Merge pull request #69 from vsoch/linting-update

updating linting

.github/workflows/main.yml

@@ -11,13 +11,13 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-
+      - uses: actions/checkout@v4
       - name: Setup black linter
         run: conda create --quiet --name black black
 
       - name: Lint python code
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate black
+          pip install black==23.3.0
           black --check scif

scif/__init__.py

@@ -1,13 +1 @@
-"""
-
-Copyright (C) 2017-2020 Vanessa Sochat.
-
-This Source Code Form is subject to the terms of the
-Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
-with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-Modified from https://github.com/Visual-mov/Colorful-Julia (MIT License)
-
-"""
-
 from scif.version import __version__

scif/client/__init__.py

@@ -2,7 +2,7 @@
 
 """
 
-Copyright (C) 2016-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -167,8 +167,7 @@ def get_parser():
 
 
 def get_subparsers(parser):
-    """get_subparser will get a dictionary of subparsers, to help with printing help
-    """
+    """get_subparser will get a dictionary of subparsers, to help with printing help"""
 
     actions = [
         action
@@ -186,16 +185,16 @@ def get_subparsers(parser):
 
 
 def main():
-    """main is the entrypoint to managing or interacting with an scif 
-       organized filesystem.
+    """main is the entrypoint to managing or interacting with an scif
+    organized filesystem.
     """
 
     parser = get_parser()
     subparsers = get_subparsers(parser)
 
     def help(return_code=0):
-        """print help, including the software version and active client 
-           and exit with return code.
+        """print help, including the software version and active client
+        and exit with return code.
         """
         version = scif.__version__
 

scif/client/dump.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     client = ScifRecipe(quiet=True, writable=False)

scif/client/execute.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     cmd = args.cmd

scif/client/help.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     apps = args.app

scif/client/inspect.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -18,7 +18,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     # Inspect choices, r, e, l, a
@@ -62,7 +61,6 @@ def main(args, parser, subparser):
 
     result = {}
     for app in apps:
-
         inspection = client.inspect(app, attributes)
         if len(inspection) > 0:
             result[app] = inspection

scif/client/install.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -16,7 +16,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     apps = args.recipe

scif/client/list.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -16,7 +16,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     client = ScifRecipe(writable=False, quiet=True)
@@ -33,7 +32,6 @@ def main(args, parser, subparser):
             result.append(app.rjust(10))
 
     if len(result) > 0:
-
         if longlist is True:
             header = "[app]              [root]"
             bot.custom(prefix="SCIF", message=header, color="CYAN")

scif/client/preview.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     apps = args.recipe

scif/client/pyshell.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -17,7 +17,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.defaults import SCIF_SHELL as shell
 
     parsed = parse_input_preferences(args.recipe, quiet=args.quiet)
@@ -54,8 +53,7 @@ def main(args, parser, subparser):
 
 
 def ipython(recipe, app=None, quiet=False, writable=True):
-    """embed the client with loaded recipe into an ipython session
-    """
+    """embed the client with loaded recipe into an ipython session"""
     from scif.main import ScifRecipe
     from IPython import embed
 

scif/client/run.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2016-2020 Vanessa Sochat.
+Copyright (C) 2016-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -16,7 +16,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     cmd = args.cmd

scif/client/shell.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -18,7 +18,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     app = args.app

scif/client/test.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2016-2020 Vanessa Sochat.
+Copyright (C) 2016-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -16,7 +16,6 @@
 
 
 def main(args, parser, subparser):
-
     from scif.main import ScifRecipe
 
     cmd = args.cmd

scif/client/utils.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -21,11 +21,11 @@
 def parse_input_preferences(recipe, quiet=False):
     """parse a recipe|app, meaning a list of one or more things that could be
 
-       any of the following:
+    any of the following:
 
-        Returns
-        =======
-        parsed: a dictionary lookup with keys for app, recipe, and quiet.
+     Returns
+     =======
+     parsed: a dictionary lookup with keys for app, recipe, and quiet.
     """
 
     # if coming from inspect, will be string
@@ -34,14 +34,12 @@ def parse_input_preferences(recipe, quiet=False):
 
     # First case: recipe and app
     if len(recipe) > 1:
-
         app = recipe[1]
         recipe = recipe[0]
         quiet = True
 
     # Second case, no input or recipe|app
     else:
-
         app = None
 
         # If no recipe provided, assume loading base

scif/defaults.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -31,14 +31,14 @@ def convert2boolean(arg):
 
 
 def getenv(variable_key, default=None, required=False, silent=True):
-    """ getenv will attempt to get an environment variable. If the variable
-        is not found, None is returned.
-
-        Paramters
-        =========
-        variable_key: the variable name
-        required: exit with error if not found
-        silent: Do not print debugging information for variable
+    """getenv will attempt to get an environment variable. If the variable
+    is not found, None is returned.
+
+    Paramters
+    =========
+    variable_key: the variable name
+    required: exit with error if not found
+    silent: Do not print debugging information for variable
     """
     variable = os.environ.get(variable_key, default)
     if variable is None and required:
@@ -52,12 +52,12 @@ def getenv(variable_key, default=None, required=False, silent=True):
 
 def getenv_namespace(namespace="SCIF", func=None):
     """return all environment variables in a particular namespace, such as for
-       SCIF apps using a filter function (func). The function should take first
-       a key in the environment, and then the namespace variable. 
-       If none provided, uses "starts with" equivalent.
+    SCIF apps using a filter function (func). The function should take first
+    a key in the environment, and then the namespace variable.
+    If none provided, uses "starts with" equivalent.
 
-        def func(key, namespace):
-            return key.startswith(namespace)
+     def func(key, namespace):
+         return key.startswith(namespace)
     """
     if func is None:
         """does key start with namespace?"""

scif/logger/message.py

@@ -1,6 +1,6 @@
 """
 
-Copyright (C) 2017-2020 Vanessa Sochat.
+Copyright (C) 2017-2024 Vanessa Sochat.
 
 This Source Code Form is subject to the terms of the
 Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
@@ -106,8 +106,7 @@ def emitOutput(self, level):
         return False
 
     def isEnabledFor(self, messageLevel):
-        """check if a messageLevel is enabled to emit a level
-        """
+        """check if a messageLevel is enabled to emit a level"""
         if messageLevel <= self.level:
             return True
         return False
@@ -262,16 +261,15 @@ def debug(self, message):
         self.emit(DEBUG, message, "DEBUG")
 
     def is_quiet(self):
-        """is_quiet returns true if the level is under 1
-        """
+        """is_quiet returns true if the level is under 1"""
         if self.level < 1:
             return False
         return True
 
     # Terminal ------------------------------------------
 
     def table(self, rows, col_width=2):
-        """table will print a table of entries. If the rows is 
+        """table will print a table of entries. If the rows is
         a dictionary, the keys are interpreted as column names. if
         not, a numbered list is used.
         """