
+      objects[prefix].forEach((array) =>
+        objectSearchCallback(prefix, array)
+      )
+    );
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch: (searchTerms, excludedTerms) => {
+    // prepare search
+    const terms = Search._index.terms;
+    const titleTerms = Search._index.titleterms;
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+
+    const scoreMap = new Map();
+    const fileMap = new Map();
+
+    // perform the search on the required terms
+    searchTerms.forEach((word) => {
+      const files = [];
+      const arr = [
+        { files: terms[word], score: Scorer.term },
+        { files: titleTerms[word], score: Scorer.title },
+      ];
+      // add support for partial matches
+      if (word.length > 2) {
+        const escapedWord = _escapeRegExp(word);
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
+      }
+
+      // no match but word was a required one
+      if (arr.every((record) => record.files === undefined)) return;
+
+      // found search word in contents
+      arr.forEach((record) => {
+        if (record.files === undefined) return;
+
+        let recordFiles = record.files;
+        if (recordFiles.length === undefined) recordFiles = [recordFiles];
+        files.push(...recordFiles);
+
+        // set score for the word in each file
+        recordFiles.forEach((file) => {
+          if (!scoreMap.has(file)) scoreMap.set(file, {});
+          scoreMap.get(file)[word] = record.score;
+        });
+      });
+
+      // create the mapping
+      files.forEach((file) => {
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
+      });
+    });
+
+    // now check if the files don't contain excluded terms
+    const results = [];
+    for (const [file, wordList] of fileMap) {
+      // check if all requirements are matched
+
+      // as search terms with length < 3 are discarded
+      const filteredTermCount = [...searchTerms].filter(
+        (term) => term.length > 2
+      ).length;
+      if (
+        wordList.length !== searchTerms.size &&
+        wordList.length !== filteredTermCount
+      )
+        continue;
+
+      // ensure that none of the excluded terms is in the search result
+      if (
+        [...excludedTerms].some(
+          (term) =>
+            terms[term] === file ||
+            titleTerms[term] === file ||
+            (terms[term] || []).includes(file) ||
+            (titleTerms[term] || []).includes(file)
+        )
+      )
+        break;
+
+      // select one (max) score for the file.
+      const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+      // add result to the result list
+      results.push([
+        docNames[file],
+        titles[file],
+        "",
+        null,
+        score,
+        filenames[file],
+        SearchResultKind.text,
+      ]);
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words.
+   */
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
+    if (text === "") return null;
+
+    const textLower = text.toLowerCase();
+    const actualStartPosition = [...keywords]
+      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .filter((i) => i > -1)
+      .slice(-1)[0];
+    const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+    const top = startWithContext === 0 ? "" : "...";
+    const tail = startWithContext + 240 < text.length ? "..." : "";
+
+    let summary = document.createElement("p");
+    summary.classList.add("context");
+    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+    return summary;
+  },
+};
+
+_ready(Search.init);

