Improvements #5

draeger-lab · Jun 25, 2024 · ef189bc · ef189bc
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diff --git a/docs/build/doctrees/cmpb/about-pipeline.doctree b/docs/build/doctrees/cmpb/about-pipeline.doctree
diff --git a/docs/build/doctrees/cmpb/cmpb-config.doctree b/docs/build/doctrees/cmpb/cmpb-config.doctree
diff --git a/docs/build/doctrees/cmpb/run-pipeline.doctree b/docs/build/doctrees/cmpb/run-pipeline.doctree
diff --git a/docs/build/doctrees/dev-notes.doctree b/docs/build/doctrees/dev-notes.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/help.doctree b/docs/build/doctrees/help.doctree
diff --git a/docs/build/doctrees/hqtb/about-pipeline.doctree b/docs/build/doctrees/hqtb/about-pipeline.doctree
diff --git a/docs/build/doctrees/hqtb/hqtb-config.doctree b/docs/build/doctrees/hqtb/hqtb-config.doctree
diff --git a/docs/build/doctrees/hqtb/run-pipeline.doctree b/docs/build/doctrees/hqtb/run-pipeline.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/analysis.doctree b/docs/build/doctrees/hqtb/step-desc/analysis.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/bidirect_blast.doctree b/docs/build/doctrees/hqtb/step-desc/bidirect_blast.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/gen_draft.doctree b/docs/build/doctrees/hqtb/step-desc/gen_draft.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/annot.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/annot.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/cleanup.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/cleanup.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/extension.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/extension.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refine-parts/smooth.doctree b/docs/build/doctrees/hqtb/step-desc/refine-parts/smooth.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/refinement.doctree b/docs/build/doctrees/hqtb/step-desc/refinement.doctree
diff --git a/docs/build/doctrees/hqtb/step-desc/validation.doctree b/docs/build/doctrees/hqtb/step-desc/validation.doctree
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/installation.doctree b/docs/build/doctrees/installation.doctree
diff --git a/docs/build/doctrees/modules/classes.doctree b/docs/build/doctrees/modules/classes.doctree
diff --git a/docs/build/doctrees/modules/cmd.doctree b/docs/build/doctrees/modules/cmd.doctree
diff --git a/docs/build/doctrees/modules/cmpb.doctree b/docs/build/doctrees/modules/cmpb.doctree
diff --git a/docs/build/doctrees/modules/core.doctree b/docs/build/doctrees/modules/core.doctree
diff --git a/docs/build/doctrees/modules/hqtb.doctree b/docs/build/doctrees/modules/hqtb.doctree
diff --git a/docs/build/doctrees/modules/util.doctree b/docs/build/doctrees/modules/util.doctree
diff --git a/docs/build/doctrees/overview-pipes.doctree b/docs/build/doctrees/overview-pipes.doctree
diff --git a/docs/build/doctrees/pipeline_idea.doctree b/docs/build/doctrees/pipeline_idea.doctree
diff --git a/docs/build/doctrees/specimen.doctree b/docs/build/doctrees/specimen.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e6df1f6e9c96870d3ba9c601c63df629
+config: 0fb85034dd4ee52eca935a0038112cc8
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -18,7 +18,7 @@
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_modules/specimen/classes/reports.html b/docs/build/html/_modules/specimen/classes/reports.html
@@ -18,7 +18,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../../../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_modules/specimen/cmpb/workflow.html b/docs/build/html/_modules/specimen/cmpb/workflow.html
diff --git a/docs/build/html/_modules/specimen/hqtb/core/analysis.html b/docs/build/html/_modules/specimen/hqtb/core/analysis.html
@@ -18,7 +18,7 @@
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
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diff --git a/docs/build/html/_modules/specimen/hqtb/core/bidirectional_blast.html b/docs/build/html/_modules/specimen/hqtb/core/bidirectional_blast.html
@@ -18,7 +18,7 @@
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../../../../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_modules/specimen/hqtb/core/generate_draft_model.html b/docs/build/html/_modules/specimen/hqtb/core/generate_draft_model.html
@@ -18,7 +18,7 @@
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../../../../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/annotation.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/annotation.html
@@ -18,7 +18,7 @@
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
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diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/cleanup.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/cleanup.html
@@ -18,7 +18,7 @@
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
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diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/extension.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/extension.html
@@ -18,7 +18,7 @@
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../../_static/doctools.js?v=888ff710"></script>
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diff --git a/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html b/docs/build/html/_modules/specimen/hqtb/core/refinement/smoothing.html
@@ -18,7 +18,7 @@
         <script src="../../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../../_static/clipboard.min.js?v=a7894cd8"></script>
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diff --git a/docs/build/html/_modules/specimen/hqtb/core/validation.html b/docs/build/html/_modules/specimen/hqtb/core/validation.html
@@ -18,7 +18,7 @@
         <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../../../../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_modules/specimen/hqtb/workflow.html b/docs/build/html/_modules/specimen/hqtb/workflow.html
@@ -18,7 +18,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
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diff --git a/docs/build/html/_modules/specimen/util/set_up.html b/docs/build/html/_modules/specimen/util/set_up.html
@@ -18,7 +18,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/doctools.js?v=888ff710"></script>
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@@ -92,9 +92,9 @@ <h1>Source code for specimen.util.set_up</h1><div class="highlight"><pre>
 <span class="c1">################################################################################</span>
 
