Merge pull request #17 from barahona-research-group/v0.2.10

V0.2.10
barahona-research-group · Jun 1, 2024 · baee4f9 · baee4f9
2 parents 1121738 + 197c244
commit baee4f9
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diff --git a/README.md b/README.md
@@ -1,24 +1,29 @@
-# RamanSPy
+<p align="center">
+  <a href="https://ramanspy.readthedocs.io/">
+    <img src="https://github.com/barahona-research-group/RamanSPy/blob/1121738ca4b8b64d938b81eefe32059ac33ace8e/docs/source/images/raman_logo_transparent.png" alt="RamanSPy logo"  width="300">
+  </a>
+</p>
 
-[![Downloads](https://static.pepy.tech/badge/ramanspy)](https://pepy.tech/project/ramanspy)   [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)]([https://github.com/dwyl/esta/issues](https://github.com/barahona-research-group/RamanSPy/issues))
+## *RamanSPy*: An open-source package for <ins>Raman</ins> <ins>S</ins>pectroscopy analytics in <ins>Py</ins>thon.
 
+[![Downloads](https://static.pepy.tech/badge/ramanspy)](https://pepy.tech/project/ramanspy)   [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)]([https://github.com/dwyl/esta/issues](https://github.com/barahona-research-group/RamanSPy/issues))
 
-*RamanSPy* is an open-source Python package for integrative
-Raman spectroscopy data analysis.
 
 ## Key features
 
+![Overview of RamanSPy](docs/source/images/ramanspy_graphical_abstract.png)
+
 - Common data format
 - Data loaders
 - Preprocessing methods
 - Preprocessing pipelining
 - Preprocessing protocols
 - Analysis methods
+- AI & ML integration
 - Visualisation tools
-- AI integration
 - Datasets
+- Synthetic data generator
 - Metrics
-- Synthetic data generator (***new in versions >= 0.2.0***)
 
 
 ## Installation
@@ -68,11 +73,11 @@ rp.plot.show()
 ## Documentation
 
 For more information about the functionalities of the package, refer to
-the [documentation](https://ramanspy.readthedocs.io).
+the [online documentation](https://ramanspy.readthedocs.io).
 
 ## Credits
 
-If you use this package for your research, please cite our paper:
+If you use *RamanSPy* for your research, please cite our paper:
 
 [Georgiev, D.; Pedersen, S. V.; Xie, R.; Fernández-Galiana, Á.; Stevens, M. M.; Barahona, M. *RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis*. ACS Analytical Chemistry **2024**, 96(21), 8492-8500, DOI: 10.1021/acs.analchem.4c00383](https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383)
 

diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
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-config: 4120cd5746195a2fc1af6c77d5dfc838
+config: ba21baef02957aa75ccaa933bdd1e25c
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diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -265,7 +265,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/_modules/ramanspy/core.html b/docs/build/html/_modules/ramanspy/core.html
@@ -192,8 +192,8 @@
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-<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.html">ramanspy.preprocessing.baseline.Poly</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.html">ramanspy.preprocessing.baseline.ModPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.PenalisedPoly.html">ramanspy.preprocessing.baseline.PenalisedPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IModPoly.html">ramanspy.preprocessing.baseline.IModPoly</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Goldindec.html">ramanspy.preprocessing.baseline.Goldindec</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IRSQR.html">ramanspy.preprocessing.baseline.IRSQR</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.CornerCutting.html">ramanspy.preprocessing.baseline.CornerCutting</a></li>
@@ -265,7 +265,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/_modules/ramanspy/load.html b/docs/build/html/_modules/ramanspy/load.html
@@ -192,8 +192,8 @@
 <li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ASPLS.html">ramanspy.preprocessing.baseline.ASPLS</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.html">ramanspy.preprocessing.baseline.ModPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.PenalisedPoly.html">ramanspy.preprocessing.baseline.PenalisedPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IModPoly.html">ramanspy.preprocessing.baseline.IModPoly</a></li>
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@@ -265,7 +265,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/_modules/ramanspy/preprocessing/baseline.html b/docs/build/html/_modules/ramanspy/preprocessing/baseline.html
@@ -265,7 +265,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/_modules/ramanspy/synth/synth.html b/docs/build/html/_modules/ramanspy/synth/synth.html
@@ -265,7 +265,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -6,6 +6,13 @@ day-to-day analyses, research applications, as well as the development and valid
 