docs/source/_build/html/_static/sphinx_highlight.js

@@ -0,0 +1,154 @@
+/* Highlighting utilities for Sphinx HTML documentation. */
+"use strict";
+
+const SPHINX_HIGHLIGHT_ENABLED = true
+
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+  if (node.nodeType === Node.TEXT_NODE) {
+    const val = node.nodeValue;
+    const parent = node.parentNode;
+    const pos = val.toLowerCase().indexOf(text);
+    if (
+      pos >= 0 &&
+      !parent.classList.contains(className) &&
+      !parent.classList.contains("nohighlight")
+    ) {
+      let span;
+
+      const closestNode = parent.closest("body, svg, foreignObject");
+      const isInSVG = closestNode && closestNode.matches("svg");
+      if (isInSVG) {
+        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+      } else {
+        span = document.createElement("span");
+        span.classList.add(className);
+      }
+
+      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
+      parent.insertBefore(
+        span,
+        parent.insertBefore(
+          rest,
+          node.nextSibling
+        )
+      );
+      node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
+
+      if (isInSVG) {
+        const rect = document.createElementNS(
+          "http://www.w3.org/2000/svg",
+          "rect"
+        );
+        const bbox = parent.getBBox();
+        rect.x.baseVal.value = bbox.x;
+        rect.y.baseVal.value = bbox.y;
+        rect.width.baseVal.value = bbox.width;
+        rect.height.baseVal.value = bbox.height;
+        rect.setAttribute("class", className);
+        addItems.push({ parent: parent, target: rect });
+      }
+    }
+  } else if (node.matches && !node.matches("button, select, textarea")) {
+    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+  }
+};
+const _highlightText = (thisNode, text, className) => {
+  let addItems = [];
+  _highlight(thisNode, addItems, text, className);
+  addItems.forEach((obj) =>
+    obj.parent.insertAdjacentElement("beforebegin", obj.target)
+  );
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const SphinxHighlight = {
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+      <li>
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+
+      <ul>
+        <li><a href="grogu.html#module-grogu.jij">module</a>
+</li>
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+        <li><a href="grogu.html#module-grogu.useful">module</a>
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+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="grogu.html#grogu.useful.hsk">hsk() (in module grogu.useful)</a>
+</li>
+  </ul></td>
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+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="grogu.html#grogu.useful.make_atran">make_atran() (in module grogu.useful)</a>
+</li>
+      <li><a href="grogu.html#grogu.useful.make_contour">make_contour() (in module grogu.useful)</a>
+</li>
+      <li><a href="grogu.html#grogu.useful.make_kset">make_kset() (in module grogu.useful)</a>
+</li>
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+
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+        <li><a href="grogu.html#module-grogu">grogu</a>
+</li>
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+<li class="toctree-l3"><a class="reference internal" href="#submodules">Submodules</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#module-grogu.example">grogu.example module</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#module-grogu.jij">grogu.jij module</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#module-grogu.useful">grogu.useful module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#grogu.useful.add"><code class="docutils literal notranslate"><span class="pre">add()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#grogu.useful.hsk"><code class="docutils literal notranslate"><span class="pre">hsk()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#grogu.useful.make_atran"><code class="docutils literal notranslate"><span class="pre">make_atran()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#grogu.useful.make_contour"><code class="docutils literal notranslate"><span class="pre">make_contour()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#grogu.useful.make_kset"><code class="docutils literal notranslate"><span class="pre">make_kset()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="#module-grogu">Module contents</a></li>
+</ul>
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <section id="grogu-package">
+<h1>grogu package<a class="headerlink" href="#grogu-package" title="Link to this heading"></a></h1>
+<section id="submodules">
+<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
+</section>
+<section id="module-grogu.example">
+<span id="grogu-example-module"></span><h2>grogu.example module<a class="headerlink" href="#module-grogu.example" title="Link to this heading"></a></h2>
+</section>
+<section id="module-grogu.jij">
+<span id="grogu-jij-module"></span><h2>grogu.jij module<a class="headerlink" href="#module-grogu.jij" title="Link to this heading"></a></h2>
+</section>
+<section id="module-grogu.useful">
+<span id="grogu-useful-module"></span><h2>grogu.useful module<a class="headerlink" href="#module-grogu.useful" title="Link to this heading"></a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="grogu.useful.add">
+<span class="sig-prename descclassname"><span class="pre">grogu.useful.</span></span><span class="sig-name descname"><span class="pre">add</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/grogu/useful.html#add"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogu.useful.add" title="Link to this definition"></a></dt>
+<dd><p>The sum of two numbers for testing.</p>
+<p>This function adds to numbers together. I only created this for testing documentation and examples.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>x</strong> (<em>float</em>) – First number</p></li>
+<li><p><strong>y</strong> (<em>float</em>) – Second number added to <cite>x</cite></p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>sum</strong> – The sum of the inputs</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>int</p>
+</dd>
+</dl>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<dl class="simple">
+<dt><code class="xref py py-obj docutils literal notranslate"><span class="pre">numpy.add</span></code></dt><dd><p>Adds more than two numbers.</p>
+</dd>
+</dl>
+</div>
+<p class="rubric">Notes</p>
+<p>We can create some latex notes here <a class="footnote-reference brackets" href="#id2" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a> :</p>
+<div class="math notranslate nohighlight">
+\[a + b = c\]</div>
+<p class="rubric">References</p>
+<aside class="footnote-list brackets">
+<aside class="footnote brackets" id="id2" role="doc-footnote">
+<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
+<p><a class="reference external" href="https://numpydoc.readthedocs.io/en/latest/format.html">https://numpydoc.readthedocs.io/en/latest/format.html</a></p>
+</aside>
+</aside>
+<p class="rubric">Examples</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">add</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="go">3</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="grogu.useful.hsk">
+<span class="sig-prename descclassname"><span class="pre">grogu.useful.</span></span><span class="sig-name descname"><span class="pre">hsk</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dh</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/grogu/useful.html#hsk"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogu.useful.hsk" title="Link to this definition"></a></dt>
+<dd><p>One way to speed up Hk and Sk generation</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="grogu.useful.make_atran">
+<span class="sig-prename descclassname"><span class="pre">grogu.useful.</span></span><span class="sig-name descname"><span class="pre">make_atran</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nauc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dirs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'xyz'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/grogu/useful.html#make_atran"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogu.useful.make_atran" title="Link to this definition"></a></dt>
+<dd><p>Simple pair generator. Depending on the value of the dirs
+argument sampling in 1,2 or 3 dimensions is generated.
+If dirs argument does not contain either of x,y or z
+a single pair is returend.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="grogu.useful.make_contour">
+<span class="sig-prename descclassname"><span class="pre">grogu.useful.</span></span><span class="sig-name descname"><span class="pre">make_contour</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">emin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">emax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">150</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/grogu/useful.html#make_contour"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogu.useful.make_contour" title="Link to this definition"></a></dt>
+<dd><p>A more sophisticated contour generator</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="grogu.useful.make_kset">
+<span class="sig-prename descclassname"><span class="pre">grogu.useful.</span></span><span class="sig-name descname"><span class="pre">make_kset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dirs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'xyz'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">NUMK</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/grogu/useful.html#make_kset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogu.useful.make_kset" title="Link to this definition"></a></dt>
+<dd><p>Simple k-grid generator. Depending on the value of the dirs
+argument k sampling in 1,2 or 3 dimensions is generated.
+If dirs argument does not contain either of x,y or z
+a kset of a single k-pont at the origin is returend.</p>
+</dd></dl>
+
+</section>
+<section id="module-grogu">
+<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-grogu" title="Link to this heading"></a></h2>
+</section>
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+</html>

