Updates for version 1.0 (#5)

* 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

Author: aabiddanda

.github/workflows/macos.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: run tests
         run: |
-          pytest
+          python -m pytest tests/
 
       - name: run flake8
         run: |

.github/workflows/ubuntu.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: run tests
         run: |
-          pytest
+          python -m pytest tests/
 
       - name: run flake8
         run: |

.github/workflows/windows.yml

@@ -1,3 +1,8 @@
 sandbox/*
 geovar/data/*.csv
 docsrc/_build/*
+.hypothesis/
+*.egg-info/
+*.coverage
+*.python-version
+build/

.gitignore

@@ -54,6 +54,7 @@ <h1>Source code for geovar.binning</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">assert</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">bins</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mf">1.0</span><span class="p">)</span>
         <span class="k">assert</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">bins</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="mf">0.0</span><span class="p">)</span>
+        <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">bins</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">bins</span> <span class="o">=</span> <span class="n">bins</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">freq_mat</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">n_variants</span> <span class="o">=</span> <span class="kc">None</span>