From 4d4178a45c95cde0b0e8803d077ce37355a4d7b1 Mon Sep 17 00:00:00 2001
From: stuchalk <stuchalk@users.noreply.github.com>
Date: Wed, 31 Jan 2024 00:05:46 +0000
Subject: [PATCH] deploy: ae401a2137fbae4d2578cd82b01d874775215f5b

---
 _sources/about_cookbook.md          |  4 ++--
 about_cookbook.html                 |  2 +-
 bibliography.html                   |  3 +++
 datasources/goldbook_api.html       |  2 +-
 datasources/pubchem_pugrest1.html   |  8 ++++++--
 manipulations/computing_inchis.html |  6 +++---
 manipulations/dataset_search.html   |  2 +-
 searchindex.js                      |  2 +-
 usecases/uvvis_metadata.html        | 12 ++++++++----
 9 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/_sources/about_cookbook.md b/_sources/about_cookbook.md
index 2e977656..a96181eb 100644
--- a/_sources/about_cookbook.md
+++ b/_sources/about_cookbook.md
@@ -8,7 +8,7 @@ smooth the adoption of best practices for sharing and reusing FAIR chemical data
 of actionable recipes for a range of tasks to prepare and deposit FAIR machine-enabled chemical data, identify 
 and extract chemically relevant metadata, and compile and validate chemical data files using online tools.
 
-FAIR data are findable, accessible, interoperable, and reusable for machine processing {cite:p}Wilkinson2016. 
+FAIR data are findable, accessible, interoperable, and reusable for machine processing {cite:p}`Wilkinson2016`. 
 FAIR chemical data need to be machine-readable, and this can be an unfamiliar scenario for many researchers 
 and other stakeholders involved with publishing and managing experimental data. This cookbook aims to support 
 best practices for sharing and reusing chemical data aligned with the technical criteria for FAIR 
@@ -17,4 +17,4 @@ online tools for working with digital content augment broader guidance.
 