docs/source/_build/html/index.html

@@ -0,0 +1,128 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>asd documentation &mdash; Grogu 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
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+</ul>
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+documentation for details.</p>
+<div class="toctree-wrapper compound">
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+</div>
+</section>
+<section id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Link to this heading"></a></h1>
+<ul class="simple">
+<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
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+<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
+</ul>
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+        <a href="modules.html" class="btn btn-neutral float-right" title="src" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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+  </script>
+
+</body>
+</html>

docs/source/_build/html/modules.html

@@ -0,0 +1,132 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>src &mdash; Grogu 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
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+      <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+    <script src="_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="grogu package" href="grogu.html" />
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+<li class="toctree-l1 current"><a class="current reference internal" href="#">src</a><ul>
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+            <a href="_sources/modules.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <section id="src">
+<h1>src<a class="headerlink" href="#src" title="Link to this heading"></a></h1>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="grogu.html">grogu package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="grogu.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grogu.html#module-grogu.example">grogu.example module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grogu.html#module-grogu.jij">grogu.jij module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="grogu.html#module-grogu.useful">grogu.useful module</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="grogu.html#grogu.useful.add"><code class="docutils literal notranslate"><span class="pre">add()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="grogu.html#grogu.useful.hsk"><code class="docutils literal notranslate"><span class="pre">hsk()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="grogu.html#grogu.useful.make_atran"><code class="docutils literal notranslate"><span class="pre">make_atran()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="grogu.html#grogu.useful.make_contour"><code class="docutils literal notranslate"><span class="pre">make_contour()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="grogu.html#grogu.useful.make_kset"><code class="docutils literal notranslate"><span class="pre">make_kset()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="grogu.html#module-grogu">Module contents</a></li>
+</ul>
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+</ul>
+</div>
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docs/source/_build/html/objects.inv

@@ -0,0 +1,7 @@
+# Sphinx inventory version 2
+# Project: Grogu
+# Version: 
+# The remainder of this file is compressed using zlib.
+xÚ•‘M
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+¨

docs/source/_build/html/py-modindex.html

@@ -0,0 +1,135 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
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+
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+
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+<ul>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">src</a></li>
+</ul>
+
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+        <div class="rst-content">
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+      <li class="wy-breadcrumbs-aside">
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+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+
+   <h1>Python Module Index</h1>
+
+   <div class="modindex-jumpbox">
+   <a href="#cap-g"><strong>g</strong></a>
+   </div>
+
+   <table class="indextable modindextable">
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-g"><td></td><td>
+       <strong>g</strong></td><td></td></tr>
+     <tr>
+       <td><img src="_static/minus.png" class="toggler"
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+       <td>
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docs/source/_build/html/search.html

