From 284a3b9281c25165389086895d8db66f6858ae2b Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Mon, 15 Jul 2024 21:12:39 +0200
Subject: [PATCH] chore(code): Move dataframe generation to module

---
 article.qmd                                   | 19 ++++++++++++++++---
 scoping_review.qmd                            | 18 ++++++++++++++++--
 .../process/generate_dataframes.py            | 10 ----------
 3 files changed, 32 insertions(+), 15 deletions(-)
 rename 01-codechunks/_prep-data.py => src/process/generate_dataframes.py (90%)

diff --git a/article.qmd b/article.qmd
index 912ce14..79b4ca4 100644
--- a/article.qmd
+++ b/article.qmd
@@ -38,12 +38,25 @@ crossref: # to fix the appendix crossrefs being separate from main
       latex-list-of-description: Appendix B Table
 ---
 
-
 ```{python}
-#| label: prep-data
+#| label: standard-imports
 #| echo: false
 #| output: false
-{{< include 01-codechunks/_prep-data.py >}}
+import src.globals as g
+from IPython.display import display, Markdown, HTML
+import numpy as np
+import pandas as pd
+from matplotlib import pyplot as plt
+from tabulate import tabulate
+import seaborn as sns
+sns.set_style("whitegrid")
+```
+
+```{python}
+#| label: load-dataframes
+#| echo: false
+#| output: false
+from src.process.generate_dataframes import df, df_by_intervention, validities
 ```
 
 {{< portrait >}}
diff --git a/scoping_review.qmd b/scoping_review.qmd
index cd0ebd0..63c206a 100644
--- a/scoping_review.qmd
+++ b/scoping_review.qmd
@@ -22,10 +22,24 @@ crossref:
 ---
 
 ```{python}
-#| label: prep-data
+#| label: standard-imports
 #| echo: false
 #| output: false
-{{< include 01-codechunks/_prep-data.py >}}
+import src.globals as g
+from IPython.display import display, Markdown, HTML
+import numpy as np
+import pandas as pd
+from matplotlib import pyplot as plt
+from tabulate import tabulate
+import seaborn as sns
+sns.set_style("whitegrid")
+```
+
+```{python}
+#| label: load-dataframes
+#| echo: false
+#| output: false
+from src.process.generate_dataframes import df, df_by_intervention, validities
 ```
 
 <!-- pagebreak to separate from TOC -->
diff --git a/01-codechunks/_prep-data.py b/src/process/generate_dataframes.py
similarity index 90%
rename from 01-codechunks/_prep-data.py
rename to src/process/generate_dataframes.py
index 8287e65..a5bab48 100644
--- a/01-codechunks/_prep-data.py
+++ b/src/process/generate_dataframes.py
@@ -1,18 +1,8 @@
 from pathlib import Path
-import os
 import re
-## standard imports
-from IPython.display import display, Markdown, HTML
-import numpy as np
-import pandas as pd
-from matplotlib import pyplot as plt
 import seaborn as sns
-from tabulate import tabulate
-import bibtexparser
 import src.globals as g
 
-sns.set_style("whitegrid")
-
 ## Creates 3 important data structures:
 # df: The main dataframe containing all final sample studies
 # df_by_intervention: The same dataframe but split up by individual interventions per study