Add Black format checking (#113)

* Run black on all python files

* Add black check to CI

* Fix CI order

.github/workflows/python-package.yml

@@ -11,10 +11,15 @@ jobs:
         python-version: [3.7, 3.8]
 
     steps:
+
     - uses: actions/checkout@v2
       with:
         path: scanpy-scripts
-
+
+    - uses: psf/black@stable
+      with:
+        options: '--check --verbose --include="\.pyi?$" .'
+
     - uses: actions/checkout@v2
       with:
         repository: theislab/scanpy 

scanpy_scripts/__init__.py

@@ -3,13 +3,15 @@
 """
 import pkg_resources
 
-__version__ = pkg_resources.get_distribution('scanpy-scripts').version
+__version__ = pkg_resources.get_distribution("scanpy-scripts").version
 
-__author__ = ', '.join([
-    'Ni Huang',
-    'Pablo Moreno',
-    'Jonathan Manning',
-    'Philipp Angerer',
-])
+__author__ = ", ".join(
+    [
+        "Ni Huang",
+        "Pablo Moreno",
+        "Jonathan Manning",
+        "Philipp Angerer",
+    ]
+)
 
 from . import lib

scanpy_scripts/cli.py

@@ -42,20 +42,20 @@
 
 @click.group(cls=NaturalOrderGroup)
 @click.option(
-    '--debug',
+    "--debug",
     is_flag=True,
     default=False,
-    help='Print debug information',
+    help="Print debug information",
 )
 @click.option(
-    '--verbosity',
+    "--verbosity",
     type=click.INT,
     default=3,
-    help='Set scanpy verbosity',
+    help="Set scanpy verbosity",
 )
 @click.version_option(
-    version='0.2.0',
-    prog_name='scanpy',
+    version="0.2.0",
+    prog_name="scanpy",
 )
 def cli(debug=False, verbosity=3):
     """
@@ -64,11 +64,12 @@ def cli(debug=False, verbosity=3):
     log_level = logging.DEBUG if debug else logging.INFO
     logging.basicConfig(
         level=log_level,
-        format=('%(asctime)s; %(levelname)s; %(filename)s; '
-                '%(funcName)s(): %(message)s'),
-        datefmt='%y-%m-%d %H:%M:%S',
+        format=(
+            "%(asctime)s; %(levelname)s; %(filename)s; " "%(funcName)s(): %(message)s"
+        ),
+        datefmt="%y-%m-%d %H:%M:%S",
     )
-    logging.debug('debugging')
+    logging.debug("debugging")
     sc.settings.verbosity = verbosity
     return 0
 
@@ -112,15 +113,18 @@ def cluster():
 def integrate():
     """Integrate cells from different experimental batches."""
 
+
 integrate.add_command(HARMONY_INTEGRATE_CMD)
 integrate.add_command(BBKNN_CMD)
 integrate.add_command(MNN_CORRECT_CMD)
 integrate.add_command(COMBAT_CMD)
 
+
 @cli.group(cls=NaturalOrderGroup)
 def multiplet():
     """Execute methods for multiplet removal."""
 
+
 multiplet.add_command(SCRUBLET_MULTIPLET_CMD)
 multiplet.add_command(SCRUBLET_MULTIPLET_SIMULATE_CMD)
 

scanpy_scripts/click_utils.py

@@ -13,6 +13,7 @@ class NaturalOrderGroup(click.Group):
 
         @click.group(cls=NaturalOrderGroup)
     """
+
     def list_commands(self, ctx):
         """List command names as they are in commands dict.
 
@@ -26,15 +27,16 @@ class CommaSeparatedText(click.ParamType):
     """
     Comma separated text
     """
+
     def __init__(self, dtype=click.STRING, simplify=False, length=None):
         self.dtype = dtype
         self.dtype_name = _get_type_name(dtype)
         self.simplify = simplify
         self.length = length
         if length and length <= 3:
-            self.name = ','.join([f'{self.dtype_name}'] * length)
+            self.name = ",".join([f"{self.dtype_name}"] * length)
         else:
-            self.name = '{}[,{}...]'.format(self.dtype_name, self.dtype_name)
+            self.name = "{}[,{}...]".format(self.dtype_name, self.dtype_name)
 
