A few minor style changes via pyupgrade (scverse#971)

Co-authored-by: Philipp A <[email protected]>
csgroen · Aug 5, 2020 · 090d577 · 090d577
1 parent f6212ce
commit 090d577
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Showing 6 changed files with 5 additions and 7 deletions.
diff --git a/scanpy/plotting/_anndata.py b/scanpy/plotting/_anndata.py
@@ -1836,7 +1836,7 @@ def _prepare_dataframe(
     if gene_symbols is not None:
         # translate the column names to the symbol names
         obs_tidy.rename(
-            columns=dict([(var_names[x], symbols[x]) for x in range(len(var_names))]),
+            columns={var_names[x]: symbols[x] for x in range(len(var_names))},
             inplace=True,
         )
     categories = obs_tidy.index.categories

diff --git a/scanpy/preprocessing/_deprecated/highly_variable_genes.py b/scanpy/preprocessing/_deprecated/highly_variable_genes.py
@@ -179,10 +179,10 @@ def filter_genes_dispersion(
         with warnings.catch_warnings():
             warnings.simplefilter('ignore')
             disp_mad_bin = disp_grouped.apply(robust.mad)
-        df['dispersion_norm'] = np.abs((
+        df['dispersion_norm'] = np.abs(
             df['dispersion'].values
             - disp_median_bin[df['mean_bin'].values].values
-        )) / disp_mad_bin[df['mean_bin'].values].values
+        ) / disp_mad_bin[df['mean_bin'].values].values
     else:
         raise ValueError('`flavor` needs to be "seurat" or "cell_ranger"')
     dispersion_norm = df['dispersion_norm'].values.astype('float32')

diff --git a/scanpy/preprocessing/_qc.py b/scanpy/preprocessing/_qc.py
@@ -390,7 +390,7 @@ def top_segment_proportions_dense(
     sums = mtx.sum(axis=1)
     partitioned = np.apply_along_axis(np.partition, 1, mtx, mtx.shape[1] - ns)[:, ::-1][:, :ns[-1]]
     values = np.zeros((mtx.shape[0], len(ns)))
-    acc = np.zeros((mtx.shape[0]))
+    acc = np.zeros(mtx.shape[0])
     prev = 0
     for j, n in enumerate(ns):
         acc += partitioned[:, prev:n].sum(axis=1)

diff --git a/scanpy/sim_models/__init__.py b/scanpy/sim_models/__init__.py
@@ -1 +0,0 @@
-

diff --git a/scanpy/tests/notebooks/test_pbmc3k.py b/scanpy/tests/notebooks/test_pbmc3k.py
@@ -1,4 +1,3 @@
-# coding: utf-8
 # *First compiled on May 5, 2017. Updated August 14, 2018.*
 # # Clustering 3k PBMCs following a Seurat Tutorial
 #

diff --git a/scanpy/tools/_dpt.py b/scanpy/tools/_dpt.py
@@ -183,7 +183,7 @@ class DPT(Neighbors):
 
     def __init__(self, adata, n_dcs=None, min_group_size=0.01,
                  n_branchings=0, allow_kendall_tau_shift=False, neighbors_key=None):
-        super(DPT, self).__init__(adata, n_dcs=n_dcs, neighbors_key=neighbors_key)
+        super().__init__(adata, n_dcs=n_dcs, neighbors_key=neighbors_key)
         self.flavor = 'haghverdi16'
         self.n_branchings = n_branchings
         self.min_group_size = min_group_size if min_group_size >= 1 else int(min_group_size * self._adata.shape[0])