Format code

README.md

@@ -47,7 +47,7 @@ Our goal is to make analyzing neural networks' predictions easy!
 
 iNNvestigate can be installed with the following commands.
 The library is based on Keras and therefore requires a supported [Keras-backend](https://keras.io/backend/)
-o(Currently only the Tensorflow backend is supported. We test with Python 3.6, Tensorflow 1.12 and Cuda 9.x.):
+o(Currently only the TensorFlow backend is supported. We test with Python 3.6, TensorFlow 1.12 and Cuda 9.x.):
 
 ```bash
 pip install innvestigate
@@ -82,7 +82,7 @@ The iNNvestigate library contains implementations for the following methods:
 * *attribution:*
   * **input_t_gradient:** Input \* Gradient
   * **deep_taylor[.bounded]:** [DeepTaylor](https://www.sciencedirect.com/science/article/pii/S0031320316303582?via%3Dihub) computes for each neuron a rootpoint, that is close to the input, but which's output value is 0, and uses this difference to estimate the attribution of each neuron recursively.
-  * **pattern.attribution:** [PatternAttribution](https://arxiv.org/abs/1705.05598) applies Deep Taylor by searching rootpoints along the singal direction of each neuron.
+  * **pattern.attribution:** [PatternAttribution](https://arxiv.org/abs/1705.05598) applies Deep Taylor by searching root points along the signal direction of each neuron.
   * **lrp.\*:** [LRP](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130140) attributes recursively to each neuron's input relevance proportional to its contribution of the neuron output.
   * **integrated_gradients:** [IntegratedGradients](https://arxiv.org/abs/1703.01365) integrates the gradient along a path from the input to a reference.
   * **deeplift.wrapper:** [DeepLIFT (wrapper around original code, slower)](http://proceedings.mlr.press/v70/shrikumar17a.html) computes a backpropagation based on "finite" gradients.

docs/source/conf.py

@@ -14,19 +14,20 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'iNNvestigate'
-copyright = '2018, Maximilian Alber'
-author = 'Maximilian Alber'
+project = "iNNvestigate"
+copyright = "2018, Maximilian Alber"
+author = "Maximilian Alber"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = 'not set'
+release = "not set"
 
 
 # -- General configuration ---------------------------------------------------
@@ -39,21 +40,21 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.mathjax',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -68,15 +69,15 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -87,7 +88,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -103,7 +104,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'iNNvestigatedoc'
+htmlhelp_basename = "iNNvestigatedoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -112,15 +113,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -130,19 +128,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'iNNvestigate.tex', 'iNNvestigate Documentation',
-     'Maximilian Alber', 'manual'),
+    (
+        master_doc,
+        "iNNvestigate.tex",
+        "iNNvestigate Documentation",
+        "Maximilian Alber",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'innvestigate', 'iNNvestigate Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "innvestigate", "iNNvestigate Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -151,10 +151,16 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'iNNvestigate', 'iNNvestigate Documentation',
-     author, 'iNNvestigate', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "iNNvestigate",
+        "iNNvestigate Documentation",
+        author,
+        "iNNvestigate",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
-# -- Extension configuration -------------------------------------------------
+# -- Extension configuration -------------------------------------------------

examples/embedding_minimal_example.py

@@ -1,18 +1,21 @@
-from keras import Sequential
-from keras.layers import Dense, Conv1D, Embedding, GlobalMaxPooling1D
 import numpy as np
+from keras import Sequential
+from keras.layers import Conv1D, Dense, Embedding, GlobalMaxPooling1D
+
 import innvestigate
 
 model = Sequential()
 model.add(Embedding(input_dim=219, output_dim=8))
-model.add(Conv1D(filters=64, kernel_size=8, padding='valid', activation='relu'))
+model.add(Conv1D(filters=64, kernel_size=8, padding="valid", activation="relu"))
