Skip to content

Commit c4acb95

Browse files
paulsaxepaulsaxe
committed
deploy: 074d9a7 
1 parent 55e0cdf commit c4acb95

26 files changed

+73
-66
lines changed

‎.buildinfo

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: d98f49351f41e2e071db314dde4f4af3
3+
config: ac5edb7f5412d38d62b0387c80a7a877
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

‎_modules/index.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>Overview: module code &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>Overview: module code &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../_static/clipboard.min.js?v=a7894cd8"></script>

‎_modules/packmol_step/installer.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>packmol_step.installer &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>packmol_step.installer &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>

‎_modules/packmol_step/packmol.html

+21-20
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>packmol_step.packmol &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>packmol_step.packmol &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -495,6 +495,7 @@ <h1>Source code for packmol_step.packmol</h1><div class="highlight"><pre>
495495
<span class="kn">import</span> <span class="nn">importlib</span>
496496
<span class="kn">import</span> <span class="nn">logging</span>
497497
<span class="kn">import</span> <span class="nn">math</span>
498+
<span class="kn">import</span> <span class="nn">os</span>
498499
<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
499500
<span class="kn">import</span> <span class="nn">pprint</span>
500501
<span class="kn">import</span> <span class="nn">shutil</span>
@@ -505,7 +506,7 @@ <h1>Source code for packmol_step.packmol</h1><div class="highlight"><pre>
505506
<span class="kn">from</span> <span class="nn">molsystem</span> <span class="kn">import</span> <span class="n">SystemDB</span>
506507
<span class="kn">import</span> <span class="nn">seamm</span>
507508
<span class="kn">import</span> <span class="nn">seamm_util</span>
508-
<span class="kn">from</span> <span class="nn">seamm_util</span> <span class="kn">import</span> <span class="n">ureg</span><span class="p">,</span> <span class="n">Q_</span><span class="p">,</span> <span class="n">units_class</span> <span class="c1"># noqa: F401</span>
509+
<span class="kn">from</span> <span class="nn">seamm_util</span> <span class="kn">import</span> <span class="n">Configuration</span><span class="p">,</span> <span class="n">ureg</span><span class="p">,</span> <span class="n">Q_</span><span class="p">,</span> <span class="n">units_class</span> <span class="c1"># noqa: F401</span>
509510
<span class="kn">import</span> <span class="nn">seamm_util.printing</span> <span class="k">as</span> <span class="nn">printing</span>
510511
<span class="kn">from</span> <span class="nn">seamm_util.printing</span> <span class="kn">import</span> <span class="n">FormattedText</span> <span class="k">as</span> <span class="n">__</span>
511512
<span class="kn">import</span> <span class="nn">packmol_step</span>
@@ -719,14 +720,19 @@ <h1>Source code for packmol_step.packmol</h1><div class="highlight"><pre>
719720
<span class="n">ini_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">seamm_options</span><span class="p">[</span><span class="s2">&quot;root&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">expanduser</span><span class="p">()</span>
720721
<span class="n">path</span> <span class="o">=</span> <span class="n">ini_dir</span> <span class="o">/</span> <span class="s2">&quot;packmol.ini&quot;</span>
721722

