deploy: 0ccd1a4

_sources/mdakits.rst.txt

@@ -318,7 +318,7 @@ Each of the MDAKits in the following table links to a page with more details abo
 .. _`propkatraj authors`:
    https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS
 
-.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-failed-red.svg
+.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
    :alt: propkatraj develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 

_sources/propkatraj.rst.txt

@@ -39,7 +39,7 @@ The source code of propkatraj can be installed using the following:
 .. _`propkatraj authors`:
    https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS
 
-.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-failed-red.svg
+.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
    :alt: propkatraj develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 

_sources/reviewersguide.rst.txt

@@ -206,6 +206,8 @@ is failing
 ``test_dependencies``: a list of commands for installing any dependencies required by the MDAKit’s tests.
 This is a *list of strings* (*AUTOMATIC CHECK*).
 
+- *note* : care should be taken to to override the underlying ``mamba`` environment. For example, this should _not_ attempt to do a ``mamba env update`` call as it will overwrite the base mamba environment and one ends up with a conda environment without the base mdakit dependencies.  
+
 
 
 *Optional* entries 

mdakits.html

@@ -262,7 +262,7 @@ <h1>Registry of MDAnalysis Toolkits (MDAKits)<a class="headerlink" href="#regist
 <tr class="row-odd"><td><p><a class="reference internal" href="propkatraj.html#propkatraj"><span class="std std-ref">propkatraj</span></a></p></td>
 <td><p>pKa, protein</p></td>
 <td><p><a class="reference external" href="https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS">propkatraj authors</a></p></td>
-<td><p><a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/latest-failed-red.svg" /></a> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/develop-passed-green.svg" /></a></p></td>
+<td><p><a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/latest-passed-green.svg" /></a> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/develop-passed-green.svg" /></a></p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="mdahole2.html#mdahole2"><span class="std std-ref">mdahole2</span></a></p></td>
 <td><p>pores, ion channels, transporters, HOLE</p></td>

propkatraj.html

@@ -166,7 +166,7 @@
 <div class="line">* <a class="reference external" href="https://doi.org/10.1021/ct200133y">https://doi.org/10.1021/ct200133y</a></div>
 <div class="line">* <a class="reference external" href="https://doi.org/10.1085/jgp.201411219">https://doi.org/10.1085/jgp.201411219</a></div>
 </div>
-<div class="line">🧪 <strong>Tests (latest):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/latest-failed-red.svg" /></a></div>
+<div class="line">🧪 <strong>Tests (latest):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/latest-passed-green.svg" /></a></div>
 <div class="line">🧪 <strong>Tests (develop):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="propkatraj develop CI status" src="https://img.shields.io/badge/develop-passed-green.svg" /></a></div>
 <div class="line"><strong>Description:</strong></div>
 <div class="line"><em>pKa estimates for proteins using an ensemble approach</em></div>

reviewersguide.html

@@ -312,6 +312,9 @@ <h4>Entries <em>required</em> for registration<a class="headerlink" href="#entri
 </ul>
 <p><code class="docutils literal notranslate"><span class="pre">test_dependencies</span></code>: a list of commands for installing any dependencies required by the MDAKit’s tests.
 This is a <em>list of strings</em> (<em>AUTOMATIC CHECK</em>).</p>
+<ul class="simple">
+<li><p><em>note</em> : care should be taken to to override the underlying <code class="docutils literal notranslate"><span class="pre">mamba</span></code> environment. For example, this should _not_ attempt to do a <code class="docutils literal notranslate"><span class="pre">mamba</span> <span class="pre">env</span> <span class="pre">update</span></code> call as it will overwrite the base mamba environment and one ends up with a conda environment without the base mdakit dependencies.</p></li>
+</ul>
 </section>
 <section id="optional-entries">
 <h4><em>Optional</em> entries<a class="headerlink" href="#optional-entries" title="Link to this heading"></a></h4>