Merge pull request #5 from scverse/design-matrix-name

Rename design to design_matrix
scverse · Dec 1, 2024 · 9d62570 · 9d62570
2 parents 66cd05f + 5cfdf83
commit 9d62570
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Showing 4 changed files with 14 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,10 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## v0.2.0
+
+-   Rename `FormulaicContrasts.design` to `FormulaicContrasts.design_matrix`
+
 ## v0.1.0
 
 Initial release
diff --git a/docs/model_usage.ipynb b/docs/model_usage.ipynb
@@ -32,7 +32,7 @@
     "\n",
     "class StatsmodelsOLS(formulaic_contrasts.FormulaicContrasts):\n",
     "    def fit(self, variable: str):\n",
-    "        self.mod = sm.OLS(self.data[variable], self.design)\n",
+    "        self.mod = sm.OLS(self.data[variable], self.design_matrix)\n",
     "        self.mod = self.mod.fit()\n",
     "\n",
     "    def t_test(self, contrast: np.ndarray):\n",
@@ -240,7 +240,7 @@
     "        self.contrast_builder = formulaic_contrasts.FormulaicContrasts(data, design)\n",
     "\n",
     "    def fit(self, variable: str):\n",
-    "        self.mod = sm.OLS(self.data[variable], self.contrast_builder.design)\n",
+    "        self.mod = sm.OLS(self.data[variable], self.contrast_builder.design_matrix)\n",
     "        self.mod = self.mod.fit()\n",
     "\n",
     "    def cond(self, **kwargs):\n",
@@ -262,7 +262,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -569,12 +569,12 @@
      "data": {
       "text/plain": [
        "defaultdict(set,\n",
-       "            {'biomarker': {'np.log(biomarker)'},\n",
-       "             'np.log': {'np.log(biomarker)'},\n",
+       "            {'np.log': {'np.log(biomarker)'},\n",
+       "             'biomarker': {'np.log(biomarker)'},\n",
        "             'C': {'C(response)',\n",
        "              \"C(treatment, contr.treatment(base='drugB'))\"},\n",
-       "             'contr.treatment': {\"C(treatment, contr.treatment(base='drugB'))\"},\n",
        "             'treatment': {\"C(treatment, contr.treatment(base='drugB'))\"},\n",
+       "             'contr.treatment': {\"C(treatment, contr.treatment(base='drugB'))\"},\n",
        "             'response': {'C(response)'}})"
       ]
      },
@@ -586,13 +586,6 @@
    "source": [
     "variables_to_factors"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/src/formulaic_contrasts/_contrasts.py b/src/formulaic_contrasts/_contrasts.py
@@ -22,13 +22,13 @@ class FormulaicContrasts:
     def __init__(self, data: pd.DataFrame, design: str):
         self.factor_storage, self.variable_to_factors, materializer_class = get_factor_storage_and_materializer()
         self.data = data
-        self.design = materializer_class(data, record_factor_metadata=True).get_model_matrix(design)
+        self.design_matrix = materializer_class(data, record_factor_metadata=True).get_model_matrix(design)
 
     @property
     def variables(self):
         """Get the names of the variables used in the model definition."""
         try:
-            return self.design.model_spec.variables_by_source["data"]
+            return self.design_matrix.model_spec.variables_by_source["data"]
         except AttributeError:
             raise ValueError(
                 "Retrieving variables is only possible if the model was initialized using a formula."
@@ -63,7 +63,7 @@ def cond(self, **kwargs):
             else:
                 cond_dict[var] = self._get_default_value(var)
         df = pd.DataFrame([kwargs])
-        return self.design.model_spec.get_model_matrix(df).iloc[0]
+        return self.design_matrix.model_spec.get_model_matrix(df).iloc[0]
 
     def contrast(self, column, baseline, group_to_compare):
         """

diff --git a/tests/test_contrasts.py b/tests/test_contrasts.py
@@ -84,4 +84,4 @@ def test_model_cond(test_dataframe, MockModel, formula, cond_kwargs, expected_co
     else:
         actual_contrast = mod.cond(**cond_kwargs)
         assert actual_contrast.tolist() == expected_contrast
-        assert actual_contrast.index.tolist() == mod.design.columns.tolist()
+        assert actual_contrast.index.tolist() == mod.design_matrix.columns.tolist()