fix tests and docs

MannLabs · Nov 18, 2024 · af7cf8b · af7cf8b
1 parent 06aa614
commit af7cf8b
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git a/docs/api_reference/dataset.rst b/docs/api_reference/dataset.rst
@@ -5,7 +5,7 @@ DataSet
 
 DataSet
 ~~~~~~~~~~~
-.. automodule:: alphastats.DataSet
+.. automodule:: alphastats.dataset.dataset.DataSet
     :members:
     :undoc-members:
     :inherited-members:
diff --git a/docs/import_data.md b/docs/import_data.md
@@ -12,7 +12,7 @@ maxquant_data = alphastats.MaxQuantLoader(
     file="testfiles/maxquant_proteinGroups.txt"
 )
 
-dataset = alphastats.DataSet(
+dataset = alphastats.dataset.dataset.DataSet(
     loader = maxquant_data,
     metadata_path_or_df="../testfiles/maxquant/metadata.xlsx",
     sample_column="sample"
@@ -115,7 +115,7 @@ To compare samples across various conditions in the downstream analysis, a metad
 
 ## Creating a DataSet
 
-The whole downstream analysis can be performed on the alphastats.DataSet. To create the DataSet you need to provide the loader object as well as the metadata.
+The whole downstream analysis can be performed on the alphastats.dataset.dataset.DataSet. To create the DataSet you need to provide the loader object as well as the metadata.
 
 ```python
 import alphastats
@@ -124,7 +124,7 @@ maxquant_data = alphastats.MaxQuantLoader(
     file="testfiles/maxquant_proteinGroups.txt"
 )
 
-dataset = alphastats.DataSet(
+dataset = alphastats.dataset.dataset.DataSet(
     loader = maxquant_data,
     metadata_path_or_df="../testfiles/maxquant/metadata.xlsx",
     sample_column="sample"

diff --git a/nbs/liu_2019.ipynb b/nbs/liu_2019.ipynb
@@ -59,7 +59,7 @@
    "metadata": {},
    "source": [
     "We are going to load the `proteinGroups.txt` and the corresponding metadatafile. You can find the data [here](https://github.com/MannLabs/alphapeptstats/tree/main/testfiles/maxquant) or on ProteomeXchange [PXD011839](http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD011839).\n",
-    "To load the proteomis data you need to create a loader object using `alphastats.MaxQuantLoader`. The whole downstream analysis will be performed on a `alphastats.DataSet`. To create the DataSet you need to provide the loader object as well as the metadata."
+    "To load the proteomis data you need to create a loader object using `alphastats.MaxQuantLoader`. The whole downstream analysis will be performed on a `alphastats.dataset.dataset.DataSet`. To create the DataSet you need to provide the loader object as well as the metadata."
    ]
   },
   {

diff --git a/nbs/ramus_2016.ipynb b/nbs/ramus_2016.ipynb
@@ -87,7 +87,7 @@
     "    filter_columns=[],\n",
     ")\n",
     "\n",
-    "ds = alphastats.DataSet(\n",
+    "ds = alphastats.dataset.dataset.DataSet(\n",
     "    loader=loader, metadata_path_or_df=\"metadata.csv\", sample_column=\"sample\"\n",
     ")"
    ]

diff --git a/tests/test_DataSet.py b/tests/test_DataSet.py
@@ -491,7 +491,7 @@ def test_preprocess_subset(self):
         self.obj.preprocess(subset=True)
         self.assertEqual(self.obj.mat.shape[0], 48)
 
-    @patch("alphastats.DataSet.DataSet.tukey_test")
+    @patch("alphastats.dataset.dataset.DataSet.tukey_test")
     def test_anova_without_tukey(self, mock):
         # TODO: Check why 4 extra rows are generated here. This is not due to changes made to 0 and nan filtering.
         anova_results = self.obj.anova(column="disease", protein_ids="all", tukey=False)