 <span class="kn">import</span> <span class="nn">click</span>
+<span class="kn">import</span> <span class="nn">logging</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">requests</span>
-<span class="kn">import</span> <span class="nn">warnings</span>
 <span class="kn">import</span> <span class="nn">yaml</span>
 
 <span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">date</span>
@@ -111,24 +111,24 @@ <h1>Source code for specimen.util.set_up</h1><div class="highlight"><pre>
 
 <span class="c1"># config keys</span>
 <span class="c1"># -----------</span>
-<span class="n">HQTB_CONFIG_PATH_OPTIONAL</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;media_gap&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_map&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_dat&#39;</span><span class="p">,</span><span class="s1">&#39;biocyc&#39;</span><span class="p">,</span><span class="s1">&#39;universal&#39;</span><span class="p">,</span><span class="s1">&#39;pan-core&#39;</span><span class="p">]</span>
+<span class="n">HQTB_CONFIG_PATH_OPTIONAL</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;media_gap&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_map&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_dat&#39;</span><span class="p">,</span><span class="s1">&#39;biocyc&#39;</span><span class="p">,</span><span class="s1">&#39;universal&#39;</span><span class="p">,</span><span class="s1">&#39;pan-core&#39;</span><span class="p">]</span> <span class="c1">#: :meta: </span>
 <span class="n">HQTB_CONFIG_PATH_REQUIRED</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;annotated_genome&#39;</span><span class="p">,</span><span class="s1">&#39;full_sequence&#39;</span><span class="p">,</span><span class="s1">&#39;model&#39;</span><span class="p">,</span><span class="s1">&#39;diamond&#39;</span><span class="p">,</span>
                              <span class="s1">&#39;mnx_chem_prop&#39;</span><span class="p">,</span> <span class="s1">&#39;mnx_chem_xref&#39;</span><span class="p">,</span><span class="s1">&#39;mnx_reac_prop&#39;</span><span class="p">,</span><span class="s1">&#39;mnx_reac_xref&#39;</span><span class="p">,</span>
-                             <span class="s1">&#39;media_analysis&#39;</span><span class="p">]</span>
+                             <span class="s1">&#39;media_analysis&#39;</span><span class="p">]</span> <span class="c1">#: :meta: </span>
 <span class="n">CMPB_CONFIG_PATHS</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;annotated_genome&#39;</span><span class="p">,</span><span class="s1">&#39;mediapath&#39;</span><span class="p">,</span><span class="s1">&#39;modelpath&#39;</span><span class="p">,</span><span class="s1">&#39;dir&#39;</span><span class="p">,</span><span class="s1">&#39;refseq_gff&#39;</span><span class="p">,</span><span class="s1">&#39;protein_fasta&#39;</span><span class="p">,</span>
-                     <span class="s1">&#39;biocyc_files&#39;</span><span class="p">,</span><span class="s1">&#39;full_genome_sequence&#39;</span><span class="p">]</span>
+                     <span class="s1">&#39;biocyc_files&#39;</span><span class="p">,</span><span class="s1">&#39;full_genome_sequence&#39;</span><span class="p">]</span> <span class="c1">#: :meta: </span>
 <span class="n">PIPELINE_PATHS</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;hqtb&#39;</span><span class="p">:</span><span class="n">HQTB_CONFIG_PATH_OPTIONAL</span><span class="o">+</span><span class="n">HQTB_CONFIG_PATH_REQUIRED</span><span class="p">,</span>
-                  <span class="s1">&#39;cmpb&#39;</span><span class="p">:</span><span class="n">CMPB_CONFIG_PATHS</span><span class="p">}</span>
+                  <span class="s1">&#39;cmpb&#39;</span><span class="p">:</span><span class="n">CMPB_CONFIG_PATHS</span><span class="p">}</span> <span class="c1">#: :meta: </span>
 