722-
<span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
723-
<span class="n">full_config</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ini_dir</span> <span class="o">/</span> <span class="s2">&quot;packmol.ini&quot;</span><span class="p">)</span>
724-
725-
<span class="c1"># If the section we need doesn&#39;t exists, get the default</span>
726-
<span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="n">executor_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">full_config</span><span class="p">:</span>
723+
<span class="c1"># If the config file doesn&#39;t exists, get the default</span>
724+
<span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
727725
<span class="n">resources</span> <span class="o">=</span> <span class="n">importlib</span><span class="o">.</span><span class="n">resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="s2">&quot;packmol_step&quot;</span><span class="p">)</span> <span class="o">/</span> <span class="s2">&quot;data&quot;</span>
728726
<span class="n">ini_text</span> <span class="o">=</span> <span class="p">(</span><span class="n">resources</span> <span class="o">/</span> <span class="s2">&quot;packmol.ini&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">read_text</span><span class="p">()</span>
729-
<span class="n">full_config</span><span class="o">.</span><span class="n">read_string</span><span class="p">(</span><span class="n">ini_text</span><span class="p">)</span>
727+
<span class="n">txt_config</span> <span class="o">=</span> <span class="n">Configuration</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
728+
<span class="n">txt_config</span><span class="o">.</span><span class="n">from_string</span><span class="p">(</span><span class="n">ini_text</span><span class="p">)</span>
729+
730+
<span class="c1"># Work out the conda info needed</span>
731+
<span class="n">txt_config</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="s2">&quot;local&quot;</span><span class="p">,</span> <span class="s2">&quot;conda&quot;</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">&quot;CONDA_EXE&quot;</span><span class="p">])</span>
732+
<span class="n">txt_config</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="s2">&quot;local&quot;</span><span class="p">,</span> <span class="s2">&quot;conda-environment&quot;</span><span class="p">,</span> <span class="s2">&quot;seamm-packmol&quot;</span><span class="p">)</span>
733+
<span class="n">txt_config</span><span class="o">.</span><span class="n">save</span><span class="p">()</span>
734+
735+
<span class="n">full_config</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ini_dir</span> <span class="o">/</span> <span class="s2">&quot;packmol.ini&quot;</span><span class="p">)</span>
730736

731737
<span class="c1"># Getting desperate! Look for an executable in the path</span>
732738
<span class="k">if</span> <span class="n">executor_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">full_config</span><span class="p">:</span>
@@ -738,17 +744,12 @@ <h1>Source code for packmol_step.packmol</h1><div class="highlight"><pre>
738744
<span class="s2">&quot;in the path!&quot;</span>
739745
<span class="p">)</span>
740746
<span class="k">else</span><span class="p">:</span>
741-
<span class="n">full_config</span><span class="p">[</span><span class="n">executor_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
742-
<span class="s2">&quot;installation&quot;</span><span class="p">:</span> <span class="s2">&quot;local&quot;</span><span class="p">,</span>
743-
<span class="s2">&quot;code&quot;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">path</span><span class="p">),</span>
744-
<span class="p">}</span>
745-
746-
<span class="c1"># If the ini file does not exist, write it out!</span>
747-
<span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
748-
<span class="k">with</span> <span class="n">path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fd</span><span class="p">:</span>
749-
<span class="n">full_config</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">fd</span><span class="p">)</span>
750-
<span class="n">printer</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Wrote the Packmol configuration file to </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
751-
<span class="n">printer</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
747+
<span class="n">txt_config</span> <span class="o">=</span> <span class="n">Configuration</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
748+
<span class="n">txt_config</span><span class="o">.</span><span class="n">add_section</span><span class="p">(</span><span class="n">executor_type</span><span class="p">)</span>
749+
<span class="n">txt_config</span><span class="o">.</span><span class="n">add_value</span><span class="p">(</span><span class="n">executor_type</span><span class="p">,</span> <span class="s2">&quot;installation&quot;</span><span class="p">,</span> <span class="s2">&quot;local&quot;</span><span class="p">)</span>
750+
<span class="n">txt_config</span><span class="o">.</span><span class="n">add_value</span><span class="p">(</span><span class="n">executor_type</span><span class="p">,</span> <span class="s2">&quot;code&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">path</span><span class="p">))</span>
751+
<span class="n">txt_config</span><span class="o">.</span><span class="n">save</span><span class="p">()</span>
752+
<span class="n">full_config</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ini_dir</span> <span class="o">/</span> <span class="s2">&quot;packmol.ini&quot;</span><span class="p">)</span>
752753

753754
<span class="n">config</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">full_config</span><span class="o">.</span><span class="n">items</span><span class="p">(</span><span class="n">executor_type</span><span class="p">))</span>
754755

‎_modules/packmol_step/packmol_parameters.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>packmol_step.packmol_parameters &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>packmol_step.packmol_parameters &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>

‎_modules/packmol_step/packmol_step.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>packmol_step.packmol_step &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>packmol_step.packmol_step &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>

‎_modules/packmol_step/tk_packmol.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<head>
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
10-
<title>packmol_step.tk_packmol &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
10+
<title>packmol_step.tk_packmol &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1111