@@ -0,0 +1,120 @@
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+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
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+      <li class="breadcrumb-item active">Search</li>
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+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <noscript>
+  <div id="fallback" class="admonition warning">
+    <p class="last">
+      Please activate JavaScript to enable the search functionality.
+    </p>
+  </div>
+  </noscript>
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+  <div id="search-results">
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+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Grogu.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script>
+  <script>
+    jQuery(function() { Search.loadIndex("searchindex.js"); });
+  </script>
+
+  <script id="searchindexloader"></script>
+
+
+
+</body>
+</html>

docs/source/_build/html/searchindex.js

@@ -0,0 +1 @@
+Search.setIndex({"alltitles": {"Contents:": [[1, null]], "Indices and tables": [[1, "indices-and-tables"]], "Module contents": [[0, "module-grogu"]], "Submodules": [[0, "submodules"]], "asd documentation": [[1, null]], "grogu package": [[0, null]], "grogu.example module": [[0, "module-grogu.example"]], "grogu.jij module": [[0, "module-grogu.jij"]], "grogu.useful module": [[0, "module-grogu.useful"]], "src": [[2, null]]}, "docnames": ["grogu", "index", "modules"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["grogu.rst", "index.rst", "modules.rst"], "indexentries": {"add() (in module grogu.useful)": [[0, "grogu.useful.add", false]], "grogu": [[0, "module-grogu", false]], "grogu.example": [[0, "module-grogu.example", false]], "grogu.jij": [[0, "module-grogu.jij", false]], "grogu.useful": [[0, "module-grogu.useful", false]], "hsk() (in module grogu.useful)": [[0, "grogu.useful.hsk", false]], "make_atran() (in module grogu.useful)": [[0, "grogu.useful.make_atran", false]], "make_contour() (in module grogu.useful)": [[0, "grogu.useful.make_contour", false]], "make_kset() (in module grogu.useful)": [[0, "grogu.useful.make_kset", false]], "module": [[0, "module-grogu", false], [0, "module-grogu.example", false], [0, "module-grogu.jij", false], [0, "module-grogu.useful", false]]}, "objects": {"": [[0, 0, 0, "-", "grogu"]], "grogu": [[0, 0, 0, "-", "example"], [0, 0, 0, "-", "jij"], [0, 0, 0, "-", "useful"]], "grogu.useful": [[0, 1, 1, "", "add"], [0, 1, 1, "", "hsk"], [0, 1, 1, "", "make_atran"], [0, 1, 1, "", "make_contour"], [0, 1, 1, "", "make_kset"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"]}, "objtypes": {"0": "py:module", "1": "py:function"}, "terms": {"0": 0, "1": 0, "150": 0, "2": 0, "20": 0, "3": 0, "42": 0, "A": 0, "If": 0, "One": 0, "The": 0, "ad": 0, "add": [0, 1, 2], "argument": 0, "b": 0, "c": 0, "can": 0, "contain": 0, "content": 2, "contour": 0, "creat": 0, "depend": 0, "detail": 1, "dh": 0, "dimens": 0, "dir": 0, "dist": 0, "document": 0, "doe": 0, "either": 0, "emax": 0, "emin": 0, "en": 0, "enum": 0, "exampl": 2, "first": 0, "float": 0, "format": 0, "function": 0, "gener": 0, "grid": 0, "grogu": [1, 2], "here": 0, "hk": 0, "hsk": [0, 2], "html": 0, "http": 0, "i": 0, "index": 1, "input": 0, "int": 0, "io": 0, "jij": 2, "k": 0, "kset": 0, "latest": 0, "latex": 0, "make_atran": [0, 2], "make_contour": [0, 2], "make_kset": [0, 2], "modul": [1, 2], "more": 0, "nauc": 0, "note": 0, "number": 0, "numk": 0, "numpi": 0, "numpydoc": 0, "onli": 0, "origin": 0, "p": 0, "packag": [1, 2], "page": 1, "pair": 0, "paramet": 0, "pont": 0, "readthedoc": 0, "refer": 0, "restructuredtext": 1, "returend": 0, "return": 0, "sampl": 0, "search": 1, "second": 0, "see": 1, "simpl": 0, "singl": 0, "sk": 0, "some": 0, "sophist": 0, "sourc": 0, "speed": 0, "src": 1, "submodul": 2, "sum": 0, "syntax": 1, "test": 0, "than": 0, "thi": 0, "togeth": 0, "two": 0, "type": 0, "up": 0, "us": [1, 2], "valu": 0, "wai": 0, "we": 0, "x": 0, "xyz": 0, "y": 0, "your": 1, "z": 0}, "titles": ["grogu package", "asd documentation", "src"], "titleterms": {"asd": 1, "content": [0, 1], "document": 1, "exampl": 0, "grogu": 0, "indic": 1, "jij": 0, "modul": 0, "packag": 0, "src": 2, "submodul": 0, "tabl": 1, "us": 0}})

docs/source/conf.py

@@ -0,0 +1,52 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Grogu"
+copyright = "2024, Grogu"
+author = "Laszlo Oroszlany, Daniel Pozsar"
+release = "0.0.1"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/grogu.rst

