Merge branch 'master' into feature/conda_forge

The-Dev-Effect · Oct 27, 2021 · 985f680 · 985f680
2 parents a6e031d + b13cf8e
commit 985f680
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Showing 7 changed files with 11 additions and 11 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,14 @@
 repos:
--   repo: https://github.com/python/black
-    rev: 20.8b1
+-   repo: https://github.com/psf/black
+    rev: 21.9b0
     hooks:
     -   id: black
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+-   repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
     hooks:
     -   id: flake8
 -   repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.5.5
+    rev: v1.5.7
     hooks:
     -   id: autopep8
         args: ["-i"]

diff --git a/pyproject.toml b/pyproject.toml
@@ -86,7 +86,7 @@ dev = [
     'docutils',
 ]
 doc = [
-    'sphinx>=4.1',
+    'sphinx>=4.1,<4.2',
     'sphinx-rtd-theme>=0.3.1',
     'sphinx-autodoc-typehints',
     'scanpydoc>=0.7.3',

diff --git a/scanpy/external/exporting.py b/scanpy/external/exporting.py
@@ -276,7 +276,7 @@ def write_hdf5_genes(E, gene_list, filename):
 
 
 def write_hdf5_cells(E, filename):
-    '''SPRING standard: filename = main_spring_dir + "counts_norm_sparse_cells.hdf5" '''
+    '''SPRING standard: filename = main_spring_dir + "counts_norm_sparse_cells.hdf5"'''
 
     E = E.tocsr()
 
@@ -298,7 +298,7 @@ def write_hdf5_cells(E, filename):
 
 
 def write_sparse_npz(E, filename, compressed=False):
-    ''' SPRING standard: filename = main_spring_dir + "/counts_norm.npz"'''
+    '''SPRING standard: filename = main_spring_dir + "/counts_norm.npz"'''
     E = E.tocsc()
     scipy.sparse.save_npz(filename, E, compressed=compressed)
 

diff --git a/scanpy/preprocessing/_deprecated/highly_variable_genes.py b/scanpy/preprocessing/_deprecated/highly_variable_genes.py
@@ -236,7 +236,7 @@ def filter_genes_dispersion(
 
 
 def filter_genes_cv_deprecated(X, Ecutoff, cvFilter):
-    """ Filter genes by coefficient of variance and mean."""
+    """Filter genes by coefficient of variance and mean."""
     return _filter_genes(X, Ecutoff, cvFilter, np.std)
 
 

diff --git a/scanpy/tests/_images/master_violin_multi_panel.png b/scanpy/tests/_images/master_violin_multi_panel.png
diff --git a/scanpy/tests/notebooks/pbmc3k_images/violin.png b/scanpy/tests/notebooks/pbmc3k_images/violin.png
diff --git a/scanpy/tools/_sim.py b/scanpy/tools/_sim.py
@@ -505,7 +505,7 @@ def Xdiff_var(self, Xt, verbosity=0):
         return Xdiff
 
     def hill_a(self, x, threshold=0.1, power=2):
-        """ Activating hill function. """
+        """Activating hill function."""
         x_pow = np.power(x, power)
         threshold_pow = np.power(threshold, power)
         return x_pow / (x_pow + threshold_pow)
@@ -520,7 +520,7 @@ def hill_i(self, x, threshold=0.1, power=2):
         return threshold_pow / (x_pow + threshold_pow)
 
     def nhill_a(self, x, threshold=0.1, power=2, ichild=2):
-        """ Normalized activating hill function. """
+        """Normalized activating hill function."""
         x_pow = np.power(x, power)
         threshold_pow = np.power(threshold, power)
         return x_pow / (x_pow + threshold_pow) * (1 + threshold_pow)