Improper LaTeX rendering in tutorial notebooks

[p16i]

Hi,

Some tutorial notebooks have this LaTeX rendering issue:

These are the notebooks that I see the problem:

• http://www.emma-project.org/v2.5.5/generated/05-pcca-tpt.html
• http://www.emma-project.org/v2.5.5/generated/07-hidden-markov-state-models.html

There might be more though: You can try to search with :raw-latex:.

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[marscher]

there are actually quite some places, where we have this improper latex rendering errors. I guess some of them are not even intended to be rendered as latex (e.g. in citations).

marscher@lounge:/web/www.emma-project.org/htdocs/v2.5.5$ grep raw-latex -R *
generated/model_selection_validation.html:<p>$ t_i = -<a href="#id1"><span class="problematic" id="id2">:raw-latex:`\tau `/ :raw-latex:`</span></a>ln <em class="xref py py-obj">|
generated/model_selection_validation.html::raw-latex:</em>lambda`_i (<a href="#id3"><span class="problematic" id="id4">:raw-latex:`\tau`</span></a>)| $</p>
generated/00-pentapeptide-showcase.html:<p><strong>Note:</strong> We will assign the integer numbers $1 <a href="#id1"><span class="problematic" id="id2">:raw-latex:`\dots `$
generated/00-pentapeptide-showcase.html:Theory:raw-latex:`textdagger`</em>.
generated/05-pcca-tpt.html:<p>⚠️ We have assigned the integer numbers $1 <a href="#id1"><span class="problematic" id="id2">:raw-latex:`\dots `$
generated/feature_selection.html:MP, Bank JA, Jumper JM, Salmon JK, Shan Y,:raw-latex:<em class="xref py py-obj">n</em>”, “Wriggers
generated/feature_selection.html:proteins.:raw-latex:<em class="xref py py-obj">n</em>”, “<em>Science</em> <strong>330</strong>:341-346 (2010). doi:
generated/feature_selection.html:10.1126/science.1187409.:raw-latex:<em class="xref py py-obj">n</em>”,</li>
generated/07-hidden-markov-state-models.html:<p>⚠️ We have assigned the integer numbers $1 <a href="#id1"><span class="problematic" id="id2">:raw-latex:`\dots `$
generated/augmented_markov_model_walkthrough.html:\[ \begin{align}\begin{aligned}\sigma_i^2(\pi) = \sum_j \pi_j(E_{ji}-e_i)^2\\where $ e\_i = :raw-latex:`\sum`\_j :raw-latex:`\pi`\ *j E*\ {ji}$ (the\end{aligned}\end{align} \]</div>
_sources/generated/feature_selection.rst.txt:   MP, Bank JA, Jumper JM, Salmon JK, Shan Y,:raw-latex:`\n`", "Wriggers
_sources/generated/feature_selection.rst.txt:   proteins.:raw-latex:`\n`", "*Science* **330**:341-346 (2010). doi:
_sources/generated/feature_selection.rst.txt:   10.1126/science.1187409.:raw-latex:`\n`",
_sources/generated/05-pcca-tpt.rst.txt:⚠️ We have assigned the integer numbers $1 :raw-latex:`\dots `$
_sources/generated/07-hidden-markov-state-models.rst.txt:⚠️ We have assigned the integer numbers $1 :raw-latex:`\dots `$
_sources/generated/00-pentapeptide-showcase.rst.txt:**Note:** We will assign the integer numbers $1 :raw-latex:`\dots `$
_sources/generated/00-pentapeptide-showcase.rst.txt:Theory:raw-latex:`\textdagger`*.
_sources/generated/model_selection_validation.rst.txt:$ t\_i = -:raw-latex:`\tau `/ :raw-latex:`\ln `\|
_sources/generated/model_selection_validation.rst.txt::raw-latex:`\lambda`\_i (:raw-latex:`\tau`)\| $
_sources/generated/augmented_markov_model_walkthrough.rst.txt: where $ e\_i = :raw-latex:`\sum`\_j :raw-latex:`\pi`\ *j E*\ {ji}$ (the