@@ -0,0 +1,37 @@
+grogu package
+=============
+
+Submodules
+----------
+
+grogu.example module
+--------------------
+
+.. automodule:: grogu.example
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+grogu.jij module
+----------------
+
+.. automodule:: grogu.jij
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+grogu.useful module
+-------------------
+
+.. automodule:: grogu.useful
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: grogu
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -0,0 +1,25 @@
+.. asd documentation master file, created by
+   sphinx-quickstart on Thu Oct 10 17:10:03 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+asd documentation
+=================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/modules.rst

@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   grogu

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "grogu"
+version = "0.0.1"
+authors = [
+  { name="Laszlo Oroszlany", email="laszlo.oroszlany@ttk.elte.hu" },
+  { name="Daniel Pozsar", email="danielpozsar@student.elte.hu" },
+]
+description = "Relativistic magnetic interactions from non-orthogonal basis sets"
+readme = "README.md"
+kewords = [
+    "DFT",
+    "physics",
+]
+requires-python = ">=3.8"
+dependencies = [
+  "numpy",
+  "scipy",
+  "sisl",
+  "mpi4py",
+  "argparse",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/pypa/sampleproject"
+Documentation = "https://readthedocs.org"
+Repository = "https://github.com/me/spam.git"
+Issues = "https://github.com/pypa/sampleproject/issues"
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+#    "--cov",
+    "--doctest-modules",
+]
+pythonpath = [
+    "src/grogu/",
+]

requirements-dev.txt

@@ -0,0 +1,17 @@
+# PyPI
+wheel
+setuptools
+build
+
+# code-linters
+black
+license-headers
+
+# dev-tools
+pre-commit
+pytest
+pytest-randomly
+pytest-cov
+doctest
+sphinx
+git

requirements.txt

@@ -0,0 +1,6 @@
+# Package dependencies
+numpy
+scipy
+sisl
+mpi4py
+argparse

src/grogu/__init__.py

@@ -0,0 +1,22 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from jij import *
+from useful import *

src/grogu/example.py

@@ -0,0 +1,19 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.

