2025-08-19: minor docs update (troubleshooting)

Author: JamieHeather

docs/_build/doctrees/environment.pickle

@@ -24,7 +24,7 @@ Stitch together TCR coding nucleotide sequences from V/J/CDR3 information
    output
    immunoglobulins
    importing
-   warnings
+   troubleshooting
    referencing
 
 Sometimes you need a complete TCR nucleotide or amino acid sequence, but all you have is limited information. This script aims to generate a coding nucleotide sequence for a given rearrangement (e.g. for use when generating TCR expression vectors) in those situations.

docs/_build/doctrees/index.doctree

@@ -1,4 +1,18 @@
 
+Troubleshooting
+===============
+
+* If you encounter a problem or error with ``stitchr`` that isn't addressed in these docs, or if there was some functionality you'd like to be considered for future releases, please `open a new issue on the GitHub repo <https://github.com/JamieHeather/stitchr/issues>`_:
+
+    * Ideally, please first search the previous issues to see whether this problem has been encountered and/or addressed before.
+
+    * When summarising your issue, include the commands used (both working and not), the environment where you're running them, and details of the available references in your ``stitchr`` data directory.
+
+    * That reference information can easily be obtained by running ``stitchr --cite``, and then copying everything below the 'Paper citation details' citation.
+
+    * Alternatively, ``stitchr`` (or general TCR-related) `queries can be be emailed to me directly <https://jamieheather.github.io/contact/>`_
+
+
 ``stitchr`` warnings
 ~~~~~~~~~~~~~~~~~~~~
 

docs/_build/doctrees/troubleshooting.doctree

@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="output.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> output modes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="immunoglobulins.html">Stitching immunoglobulins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="importing.html">Importing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> for use in other Python scripts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="warnings.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> warnings</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html">Citing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html#licensing-information">Licensing information</a></li>
 </ul>

docs/_build/html/_sources/index.rst.txt

@@ -51,7 +51,7 @@
 <li class="toctree-l1"><a class="reference internal" href="output.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> output modes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="immunoglobulins.html">Stitching immunoglobulins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="importing.html">Importing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> for use in other Python scripts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="warnings.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> warnings</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html">Citing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html#licensing-information">Licensing information</a></li>
 </ul>
@@ -122,7 +122,10 @@ <h2>Stitch together TCR coding nucleotide sequences from V/J/CDR3 information<a
 </li>
 <li class="toctree-l1"><a class="reference internal" href="immunoglobulins.html">Stitching immunoglobulins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="importing.html">Importing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> for use in other Python scripts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="warnings.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> warnings</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="troubleshooting.html#stitchr-warnings"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> warnings</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html">Citing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html#licensing-information">Licensing information</a></li>
 </ul>

docs/warnings.rst …ld/html/_sources/troubleshooting.rst.txtdocs/warnings.rst renamed to docs/_build/html/_sources/troubleshooting.rst.txt docs/warnings.rst renamed to docs/_build/html/_sources/troubleshooting.rst.txt

@@ -2,5 +2,7 @@
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docs/_build/html/genindex.html

@@ -52,7 +52,7 @@
 <li class="toctree-l1"><a class="reference internal" href="output.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> output modes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="immunoglobulins.html">Stitching immunoglobulins</a></li>
 <li class="toctree-l1"><a class="reference internal" href="importing.html">Importing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code> for use in other Python scripts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="warnings.html"><code class="docutils literal notranslate"><span class="pre">stitchr</span></code> warnings</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html">Citing <code class="docutils literal notranslate"><span class="pre">stitchr</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="referencing.html#licensing-information">Licensing information</a></li>
 </ul>