 |
 
+.. image:: images/ramanspy_graphical_abstract.png
+  :width: 600
+  :align: center
+  :alt: Overview of RamanSPy's functionalities
+
+|
+
 Key features
 -----------------
 - Common data format
@@ -14,11 +21,11 @@ Key features
 - Preprocessing pipelining
 - Preprocessing protocols
 - Analysis methods
+- AI and ML integration
 - Visualisation tools
-- AI integration
 - Datasets
+- Synthetic data generator
 - Metrics
-- Synthetic data generator (**new in versions >= 0.2.0**)
 
 |
 
@@ -34,7 +41,20 @@ Credits
 -----------------
 If you use this package for your research, please cite our paper:
 
-`Georgiev, D., Pedersen, S., Xie, R., Fernández-Galiana, Á., Stevens, M., & Barahona, M. (2023). RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis. ChemRxiv. doi:10.26434/chemrxiv-2023-m3xlm <https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51>`_
+`Georgiev, D.; Pedersen, S. V.; Xie, R.; Fernández-Galiana, Á.; Stevens, M. M.; Barahona, M. RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis. ACS Analytical Chemistry 2024, 96(21), 8492-8500, DOI: 10.1021/acs.analchem.4c00383 <https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383>`_
+
+.. code-block:: latex
+
+    @article{georgiev2024ramanspy,
+        title={RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis},
+        author={Georgiev, Dimitar and Pedersen, Simon Vilms and Xie, Ruoxiao and Fern{\'a}ndez-Galiana, Alvaro and Stevens, Molly M and Barahona, Mauricio},
+        journal={Analytical Chemistry},
+        volume={96},
+        number={21},
+        pages={8492-8500},
+        year={2024},
+        doi={10.1021/acs.analchem.4c00383}
+    }
 
 |
 
@@ -88,4 +108,4 @@ Also, if you find *RamanSPy* useful, please consider leaving a star on GitHub:
    :hidden:
 
    GitHub repository <https://github.com/barahona-research-group/RamanSPy>
-   Paper <https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51>
+   Paper <https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383>
diff --git a/docs/build/html/_templates/autosummary/class.html b/docs/build/html/_templates/autosummary/class.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/analysis.html b/docs/build/html/analysis.html
@@ -266,7 +266,7 @@
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 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/index.html b/docs/build/html/auto_examples/index.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/plot_i_package_overview.html b/docs/build/html/auto_examples/plot_i_package_overview.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/plot_i_preprocessing_pipelines.html b/docs/build/html/auto_examples/plot_i_preprocessing_pipelines.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/plot_ii_dl_denoising.html b/docs/build/html/auto_examples/plot_ii_dl_denoising.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/plot_iii_bacteria_classification.html b/docs/build/html/auto_examples/plot_iii_bacteria_classification.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_examples/sg_execution_times.html b/docs/build/html/auto_examples/sg_execution_times.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/i-classes/plot_i_generic_container.html b/docs/build/html/auto_tutorials/i-classes/plot_i_generic_container.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/i-classes/plot_ii_spectrum_container.html b/docs/build/html/auto_tutorials/i-classes/plot_ii_spectrum_container.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/i-classes/plot_iii_image_container.html b/docs/build/html/auto_tutorials/i-classes/plot_iii_image_container.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/i-classes/plot_iv_volume_container.html b/docs/build/html/auto_tutorials/i-classes/plot_iv_volume_container.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/i-classes/sg_execution_times.html b/docs/build/html/auto_tutorials/i-classes/sg_execution_times.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/ii-instrumental/i_witec.html b/docs/build/html/auto_tutorials/ii-instrumental/i_witec.html
@@ -266,7 +266,7 @@
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 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/ii-instrumental/ii_renishaw.html b/docs/build/html/auto_tutorials/ii-instrumental/ii_renishaw.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>

diff --git a/docs/build/html/auto_tutorials/ii-instrumental/iii_ocean_insight.html b/docs/build/html/auto_tutorials/ii-instrumental/iii_ocean_insight.html
@@ -266,7 +266,7 @@
 <p class="caption" role="heading"><span class="caption-text">Links</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/barahona-research-group/RamanSPy">GitHub repository</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51">Paper</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00383">Paper</a></li>
 </ul>
 
 </div>