src/grogu/jij.py

@@ -0,0 +1,294 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+if __name__ == "__main__":
+    import argparse
+    import sys
+    from itertools import permutations, product
+    from timeit import default_timer as timer
+
+    import numpy as np
+    import numpy.linalg as nl
+    import sisl
+    import tqdm
+    from mpi4py import MPI
+    from scipy.special import roots_legendre
+
+    from grogu.useful import hsk, make_atran, make_contour, make_kset
+
+    start = timer()
+
+    # Some input parsing
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--kset",
+        dest="kset",
+        default=2,
+        type=int,
+        help="k-space resolution of Jij calculation",
+    )
+    parser.add_argument(
+        "--kdirs",
+        dest="kdirs",
+        default="xyz",
+        help="Definition of k-space dimensionality",
+    )
+    parser.add_argument(
+        "--eset",
+        dest="eset",
+        default=42,
+        type=int,
+        help="Number of energy points on the contour",
+    )
+    parser.add_argument(
+        "--eset-p",
+        dest="esetp",
+        default=10,
+        type=int,
+        help="Parameter tuning the distribution on the contour",
+    )
+    parser.add_argument("--input", dest="infile", required=True, help="Input file name")
+    parser.add_argument(
+        "--output", dest="outfile", required=True, help="Output file name"
+    )
+    parser.add_argument(
+        "--Ebot",
+        dest="Ebot",
+        default=-20.0,
+        type=float,
+        help="Bottom energy of the contour",
+    )
+    parser.add_argument(
+        "--npairs",
+        dest="npairs",
+        default=1,
+        type=int,
+        help="Number of unitcell pairs in each direction for Jij calculation",
+    )
+    parser.add_argument(
+        "--adirs", dest="adirs", default=False, help="Definition of pair directions"
+    )
+    parser.add_argument(
+        "--use-tqdm",
+        dest="usetqdm",
+        default="not",
+        help="Use tqdm for progressbars or not",
+    )
+    parser.add_argument(
+        "--cutoff",
+        dest="cutoff",
+        default=100.0,
+        type=float,
+        help="Real space cutoff for pair generation in Angs",
+    )
+    parser.add_argument(
+        "--pairfile",
+        dest="pairfile",
+        default=False,
+        help="File to read pair information",
+    )
+    args = parser.parse_args()
+    # ----------------------------------------------------------------------
+
+    # MPI init
+    comm = MPI.COMM_WORLD
+    size = comm.Get_size()
+    rank = comm.Get_rank()
+    root_node = 0
+    if rank == root_node:
+        print("Number of nodes in the parallel cluster: ", size)
+    # ----------------------------------------------------------------------
+
+    # importing the necessary structures from SIESTA output
+    dat = sisl.get_sile(args.infile)
+    dh = dat.read_hamiltonian()
+    # update datastructure of the hamiltonian
+    # this is needed for quick Hk building
+    dh.hup = (
+        dh.tocsr(0)
+        .toarray()
+        .reshape(dh.no, dh.n_s, dh.no)
+        .transpose(0, 2, 1)
+        .astype("complex128")
+    )
+    dh.hdo = (
+        dh.tocsr(1)
+        .toarray()
+        .reshape(dh.no, dh.n_s, dh.no)
+        .transpose(0, 2, 1)
+        .astype("complex128")
+    )
+    dh.sov = (
+        dh.tocsr(2)
+        .toarray()
+        .reshape(dh.no, dh.n_s, dh.no)
+        .transpose(0, 2, 1)
+        .astype("complex128")
+    )
+    # ----------------------------------------------------------------------
+
+    # generate k space sampling
+    kset = make_kset(dirs=args.kdirs, NUMK=args.kset)
+    wk = 1 / len(kset)  # weight of a kpoint in BZ integral
+    kpcs = np.array_split(kset, size)
+    if "k" in args.usetqdm:
+        kpcs[root_node] = tqdm.tqdm(kpcs[root_node], desc="k loop")
+    # ----------------------------------------------------------------------
+    # define pairs
+
+    if args.pairfile:
+        # if pair file is specified read in pair information from pairfile
+        if rank == root_node:
+            # read in pair on root node file in a format of five integer columns
+            # first two integers define sublattice
+            # second three define distance vectors of unitcells
+            dummy = np.loadtxt(args.pairfile, dtype=int)
+            atran = [
+                (dummy[p, 0], dummy[p, 1], [dummy[p, 2], dummy[p, 3], dummy[p, 4]])
+                for p in range(len(dummy))
+            ]
+        else:
+            atran = None
+        # syncronize atran over all nodes
+        atran = comm.bcast(atran, root=root_node)
+    else:
+        # if pairfile is not specified generate pair as defined by npairs and adirs
+        # Take pair directions for k directions if adirs is not set
+        args.adirs = args.adirs if args.adirs else args.kdirs
+        # definition of pairs in terms of integer coordinates refering
+        # to unicell distances and atomic positions