 
 <span class="c1"># external databases</span>
 <span class="c1"># ------------------</span>
-<span class="n">MNX_CHEM_XREF_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv&#39;</span>
-<span class="n">MNX_CHEM_PROP_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_prop.tsv&#39;</span>
-<span class="n">MNX_REAC_XREF_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv&#39;</span>
-<span class="n">MNX_REAC_PROP_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_prop.tsv&#39;</span>
+<span class="n">MNX_CHEM_XREF_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv&#39;</span> <span class="c1">#: :meta: </span>
+<span class="n">MNX_CHEM_PROP_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_prop.tsv&#39;</span> <span class="c1">#: :meta: </span>
+<span class="n">MNX_REAC_XREF_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv&#39;</span> <span class="c1">#: :meta: </span>
+<span class="n">MNX_REAC_PROP_URL</span> <span class="o">=</span> <span class="s1">&#39;https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_prop.tsv&#39;</span> <span class="c1">#: :meta: </span>
 <span class="n">MNX_URL_DICT</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;chem_prop.tsv&#39;</span><span class="p">:</span><span class="n">MNX_CHEM_PROP_URL</span><span class="p">,</span> <span class="s1">&#39;chem_xref.tsv&#39;</span><span class="p">:</span><span class="n">MNX_CHEM_XREF_URL</span><span class="p">,</span>
-                <span class="s1">&#39;reac_prop.tsv&#39;</span><span class="p">:</span><span class="n">MNX_REAC_PROP_URL</span><span class="p">,</span> <span class="s1">&#39;reac_xref.tsv&#39;</span><span class="p">:</span><span class="n">MNX_REAC_XREF_URL</span><span class="p">}</span>
+                <span class="s1">&#39;reac_prop.tsv&#39;</span><span class="p">:</span><span class="n">MNX_REAC_PROP_URL</span><span class="p">,</span> <span class="s1">&#39;reac_xref.tsv&#39;</span><span class="p">:</span><span class="n">MNX_REAC_XREF_URL</span><span class="p">}</span> <span class="c1">#: :meta: </span>
 
 <span class="c1">################################################################################</span>
 <span class="c1"># functions</span>
@@ -351,8 +351,8 @@ <h1>Source code for specimen.util.set_up</h1><div class="highlight"><pre>
             <span class="c1"># optional/requires stuff </span>
             <span class="k">elif</span> <span class="n">dictA</span> <span class="o">==</span> <span class="s1">&#39;USER&#39;</span><span class="p">:</span>
                 <span class="c1"># @TODO </span>
-                <span class="n">mes</span> <span class="o">=</span> <span class="s1">&#39;Keyword USER detected in config. Either due to skipped options or missing required information.&#39;</span>
-                <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="n">mes</span><span class="p">)</span>
+                <span class="n">mes</span> <span class="o">=</span> <span class="s1">&#39;Keyword USER detected in config. Either due to skipped options or missing required information.</span><span class="se">\n</span><span class="s1">Reminder: this may lead to downstream problems.&#39;</span>
+                <span class="n">logging</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">mes</span><span class="p">)</span>
 
             <span class="c1"># check paths</span>
             <span class="k">elif</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">PIPELINE_PATHS</span><span class="p">[</span><span class="n">pipeline</span><span class="p">]</span> <span class="ow">and</span> <span class="n">dictA</span><span class="p">:</span>

diff --git a/docs/build/html/_modules/specimen/util/util.html b/docs/build/html/_modules/specimen/util/util.html
@@ -18,7 +18,7 @@
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/doctools.js?v=888ff710"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
         <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
         <script src="../../../_static/copybutton.js?v=7859de39"></script>

diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer