changed default of two sample to t-test

Author: davidsebfischer

diffxpy/testing/tests.py

@@ -699,7 +699,7 @@ def two_sample(
         data: Union[anndata.AnnData, anndata.base.Raw, xr.DataArray, xr.Dataset, np.ndarray, scipy.sparse.csr_matrix],
         grouping: Union[str, np.ndarray, list],
         as_numeric: Union[List[str], Tuple[str], str] = (),
-        test: str = None,
+        test: str = "t-test",
         gene_names: Union[np.ndarray, list] = None,
         sample_description: pd.DataFrame = None,
         noise_model: str = None,
@@ -797,10 +797,6 @@ def two_sample(
     if groups.size < 2:
         raise ValueError("Less than two groups detected:\n\t%s", groups)
 
-    # Set default test:
-    if test is None:
-        test = 'wald'
-
     if test.lower() == 'wald':
         if noise_model is None:
             raise ValueError("Please specify noise_model")
@@ -862,7 +858,7 @@ def two_sample(
             dtype=dtype
         )
     else:
-        raise ValueError('base.two_sample(): Parameter `test="%s"` not recognized.' % test)
+        raise ValueError('two_sample(): Parameter `test="%s"` not recognized.' % test)
 
     return de_test
 

docs/api/index.rst

@@ -27,7 +27,7 @@ diffxpy provies infrastructure for likelihood ratio tests, Wald tests, t-tests a
    test.wald
    test.lrt
    test.t_test
-   test.wilcoxon
+   test.rank_test
 
 Multiple tests per gene
 ~~~~~~~~~~~~~~~~~~~~~~~

docs/conf.py

@@ -23,9 +23,9 @@
 
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE.parent))
-import diffxpy  # noqa
+import diffxpy
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("diffxpy")
 
 # -- General configuration ------------------------------------------------
 
@@ -67,7 +67,7 @@
 templates_path = ['_templates']
 
 project = 'diffxpy'
-author = 'Florian R. Hölzlwimmer, David S. Fischer'
+author = 'David S. Fischer, Florian R. Hölzlwimmer'
 
 source_suffix = '.rst'
 master_doc = 'index'
@@ -129,7 +129,7 @@ def setup(app):
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'diffxpy.tex', 'diffxpy Documentation',
-     'Florian R. Hölzlwimmer, David S. Fischer', 'manual'),
+     'David S. Fischer, Florian R. Hölzlwimmer', 'manual'),
 ]
 
 # -- Options for manual page output ------------------------------------------

docs/requires.txt

@@ -2,7 +2,7 @@ numpy>=1.14.0
 scipy
 pandas
 patsy>=0.5.0
-batchglm>=0.4.0
+batchglm>=0.6.0
 xarray
 statsmodels
 anndata

setup.py

@@ -21,18 +21,14 @@
         'scipy',
         'pandas',
         'patsy>=0.5.0',
-        'batchglm>=0.4.0',
+        'batchglm>=0.6.0',
         'xarray',
         'statsmodels',
     ],
     extras_require={
         'optional': [
             'anndata',
         ],
-        # 'scanpy_deps': [
-        #     "scanpy",
-        #     "anndata"
-        # ],
         'plotting_deps': [
             "seaborn",
             "matplotlib"