 The IUPAC FAIR Chemistry Cookbook is designed to be an evolving resource for the chemistry community. It is 
 supported by the International Union of Pure and Applied Chemistry (IUPAC) as part of the WorldFAIR 
-Initiative (see About this project).
\ No newline at end of file
+Initiative (see About this project).
diff --git a/about_cookbook.html b/about_cookbook.html
index 005c406c..4ada82ce 100644
--- a/about_cookbook.html
+++ b/about_cookbook.html
@@ -397,7 +397,7 @@ <h1>About this Cookbook<a class="headerlink" href="#about-this-cookbook" title="
 smooth the adoption of best practices for sharing and reusing FAIR chemical data. The content primarily consists
 of actionable recipes for a range of tasks to prepare and deposit FAIR machine-enabled chemical data, identify
 and extract chemically relevant metadata, and compile and validate chemical data files using online tools.</p>
-<p>FAIR data are findable, accessible, interoperable, and reusable for machine processing {cite:p}Wilkinson2016.
+<p>FAIR data are findable, accessible, interoperable, and reusable for machine processing <span id="id1">[<a class="reference internal" href="bibliography.html#id2" title="Mark D. et al. Wilkinson. The fair guiding principles for scientific data management and stewardship. Scientific Data, 3:160018, 2016. doi:10.1038/sdata.2016.18.">Wil16</a>]</span>.
 FAIR chemical data need to be machine-readable, and this can be an unfamiliar scenario for many researchers
 and other stakeholders involved with publishing and managing experimental data. This cookbook aims to support
 best practices for sharing and reusing chemical data aligned with the technical criteria for FAIR
diff --git a/bibliography.html b/bibliography.html
index db31853c..7290839a 100644
--- a/bibliography.html
+++ b/bibliography.html
@@ -404,6 +404,9 @@ <h1>Bibliography<a class="headerlink" href="#bibliography" title="Permalink to t
 <dt class="label" id="id6"><span class="brackets">KCH+22</span></dt>
 <dd><p>Sunghwan Kim, Tiejun Cheng, Siqian He, Paul A. Thiessen, Qingliang Li, Asta Gindulyte, and Evan E. Bolton. Pubchem protein, gene, pathway, and taxonomy data collections: bridging biology and chemistry through target-centric views of pubchem data. <em>Journal of Molecular Biology</em>, 434(11):167514, 2022. URL: <a class="reference external" href="https://doi.org/10.1016/j.jmb.2022.167514">https://doi.org/10.1016/j.jmb.2022.167514</a>.</p>
 </dd>
+<dt class="label" id="id2"><span class="brackets">Wil16</span></dt>
+<dd><p>Mark D. et al. Wilkinson. The fair guiding principles for scientific data management and stewardship. <em>Scientific Data</em>, 3:160018, 2016. <a class="reference external" href="https://doi.org/10.1038/sdata.2016.18">doi:10.1038/sdata.2016.18</a>.</p>
+</dd>
 </dl>
 </div>
 </section>
diff --git a/datasources/goldbook_api.html b/datasources/goldbook_api.html
index 40d60f48..b2f34ad8 100644
--- a/datasources/goldbook_api.html
+++ b/datasources/goldbook_api.html
@@ -574,7 +574,7 @@ <h2>Step 5: Use the term code to retrieve its definition<a class="headerlink" hr
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-30T22:39:59+00:00&#39;}}
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-31T00:04:49+00:00&#39;}}
 </pre></div>
 </div>
 </div>
diff --git a/datasources/pubchem_pugrest1.html b/datasources/pubchem_pugrest1.html
index fc5c4310..b5c1b2a4 100644
--- a/datasources/pubchem_pugrest1.html
+++ b/datasources/pubchem_pugrest1.html
@@ -657,11 +657,15 @@ <h3>4. Getting Chemical Structures<a class="headerlink" href="#getting-chemical-
 </div>
 <div class="cell_output docutils container">
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Canonical SMILES: CC(C)C1=NC(=NC(=C1C=CC(CC(CC(=O)O)O)O)C2=CC=C(C=C2)F)N(C)S(=O)(=O)C
-Isomeric SMILES : CC(C)C1=NC(=NC(=C1/C=C/[C@H](C[C@H](CC(=O)O)O)O)C2=CC=C(C=C2)F)N(C)S(=O)(=O)C
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Isomeric SMILES : CC(C)C1=NC(=NC(=C1/C=C/[C@H](C[C@H](CC(=O)O)O)O)C2=CC=C(C=C2)F)N(C)S(=O)(=O)C
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>InChI           : InChI=1S/C22H28FN3O6S/c1-13(2)20-18(10-9-16(27)11-17(28)12-19(29)30)21(14-5-7-15(23)8-6-14)25-22(24-20)26(3)33(4,31)32/h5-10,13,16-17,27-28H,11-12H2,1-4H3,(H,29,30)/b10-9+/t16-,17-/m1/s1
-InChIKey        : BPRHUIZQVSMCRT-VEUZHWNKSA-N
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>InChIKey        : BPRHUIZQVSMCRT-VEUZHWNKSA-N
 </pre></div>
 </div>
 </div>
diff --git a/manipulations/computing_inchis.html b/manipulations/computing_inchis.html
index d8b469f0..8029aeed 100644
--- a/manipulations/computing_inchis.html
+++ b/manipulations/computing_inchis.html
@@ -526,7 +526,7 @@ <h3>1.2 Create a Molecular Object from SMILES<a class="headerlink" href="#create
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c0f20&gt;
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd4eb0&gt;
 </pre></div>
 </div>
 </div>
@@ -607,7 +607,7 @@ <h3>1.4 Calculate InChIs for a List of Molecules<a class="headerlink" href="#cal
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c11c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c13f0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c18c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c1930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c19a0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7ff8700c1a10&gt;]
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd5380&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd5460&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd5850&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd58c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd5930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7fbe8ffd59a0&gt;]
 </pre></div>
 </div>
 </div>
@@ -766,7 +766,7 @@ <h3>2.4 Calculate InChIs for a List of Molecules<a class="headerlink" href="#id3
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7ff861bfbc90&gt;, &lt;openbabel.pybel.Molecule object at 0x7ff861bfbd10&gt;, &lt;openbabel.pybel.Molecule object at 0x7ff861bfbe10&gt;, &lt;openbabel.pybel.Molecule object at 0x7ff861bfbe90&gt;, &lt;openbabel.pybel.Molecule object at 0x7ff861bfbfd0&gt;, &lt;openbabel.pybel.Molecule object at 0x7ff861bf9290&gt;]
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7fbe8eb84910&gt;, &lt;openbabel.pybel.Molecule object at 0x7fbe8ebb6990&gt;, &lt;openbabel.pybel.Molecule object at 0x7fbe8ebb5710&gt;, &lt;openbabel.pybel.Molecule object at 0x7fbe8ebb5290&gt;, &lt;openbabel.pybel.Molecule object at 0x7fbe8ebb5310&gt;, &lt;openbabel.pybel.Molecule object at 0x7fbe8ebb5550&gt;]
 </pre></div>
 </div>
 </div>
diff --git a/manipulations/dataset_search.html b/manipulations/dataset_search.html
index 22a63c58..5a203298 100644
--- a/manipulations/dataset_search.html
+++ b/manipulations/dataset_search.html
@@ -1015,7 +1015,7 @@ <h3>2.1 - Authentication to the FAIRSharing API<a class="headerlink" href="#auth
 </div>
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@@ -693,13 +693,17 @@ <h3>4.2 Exemplar code for data reporting<a class="headerlink" href="#exemplar-co
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+Requirement already satisfied: numpy in /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages (from jcamp) (1.26.2)
 Requirement already satisfied: datetime in /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages (from jcamp) (5.4)
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-Requirement already satisfied: setuptools in /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages (from zope.interface-&gt;datetime-&gt;jcamp) (65.5.0)
+</pre></div>
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+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Requirement already satisfied: setuptools in /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages (from zope.interface-&gt;datetime-&gt;jcamp) (65.5.0)
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span><span class=" -Color -Color-Bold">[</span><span class=" -Color -Color-Blue">notice</span><span class=" -Color -Color-Bold">]</span> A new release of pip is available: <span class=" -Color -Color-Red">23.2.1</span> -&gt; <span class=" -Color -Color-Green">23.3.2</span>
+<span class=" -Color -Color-Bold">[</span><span class=" -Color -Color-Blue">notice</span><span class=" -Color -Color-Bold">]</span> To update, run: <span class=" -Color -Color-Green">pip install --upgrade pip</span>
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