     def convert(self, value, param, ctx):
         """
@@ -67,23 +69,25 @@ def convert(self, value, param, ctx):
             if value is None:
                 converted = None
             else:
-                converted = list(map(self.dtype, str(value).split(',')))
+                converted = list(map(self.dtype, str(value).split(",")))
                 if self.simplify and len(converted) == 1:
                     converted = converted[0]
         except ValueError:
             self.fail(
-                '{} is not a valid comma separated list of {}'.format(
-                    value, self.dtype_name),
+                "{} is not a valid comma separated list of {}".format(
+                    value, self.dtype_name
+                ),
                 param,
-                ctx
+                ctx,
             )
         if self.length:
             if len(converted) != self.length:
                 self.fail(
-                    '{} is not a valid comma separated list of length {}'.format(
-                        value, self.length),
+                    "{} is not a valid comma separated list of length {}".format(
+                        value, self.length
+                    ),
                     param,
-                    ctx
+                    ctx,
                 )
         return converted
 
@@ -92,8 +96,9 @@ class Dictionary(click.ParamType):
     """
     Text to be parsed as a python dict definition
     """
+
     def __init__(self, keys=None):
-        self.name = 'TEXT:VAL[,TEXT:VAL...]'
+        self.name = "TEXT:VAL[,TEXT:VAL...]"
         self.keys = keys
 
     def convert(self, value, param, ctx):
@@ -122,19 +127,19 @@ def convert(self, value, param, ctx):
         """
         try:
             converted = dict()
-            for token in value.split(','):
-                if ':' not in token:
+            for token in value.split(","):
+                if ":" not in token:
                     raise ValueError
-                key, _, value = token.partition(':')
+                key, _, value = token.partition(":")
                 if not key:
                     raise ValueError
                 if isinstance(self.keys, (list, tuple)) and key not in self.keys:
-                    self.fail(f'{key} is not a valid key ({self.keys})')
-                if value == 'None':
+                    self.fail(f"{key} is not a valid key ({self.keys})")
+                if value == "None":
                     value = None
-                elif value.lower() == 'true':
+                elif value.lower() == "true":
                     value = True
-                elif value.lower() == 'false':
+                elif value.lower() == "false":
                     value = False
                 else:
                     try:
@@ -144,19 +149,15 @@ def convert(self, value, param, ctx):
                 converted[key] = value
             return converted
         except ValueError:
-            self.fail(
-                f'{value} is not a valid python dict definition',
-                param,
-                ctx
-            )
+            self.fail(f"{value} is not a valid python dict definition", param, ctx)
 
 
 def _get_type_name(obj):
-    name = 'text'
+    name = "text"
     try:
-        name = getattr(obj, 'name')
+        name = getattr(obj, "name")
     except AttributeError:
-        name = getattr(obj, '__name__')
+        name = getattr(obj, "__name__")
     return name
 
 
@@ -181,8 +182,7 @@ def valid_limit(ctx, param, value):
     [0.0125, 0.0125]
     """
     if value[0] > value[1]:
-        param.type.fail(
-            'lower limit must not exceed upper limit', param, ctx)
+        param.type.fail("lower limit must not exceed upper limit", param, ctx)
     return value
 
 
@@ -212,13 +212,13 @@ def valid_parameter_limits(ctx, param, value):
     """
     for val in value:
         if val[1] > val[2]:
-            param.type.fail(
-                'lower limit must not exceed upper limit', param, ctx)
+            param.type.fail("lower limit must not exceed upper limit", param, ctx)
     return value
 
 
 def mutually_exclusive_with(param_name):
-    internal_name = param_name.strip('-').replace('-', '_').lower()
+    internal_name = param_name.strip("-").replace("-", "_").lower()
+
     def valid_mutually_exclusive(ctx, param, value):
         try:
             other_value = ctx.params[internal_name]
@@ -227,27 +227,35 @@ def valid_mutually_exclusive(ctx, param, value):
         if (value is None) == (other_value is None):
             param.type.fail(
                 'mutually exclusive with "{}", one and only one must be '
-                'specified.'.format(param_name),
+                "specified.".format(param_name),
                 param,
                 ctx,
             )
         return value
+
     return valid_mutually_exclusive
 
 
 def required_by(param_name):
-    internal_name = param_name.strip('-').replace('-', '_').lower()
+    internal_name = param_name.strip("-").replace("-", "_").lower()
+
     def required(ctx, param, value):
         try:
             other_value = ctx.params[internal_name]
         except KeyError:
             return value
         if other_value and not value:
-            param.type.fail('required by "{}".'.format(param_name), param, ctx,)
+            param.type.fail(
+                'required by "{}".'.format(param_name),
+                param,
+                ctx,
+            )
         return value
+
     return required
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import doctest
+
     sys.exit(doctest.testmod(verbose=True)[0])