Merge pull request #1 from Genentech/dev

v0.0.1

Author: ofajardo

README.md

@@ -20,12 +20,11 @@ Let's take a look at the data:
 
 ```python
 import pandas as pd
-from IPython.display import display, Markdown
 
 from pysummaries import get_table_summary, get_sample_data
 
 df = get_sample_data()
-display(df)
+df
 ```
 
 ![alt text](documentation/images/pysummaries_sample_data.png)
@@ -39,7 +38,7 @@ Let's start first with the PySummaries native backend:
 
 ```python
 summary_table = get_table_summary(df, strata='group', backend='native')  
-display(summary_table)
+summary_table
 ```
 
 ![alt text](documentation/images/pysummaries_native_backend.png)
@@ -48,7 +47,7 @@ And now, let's try the great tables backend!
 
 ```python
 summary_table = get_table_summary_gt(df, strata='group', backend='gt')  
-display(summary_table)
+summary_table
 ```
 
 ![alt text](documentation/images/pysummaries_gt_backend.png)

changelog.txt

@@ -1,2 +1,5 @@
 # 0.0.1
+* Added support for pyarrow pandas dtypes
+
+# 0.0.1b1
 * First version

docs/_sources/index.py

@@ -36,12 +36,11 @@
 
 # %%
 import pandas as pd
-from IPython.display import display, Markdown
 
 from pysummaries import get_table_summary, get_sample_data
 
 df = get_sample_data()
-display(df)
+df
 
 # %% [markdown]
 # Now, let's do a table one stratifying by group 
@@ -54,14 +53,14 @@
 
 # %%
 summary_table = get_table_summary(df, strata='group', backend='native')  
-display(summary_table)
+summary_table
 
 # %% [markdown]
 # And now, let's try the great tables backend!
 
 # %%
 summary_table = get_table_summary(df, strata='group', backend='gt')  
-display(summary_table)
+summary_table
 
 # %% [markdown]
 # In both cases you can enhance the table with more features. For example, let's add a title and footer to the table.
@@ -73,7 +72,7 @@
 
 # %%
 summary_table = get_table_summary(df, strata='group', backend='native', caption="<strong>Table 1</strong>", footer="This is the footer")  
-display(summary_table)
+summary_table
 
 # %% [markdown]
 # And now, with the great tables backend:
@@ -86,7 +85,7 @@
                         .tab_source_note(source_note = "This is the footer")
                         .cols_align('center')
 )
-display(summary_table)
+summary_table
 
 # %% [markdown]
 # ## More features
@@ -126,10 +125,10 @@
 # Let's bring nice labels for gender and age and exclude region
 labels = {'gender': 'Birth gender, n (%)', 
         "age": 'Age at Index'}
-# we could also specify columns_include
-# column_include = ['age', 'gender']
-cols_exclude = ['region']
-summary_table = get_table_summary(df, strata='group', columns_exclude=cols_exclude, columns_labels=labels)  
+# we could also specify columns_exclude
+cols_include = ['age', 'gender']
+#cols_exclude = ['region']
+summary_table = get_table_summary(df, strata='group', columns_include=cols_include, columns_labels=labels)  
 summary_table
 
 # %% [markdown]

docs/api.html

@@ -348,6 +348,7 @@ <h2> Contents </h2>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_sample_data"><code class="docutils literal notranslate"><span class="pre">get_sample_data()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_styles"><code class="docutils literal notranslate"><span class="pre">get_styles()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_table_summary"><code class="docutils literal notranslate"><span class="pre">get_table_summary()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_test_data"><code class="docutils literal notranslate"><span class="pre">get_test_data()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_mean_sd"><code class="docutils literal notranslate"><span class="pre">numerical_mean_sd()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_median_iqr"><code class="docutils literal notranslate"><span class="pre">numerical_median_iqr()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_median_q1q3"><code class="docutils literal notranslate"><span class="pre">numerical_median_q1q3()</span></code></a></li>
@@ -578,6 +579,20 @@ <h2> Contents </h2>
 </div>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="pysummaries.get_test_data">
+<span class="sig-prename descclassname"><span class="pre">pysummaries.</span></span><span class="sig-name descname"><span class="pre">get_test_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pysummaries.get_test_data" title="Link to this definition">#</a></dt>
+<dd><p>Enriches the sample data with further column for testing</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>sample data</p>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p>pandas dataframe</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="pysummaries.numerical_mean_sd">
 <span class="sig-prename descclassname"><span class="pre">pysummaries.</span></span><span class="sig-name descname"><span class="pre">numerical_mean_sd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">curseries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rounding</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pysummaries.numerical_mean_sd" title="Link to this definition">#</a></dt>
@@ -789,6 +804,7 @@ <h2> Contents </h2>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_sample_data"><code class="docutils literal notranslate"><span class="pre">get_sample_data()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_styles"><code class="docutils literal notranslate"><span class="pre">get_styles()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_table_summary"><code class="docutils literal notranslate"><span class="pre">get_table_summary()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.get_test_data"><code class="docutils literal notranslate"><span class="pre">get_test_data()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_mean_sd"><code class="docutils literal notranslate"><span class="pre">numerical_mean_sd()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_median_iqr"><code class="docutils literal notranslate"><span class="pre">numerical_median_iqr()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#pysummaries.numerical_median_q1q3"><code class="docutils literal notranslate"><span class="pre">numerical_median_q1q3()</span></code></a></li>

docs/genindex.html

@@ -330,6 +330,8 @@ <h2 id="G">G</h2>
       <li><a href="api.html#pysummaries.get_styles">get_styles() (in module pysummaries)</a>
 </li>
       <li><a href="api.html#pysummaries.get_table_summary">get_table_summary() (in module pysummaries)</a>
+</li>
+      <li><a href="api.html#pysummaries.get_test_data">get_test_data() (in module pysummaries)</a>
 </li>
   </ul></td>
 </tr></table>