refactor: update scripts to store downloaded data in a subfolder (#8)

this includes a new .gitignore file, and a change to the old one

# Description

This PR will create a downloaded folder to store the original files
(both the zipped file and the unzipped data files).

Closes #9

<!-- Select quick/in-depth as necessary -->
This PR needs a quick review.

## Checklist

- [x] Read through for typos, added new words to the dictionary
- [x] Checked that the README is up to date
- [x] Resolved any Ruff errors / formatted in Markdown

data-raw/.gitignore

@@ -1,2 +1,3 @@
 *
 !.gitignore
+!downloaded/

data-raw/downloaded/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

scripts/convert-with-core.py

@@ -5,8 +5,9 @@
 
 resource_dir = Path(__file__).resolve().parent.parent
 folder_path = resource_dir / "data-raw"
+downloaded_path = folder_path / "downloaded"
 
-df_experiment1 = pl.read_csv(folder_path / "Expe1.csv", infer_schema_length=100_000)
+df_experiment1 = pl.read_csv(downloaded_path / "Expe1.csv", infer_schema_length=100_000)
 
 df_experiment1 = df_experiment1.rename(
     {
@@ -24,7 +25,7 @@
 )
 df_experiment1.write_csv(folder_path / "data-experiment1-ready.csv")
 
-df_experiment2 = pl.read_csv(folder_path / "Expe2.csv", infer_schema_length=100_000)
+df_experiment2 = pl.read_csv(downloaded_path / "Expe2.csv", infer_schema_length=100_000)
 
 treatment_mapping1 = {
     "masHmasE": "with_feces_cover_after_48h",
@@ -51,7 +52,7 @@
 df_experiment2.write_csv(folder_path / "data-experiment2-ready.csv")
 
 df_abundance = pl.read_csv(
-    folder_path / "Expe3Abundance.csv", infer_schema_length=100_000
+    downloaded_path / "Expe3Abundance.csv", infer_schema_length=100_000
 )
 
 treatment_mapping2 = {
@@ -66,7 +67,7 @@
 )
 
 df_richness = pl.read_csv(
-    folder_path / "Expe3Richness.csv", infer_schema_length=100_000
+    downloaded_path / "Expe3Richness.csv", infer_schema_length=100_000
 )
 
 df_experiment3_all = pl.concat([df_abundance, df_richness], how="align")  # concat wide

scripts/download-data.py

@@ -5,14 +5,15 @@
 
 resource_dir = Path(__file__).resolve().parent.parent
 folder_path = resource_dir / "data-raw"
+download_path = folder_path / "downloaded"
 
 # Download and save the zip file
 all_files = requests.get("https://zenodo.org/api/records/4965431/files-archive")
 
-all_files_path = folder_path / "all_files.zip"
+all_files_path = download_path / "all_files.zip"
 with open(all_files_path, "wb") as file:
     file.write(all_files.content)
 
 # Extract the zip file
 with ZipFile(all_files_path, "r") as zip_ref:
-    zip_ref.extractall(folder_path)
+    zip_ref.extractall(download_path)