+        atran = make_atran(len(dh.atoms), args.adirs, dist=args.npairs)
+    pairs = []
+    for i, j, uc in atran:
+        if nl.norm(np.dot(uc, dh.cell)) < args.cutoff:
+            pairs.append(
+                dict(
+                    offset=uc,  # lattice vector offset between the unitcells the two atoms are
+                    aiij=[i, j],  # indecies of the atoms in the unitcell
+                    noij=[
+                        dh.atoms.orbitals[i],
+                        dh.atoms.orbitals[j],
+                    ],  # number of orbitals on the appropriate atoms
+                    slij=[
+                        slice(
+                            *(lambda x: [min(x), max(x) + 1])(dh.a2o(i, all=True))
+                        ),  # slices for
+                        slice(*(lambda x: [min(x), max(x) + 1])(dh.a2o(j, all=True))),
+                    ],  # appropriate orbitals
+                    rirj=[
+                        dh.axyz()[i],
+                        dh.axyz()[j],
+                    ],  # real space vectors of atoms in the unit cell
+                    Rij=np.dot(
+                        uc, dh.cell
+                    ),  # real space distance vector between unit cells
+                    rij=np.dot(uc, dh.cell)
+                    - dh.axyz()[i]
+                    + dh.axyz()[j],  # real space vector between atoms
+                    Jijz=[],  # in this empty list are we going to gather the integrad of the energy integral
+                    Jij=0,  # the final results of the calculation are going to be here on the root node
+                )
+            )
+
+    if rank == root_node:
+        print("Number of pairs beeing calculated: ", len(pairs))
+
+    comm.Barrier()
+    # ----------------------------------------------------------------------
+
+    # make energy contour
+    # we are working in eV now  !
+    # and sisil shifts E_F to 0 !
+    cont = make_contour(emin=args.Ebot, enum=args.eset, p=args.esetp)
+    eran = cont.ze
+    # ----------------------------------------------------------------------
+
+    # generating onsite matrix and overalp elements of all the atoms in the unitcell
+    # onsite of the origin supercell
+    orig_indx = np.arange(0, dh.no) + dh.sc_index([0, 0, 0]) * dh.no
+    # spin up
+    uc_up = dh.tocsr(dh.UP)[:, orig_indx].toarray()
+    # spin down
+    uc_down = dh.tocsr(dh.DOWN)[:, orig_indx].toarray()
+    Hs = []
+    # get number of atoms in the unit cell
+    for i in range(len(dh.atoms)):
+        at_indx = dh.a2o(i, all=True)
+        Hs.append(uc_up[:, at_indx][at_indx, :] - uc_down[:, at_indx][at_indx, :])
+
+    # ----------------------------------------------------------------------
+
+    # sampling the integrand on the contour and the BZ
+
+    for pair in pairs:
+        noi, noj = pair["noij"]
+        pair["Guij"] = np.zeros((args.eset, noi, noj), dtype="complex128")
+        pair["Gdji"] = np.zeros((args.eset, noj, noi), dtype="complex128")
+        pair["Guij_tmp"] = np.zeros((args.eset, noi, noj), dtype="complex128")
+        pair["Gdji_tmp"] = np.zeros((args.eset, noj, noi), dtype="complex128")
+
+    for k in kpcs[rank]:
+        HKU, HKD, SK = hsk(dh, k)
+        Gku = nl.inv(SK * eran.reshape(args.eset, 1, 1) - HKU)
+        Gkd = nl.inv(SK * eran.reshape(args.eset, 1, 1) - HKD)
+        for pair in pairs:
+            phase = np.exp(1j * np.dot(np.dot(k, dh.rcell), pair["Rij"]))
+            si, sj = pair["slij"]
+            pair["Guij_tmp"] += Gku[:, si, sj] * phase * wk
+            pair["Gdji_tmp"] += Gkd[:, sj, si] / phase * wk
+
+    # summ reduce partial results of mpi nodes
+    for pair in pairs:
+        comm.Reduce(pair["Guij_tmp"], pair["Guij"], root=root_node)
+        comm.Reduce(pair["Gdji_tmp"], pair["Gdji"], root=root_node)
+
+    if rank == root_node:
+        for pair in pairs:
+            i, j = pair["aiij"]
+            # The Szunyogh-Lichtenstein formula
+            pair["Jijz"] = np.trace(
+                (Hs[i] @ pair["Guij"]) @ (Hs[j] @ pair["Gdji"]), axis1=1, axis2=2
+            )
+            # evaluation of the contour integral
+            pair["Jij"] = np.trapz(np.imag(pair["Jijz"] * cont.we) / (2 * np.pi))
+        end = timer()
+
+        # ----------------------------------------------------------------------
+        # and saveing output of the calculation
+        np.savetxt(
+            args.outfile,
+            np.array(
+                [
+                    [nl.norm(p["rij"]), p["Jij"] * sisl.unit_convert("eV", "Ry") * 1000]
+                    + p["aiij"]
+                    + list(p["offset"])
+                    + list(p["rij"])
+                    for p in pairs
+                ],
+                dtype=object,
+            ),
+            header=str(args)
+            + "\nnumber of cores = "
+            + str(size)
+            + "\ntime of calculation = "
+            + str(end - start)
+            + "\nnorm(rij),Jij[mRy],aiij,offset,rij",
+            fmt="%s",
+        )