1212

1313

@@ -45,7 +45,7 @@
4545
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4646
<!-- End Google Tag Manager -->
4747

48-
<script src="../../_static/documentation_options.js?v=4a368e61"></script>
48+
<script src="../../_static/documentation_options.js?v=87129bd3"></script>
4949
<script src="../../_static/doctools.js?v=9a2dae69"></script>
5050
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
5151
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>

‎_static/documentation_options.js

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
const DOCUMENTATION_OPTIONS = {
2-
VERSION: '2024.6.29',
2+
VERSION: '2024.7.25',
33
LANGUAGE: 'en',
44
COLLAPSE_INDEX: false,
55
BUILDER: 'html',

‎_static/searchtools.js

+4-3
Original file line numberDiff line numberDiff line change
@@ -178,7 +178,7 @@ const Search = {
178178

179179
htmlToText: (htmlString, anchor) => {
180180
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
181-
for (const removalQuery of [".headerlinks", "script", "style"]) {
181+
for (const removalQuery of [".headerlink", "script", "style"]) {
182182
htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
183183
}
184184
if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
328328
for (const [title, foundTitles] of Object.entries(allTitles)) {
329329
if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
330330
for (const [file, id] of foundTitles) {
331-
let score = Math.round(100 * queryLower.length / title.length)
331+
const score = Math.round(Scorer.title * queryLower.length / title.length);
332+
const boost = titles[file] === title ? 1 : 0; // add a boost for document titles
332333
normalResults.push([
333334
docNames[file],
334335
titles[file] !== title ? `${titles[file]} > ${title}` : title,
335336
id !== null ? "#" + id : "",
336337
null,
337-
score,
338+
score + boost,
338339
filenames[file],
339340
]);
340341
}

‎api/index.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
1010

11-
<title>API Documentation &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
11+
<title>API Documentation &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1212

1313

1414

@@ -46,7 +46,7 @@
4646
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4747
<!-- End Google Tag Manager -->
4848

49-
<script src="../_static/documentation_options.js?v=4a368e61"></script>
49+
<script src="../_static/documentation_options.js?v=87129bd3"></script>
5050
<script src="../_static/doctools.js?v=9a2dae69"></script>
5151
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
5252
<script src="../_static/clipboard.min.js?v=a7894cd8"></script>

‎api/modules.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
1010

11-
<title>packmol_step &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
11+
<title>packmol_step &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1212

1313

1414

@@ -46,7 +46,7 @@
4646
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4747
<!-- End Google Tag Manager -->
4848

49-
<script src="../_static/documentation_options.js?v=4a368e61"></script>
49+
<script src="../_static/documentation_options.js?v=87129bd3"></script>
5050
<script src="../_static/doctools.js?v=9a2dae69"></script>
5151
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
5252
<script src="../_static/clipboard.min.js?v=a7894cd8"></script>

‎api/packmol_step.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
1010

11-
<title>packmol_step package &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
11+
<title>packmol_step package &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1212

1313

1414

@@ -46,7 +46,7 @@
4646
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4747
<!-- End Google Tag Manager -->
4848

49-
<script src="../_static/documentation_options.js?v=4a368e61"></script>
49+
<script src="../_static/documentation_options.js?v=87129bd3"></script>
5050
<script src="../_static/doctools.js?v=9a2dae69"></script>
5151
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
5252
<script src="../_static/clipboard.min.js?v=a7894cd8"></script>

‎authors.html

+2-2
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
<meta charset="utf-8" />
99
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
1010

11-
<title>Development Team &#8212; SEAMM Packmol Plug-in 2024.6.29 documentation</title>
11+
<title>Development Team &#8212; SEAMM Packmol Plug-in 2024.7.25 documentation</title>
1212

1313

1414

@@ -46,7 +46,7 @@
4646
})(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
4747
<!-- End Google Tag Manager -->
4848

49-
<script src="_static/documentation_options.js?v=4a368e61"></script>
49+
<script src="_static/documentation_options.js?v=87129bd3"></script>
5050
<script src="_static/doctools.js?v=9a2dae69"></script>
5151
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
5252
<script src="_static/clipboard.min.js?v=a7894cd8"></script>

0 commit comments

Comments
 (0)