Dev (#6)

* setup initial tests * test: updated testing actions and test structure * feat: added in some tests for utils * feat: added in function for reading in population panel files separately * draft: updated some tests * test: population panel testing * feat: new function to add in population handling * test: added in test for verification of samples * feat: vcf2frequency table now uses cyvcf2 * draft: small commit - still needs some fixing on docs * test: some refactoring and some testing * doc: some additional docstrings * feat: updated to include data in installation * feat: finally got cyvcf2 features working * feat: not supporting windows due to cyvcf2 * feat: added update to make custom lists a little bit easier * doc: cleaned up a lot of the original documentation
aabiddanda · Nov 10, 2022 · 1703ff0 · 1703ff0
1 parent 30d7ec0
commit 1703ff0
Show file tree

Hide file tree

Showing 50 changed files with 42 additions and 94,215 deletions.
diff --git a/docs/_images/notebooks_getting-started_11_0.png b/docs/_images/notebooks_getting-started_11_0.png
diff --git a/docs/_images/notebooks_getting-started_11_0.svg b/docs/_images/notebooks_getting-started_11_0.svg
diff --git a/docs/_images/notebooks_getting-started_12_0.png b/docs/_images/notebooks_getting-started_12_0.png
diff --git a/docs/_images/notebooks_getting-started_12_0.svg b/docs/_images/notebooks_getting-started_12_0.svg
diff --git a/docs/_images/notebooks_getting-started_12_1.svg b/docs/_images/notebooks_getting-started_12_1.svg
diff --git a/docs/_images/notebooks_getting-started_13_0.png b/docs/_images/notebooks_getting-started_13_0.png
diff --git a/docs/_images/notebooks_getting-started_13_0.svg b/docs/_images/notebooks_getting-started_13_0.svg
diff --git a/docs/_images/notebooks_getting-started_14_0.png b/docs/_images/notebooks_getting-started_14_0.png
diff --git a/docs/_images/notebooks_getting-started_14_0.svg b/docs/_images/notebooks_getting-started_14_0.svg
diff --git a/docs/_images/notebooks_getting-started_15_0.svg b/docs/_images/notebooks_getting-started_15_0.svg
diff --git a/docs/_images/notebooks_getting-started_17_0.png b/docs/_images/notebooks_getting-started_17_0.png
diff --git a/docs/_images/notebooks_getting-started_17_0.svg b/docs/_images/notebooks_getting-started_17_0.svg
diff --git a/docs/_images/notebooks_getting-started_18_0.png b/docs/_images/notebooks_getting-started_18_0.png
diff --git a/docs/_images/notebooks_getting-started_18_0.svg b/docs/_images/notebooks_getting-started_18_0.svg
diff --git a/docs/_images/notebooks_getting-started_19_0.svg b/docs/_images/notebooks_getting-started_19_0.svg
diff --git a/docs/_images/notebooks_getting-started_23_0.png b/docs/_images/notebooks_getting-started_23_0.png
diff --git a/docs/_images/notebooks_getting-started_23_0.svg b/docs/_images/notebooks_getting-started_23_0.svg
diff --git a/docs/_images/notebooks_getting-started_24_0.svg b/docs/_images/notebooks_getting-started_24_0.svg
diff --git a/docs/_images/notebooks_getting-started_25_0.svg b/docs/_images/notebooks_getting-started_25_0.svg
diff --git a/docs/_images/notebooks_simulated-data_12_0.svg b/docs/_images/notebooks_simulated-data_12_0.svg
diff --git a/docs/_images/notebooks_simulated-data_14_0.svg b/docs/_images/notebooks_simulated-data_14_0.svg
diff --git a/docs/_images/notebooks_simulated-data_18_0.svg b/docs/_images/notebooks_simulated-data_18_0.svg
diff --git a/docs/_modules/geovar/geovar.html b/docs/_modules/geovar/geovar.html
diff --git a/docs/_modules/geovar/utils.html b/docs/_modules/geovar/utils.html
@@ -105,7 +105,7 @@ <h1>Source code for geovar.utils</h1><div class="highlight"><pre>
     <span class="n">idx</span> <span class="o">=</span> <span class="o">~</span><span class="n">np</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">colnames</span><span class="p">,</span> <span class="n">known_cols</span><span class="p">)</span>
     <span class="c1"># Generate frequency matrix and the population names</span>
     <span class="n">freq_mat</span> <span class="o">=</span> <span class="n">af_df</span><span class="p">[</span><span class="n">af_df</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="n">idx</span><span class="p">]]</span><span class="o">.</span><span class="n">values</span>
-    <span class="n">pop_names</span> <span class="o">=</span> <span class="n">af_df</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+    <span class="n">pop_names</span> <span class="o">=</span> <span class="n">af_df</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
     <span class="k">return</span> <span class="p">(</span><span class="n">pop_names</span><span class="p">,</span> <span class="n">freq_mat</span><span class="p">)</span></div>
 
 

diff --git a/docs/_modules/geovar/viz.html b/docs/_modules/geovar/viz.html
@@ -241,7 +241,7 @@ <h1>Source code for geovar.viz</h1><div class="highlight"><pre>
         <span class="sd">&quot;&quot;&quot;Add population labels from a file for GeoVar plot.</span>
 
 <span class="sd">        Args:</span>
-<span class="sd">            popfile (:obj:`string`): path to population list file with one file per line.</span>
+<span class="sd">            popfile (:obj:`string`): path to population list file with one population per line.</span>
 
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">geodist</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>

diff --git a/docs/_sources/notebooks/getting-started.ipynb.txt b/docs/_sources/notebooks/getting-started.ipynb.txt
diff --git a/docs/_sources/notebooks/simulated-data.ipynb.txt b/docs/_sources/notebooks/simulated-data.ipynb.txt
diff --git a/docs/_sources/stubs/geovar.binning.GeoVar.rst.txt b/docs/_sources/stubs/geovar.binning.GeoVar.rst.txt
diff --git a/docs/_sources/stubs/geovar.geovar.GeoVar.rst.txt b/docs/_sources/stubs/geovar.geovar.GeoVar.rst.txt
diff --git a/docs/_sources/stubs/geovar.viz.GeoVarPlot.rst.txt b/docs/_sources/stubs/geovar.viz.GeoVarPlot.rst.txt
diff --git a/docs/_static/contents.png b/docs/_static/contents.png