src/grogu/useful.py

@@ -0,0 +1,167 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from itertools import permutations, product
+
+import numpy as np
+from scipy.special import roots_legendre
+
+
+# define some useful functions
+def hsk(dh, k=(0, 0, 0)):
+    """
+    One way to speed up Hk and Sk generation
+    """
+    k = np.asarray(k, np.float64)  # this two conversion lines
+    k.shape = (-1,)  # are from the sisl source
+
+    # this generates the list of phases
+    phases = np.exp(-1j * np.dot(np.dot(np.dot(dh.rcell, k), dh.cell), dh.sc.sc_off.T))
+
+    HKU = np.einsum("abc,c->ab", dh.hup, phases)
+    HKD = np.einsum("abc,c->ab", dh.hdo, phases)
+    SK = np.einsum("abc,c->ab", dh.sov, phases)
+
+    return HKU, HKD, SK
+
+
+def make_contour(emin=-20, emax=0.0, enum=42, p=150):
+    """
+    A more sophisticated contour generator
+    """
+
+    x, wl = roots_legendre(enum)
+    R = (emax - emin) / 2
+    z0 = (emax + emin) / 2
+    y1 = -np.log(1 + np.pi * p)
+    y2 = 0
+
+    y = (y2 - y1) / 2 * x + (y2 + y1) / 2
+    phi = (np.exp(-y) - 1) / p
+    ze = z0 + R * np.exp(1j * phi)
+    we = -(y2 - y1) / 2 * np.exp(-y) / p * 1j * (ze - z0) * wl
+
+    class ccont:
+        # just an empty container class
+        pass
+
+    cont = ccont()
+    cont.R = R
+    cont.z0 = z0
+    cont.ze = ze
+    cont.we = we
+    cont.enum = enum
+
+    return cont
+
+
+def make_kset(dirs="xyz", NUMK=20):
+    """
+    Simple k-grid generator. Depending on the value of the dirs
+    argument k sampling in 1,2 or 3 dimensions is generated.
+    If dirs argument does not contain either of x,y or z
+    a kset of a single k-pont at the origin is returend.
+    """
+    if not (sum([d in dirs for d in "xyz"])):
+        return np.array([[0, 0, 0]])
+
+    kran = len(dirs) * [np.linspace(0, 1, NUMK, endpoint=False)]
+    mg = np.meshgrid(*kran)
+    dirsdict = dict()
+
+    for d in enumerate(dirs):
+        dirsdict[d[1]] = mg[d[0]].flatten()
+    for d in "xyz":
+        if not (d in dirs):
+            dirsdict[d] = 0 * dirsdict[dirs[0]]
+    kset = np.array([dirsdict[d] for d in "xyz"]).T
+
+    return kset
+
+
+def make_atran(nauc, dirs="xyz", dist=1):
+    """
+    Simple pair generator. Depending on the value of the dirs
+    argument sampling in 1,2 or 3 dimensions is generated.
+    If dirs argument does not contain either of x,y or z
+    a single pair is returend.
+    """
+    if not (sum([d in dirs for d in "xyz"])):
+        return (0, 0, [1, 0, 0])
+
+    dran = len(dirs) * [np.arange(-dist, dist + 1)]
+    mg = np.meshgrid(*dran)
+    dirsdict = dict()
+
+    for d in enumerate(dirs):
+        dirsdict[d[1]] = mg[d[0]].flatten()
+    for d in "xyz":
+        if not (d in dirs):
+            dirsdict[d] = 0 * dirsdict[dirs[0]]
+
+    ucran = np.array([dirsdict[d] for d in "xyz"]).T
+    atran = []
+    for i, j in list(product(range(nauc), repeat=2)):
+        for u in ucran:
+            if (abs(i - j) + sum(abs(u))) > 0:
+                atran.append((i, j, list(u)))
+
+    return atran
+
+
+def add(x, y):
+    """The sum of two numbers for testing.
+
+    This function adds to numbers together. I only created this for testing documentation and examples.
+
+    Parameters
+    ----------
+    x : float
+        First number
+    y : float
+        Second number added to `x`
+
+    Returns
+    -------
+    sum : int
+        The sum of the inputs
+
+    See Also
+    --------
+    numpy.add : Adds more than two numbers.
+
+    Notes
+    -----
+    We can create some latex notes here [1]_ :
+
+    .. math:: a + b = c
+
+    References
+    ----------
+    .. [1] https://numpydoc.readthedocs.io/en/latest/format.html
+
+
+    Examples
+    --------
+    >>> add(1, 2)
+    3
+
+    """
+    return x + y

tests/__init__.py

@@ -0,0 +1,19 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.

tests/test_jij.py

@@ -0,0 +1,19 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.

tests/test_useful.py

@@ -0,0 +1,29 @@
+# Copyright (c) [2024] [Daniel Pozsar]
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import pytest
+from useful import add
+
+
+@pytest.mark.parametrize(
+    "a, b, c, expected_out", [(1, 2, 3, True), (6, 7, 13, True), (1, 2, 10, False)]
+)
+def test_add(a, b, c, expected_out):
+    assert (add(a, b) == c) == expected_out