Fixing typos, code formatting

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+extend-ignore = E203,E501
+exclude = .git,__pycache__,docs/source/conf.py,old,build,dist
+max-complexity = 10

.github/workflows/build_check.yml

@@ -2,14 +2,14 @@ name: build_and_test
 
 on:
   push:
-    branches: 
+    branches:
       - master
   workflow_dispatch:
 
 jobs:
   build_and_test:
     runs-on: ubuntu-20.04
-    timeout-minutes: 60    
+    timeout-minutes: 60
     steps:
       - uses: actions/checkout@v2
       - name: Setup conda, install packages, and test celloracle
@@ -29,7 +29,7 @@ jobs:
             # command to install dependencies
             conda activate test-environment
             conda install cython numpy pytest
-            
+
             # Check pip
             echo pip_path
             which pip

.github/workflows/build_weekly_check.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   build_and_test:
     runs-on: ubuntu-20.04
-    timeout-minutes: 60    
+    timeout-minutes: 60
     steps:
       - uses: actions/checkout@v2
       - name: Setup conda, install packages, and test celloracle
@@ -28,13 +28,13 @@ jobs:
             # command to install dependencies
             conda activate test-environment
             conda install cython numpy pytest
-            
+
             conda list
             ls /home/runner/miniconda
             ls /home/runner/miniconda/bin
-            
+
             python --version
-            
+
             which pip
             #Install fa2 for tutorial
             pip install fa2
@@ -44,5 +44,3 @@ jobs:
             pip install .
             # command to run tests
             pytest -v
-
-

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+    - id: black
+#-   repo: https://github.com/PyCQA/flake8
+#    rev: 5.0.4
+#    hooks:
+#    - id: flake8
+#      additional_dependencies:
+#      - Flake8-pyproject
+#      - flake8-bugbear
+#      - flake8-comprehensions
+#      - flake8-executable
+#      - mccabe

celloracle/__init__.py

@@ -5,39 +5,55 @@
 import warnings
 import logging
 
-from . import utility, network, network_analysis, go_analysis, data, data_conversion, oracle_utility
+from . import (
+    utility,
+    network,
+    network_analysis,
+    go_analysis,
+    data,
+    data_conversion,
+    oracle_utility,
+)
 from .trajectory.oracle_core import Oracle
 from .network import Net
 from .network_analysis import Links
 from .utility.load_hdf5 import load_hdf5
 from .utility import check_python_requirements
 from .network_analysis import test_R_libraries_installation
 from .version import __version__
-#from . import motif_analysis
+
+# from . import motif_analysis
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.StreamHandler())
 logger.setLevel(logging.INFO)
 
 
 # Make sure that DeprecationWarning within this package always gets printed
-warnings.filterwarnings('always', category=DeprecationWarning,
-                        module=r'^{0}\.'.format(re.escape(__name__)))
-
-__copyright__    = 'Copyright (C) 2020 Kenji Kamimoto'
-__license__      = 'Apache License Version 2.0'
-__author__       = 'Kenji Kamimoto'
-__author_email__ = 'kamimoto@wustl.edu'
-__url__          = 'https://github.com/morris-lab/CellOracle'
-#__version__ = "0.10.2"
-__all__ = ["utility", "motif_analysis", "network", "network_analysis",
-           "go_analysis", "data", "data_conversion",
-           "Oracle",
-           "Links",
-           "Net",
-           "load_hdf5",
-           "test_R_libraries_installation",
-           "check_python_requirements"
-           ]
+warnings.filterwarnings(
+    "always", category=DeprecationWarning, module=r"^{0}\.".format(re.escape(__name__))
+)
+
+__copyright__ = "Copyright (C) 2020 Kenji Kamimoto"
+__license__ = "Apache License Version 2.0"
+__author__ = "Kenji Kamimoto"
+__author_email__ = "kamimoto@wustl.edu"
+__url__ = "https://github.com/morris-lab/CellOracle"
+# __version__ = "0.10.2"
+__all__ = [
+    "utility",
+    "motif_analysis",
+    "network",
+    "network_analysis",
+    "go_analysis",
+    "data",
+    "data_conversion",
+    "Oracle",
+    "Links",
+    "Net",
+    "load_hdf5",
+    "test_R_libraries_installation",
+    "check_python_requirements",
+]
 
 check_python_requirements(return_detail=False, print_warning=True)

celloracle/applications/__init__.py

@@ -4,14 +4,23 @@
 
 """
 
-#from .interactive_simulation_and_plot import Oracle_extended, DEFAULT_PARAMETERS
-#from .development_analysis import Oracle_development_module, subset_oracle_for_development_analysiis
+# from .interactive_simulation_and_plot import Oracle_extended, DEFAULT_PARAMETERS
+# from .development_analysis import Oracle_development_module, subset_oracle_for_development_analysiis
 from .pseudotime import Pseudotime_calculator
-from .differentiation_flow import load_gradient, Gradient_calculator, aggregate_Gradient_objects
+from .differentiation_flow import (
+    load_gradient,
+    Gradient_calculator,
+    aggregate_Gradient_objects,
+)
 from .development_module import Oracle_development_module
 from .systematic_analysis_helper import Oracle_systematic_analysis_helper
 
 
-__all__ = ["Pseudotime_calculator",
-            "load_gradient", "Gradient_calculator", "aggregate_Gradient_objects",
-           "Oracle_development_module", "Oracle_systematic_analysis_helper"]
+__all__ = [
+    "Pseudotime_calculator",
+    "load_gradient",
+    "Gradient_calculator",
+    "aggregate_Gradient_objects",
+    "Oracle_development_module",
+    "Oracle_systematic_analysis_helper",
+]