 model.add(GlobalMaxPooling1D())
-model.add(Dense(16, activation='relu'))
+model.add(Dense(16, activation="relu"))
 model.add(Dense(2, activation=None))
 
-#test
-model.predict(np.random.randint(1, 219, (1,100)))  # [[0.04913538 0.04234646]]
+# test
+model.predict(np.random.randint(1, 219, (1, 100)))  # [[0.04913538 0.04234646]]
 
-analyzer = innvestigate.create_analyzer('lrp.epsilon', model, neuron_selection_mode='max_activation', **{'epsilon': 1})
-a = analyzer.analyze(np.random.randint(1, 219, (1,100)))
+analyzer = innvestigate.create_analyzer(
+    "lrp.epsilon", model, neuron_selection_mode="max_activation", **{"epsilon": 1}
+)
+a = analyzer.analyze(np.random.randint(1, 219, (1, 100)))
 print(a[0], a[0].shape)

examples/nbconvert.py

@@ -1,12 +1,19 @@
 # Begin: Python 2/3 compatibility header small
 # Get Python 3 functionality:
-from __future__ import\
-    absolute_import, print_function, division, unicode_literals
-from future.utils import raise_with_traceback, raise_from
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+import argparse
+import os
+import subprocess
+import sys
+
 # catch exception with: except Exception as e
-from builtins import range, map, zip, filter
+from builtins import filter, map, range, zip
 from io import open
+
 import six
+from future.utils import raise_from, raise_with_traceback
+
 # End: Python 2/3 compatability header small
 
 
@@ -15,20 +22,15 @@
 ###############################################################################
 
 
-import argparse
-import os
-import sys
-import subprocess
-
-
 ###############################################################################
 ###############################################################################
 ###############################################################################
 
 
 if __name__ == "__main__":
+
     def is_executable(filepath):
-        #determine whether the target file exists and is executable
+        # determine whether the target file exists and is executable
         return os.path.isfile(filepath) and os.access(filepath, os.X_OK)
 
     # Try jupyter binary that is the same directory as the running python.
@@ -38,13 +40,14 @@ def is_executable(filepath):
 
     if not is_executable(jupyter_executable):
         # Fallback to find any jupyter (and hope for the best).
-        jupyter_executable = subprocess.check_output(["which jupyter"],
-                                                     shell=True).strip()
-
-    #assert a valid executable of jupyter has been found
-    assert is_executable(jupyter_executable), 'No executable for "jupyter" could be found'
-
+        jupyter_executable = subprocess.check_output(
+            ["which jupyter"], shell=True
+        ).strip()
 
+    # assert a valid executable of jupyter has been found
+    assert is_executable(
+        jupyter_executable
+    ), 'No executable for "jupyter" could be found'
 
     # Get all notebooks
     notebook_dir = os.path.join(os.path.dirname(__file__), "notebooks")
@@ -55,10 +58,13 @@ def is_executable(filepath):
         os.makedirs(output_dir)
 
     parser = argparse.ArgumentParser(
-        description="Script to handle the example notebooks via command line.")
+        description="Script to handle the example notebooks via command line."
+    )
     parser.add_argument(
-        'command', choices=["execute", "to_script", "to_script_and_execute"],
-        help="What to do.")
+        "command",
+        choices=["execute", "to_script", "to_script_and_execute"],
+        help="What to do.",
+    )
     args = parser.parse_args()
 
     if args.command == "execute":
@@ -71,24 +77,28 @@ def is_executable(filepath):
             print()
 
             call = [
-                jupyter_executable, "nbconvert",
+                jupyter_executable,
+                "nbconvert",
                 "--output-dir='%s'" % output_dir,
                 "--ExecutePreprocessor.timeout=-1",
-                "--to", "notebook", "--execute",
-                os.path.join(notebook_dir, notebook)
+                "--to",
+                "notebook",
+                "--execute",
+                os.path.join(notebook_dir, notebook),
             ]
             subprocess.check_call(call)
     elif args.command in ["to_script", "to_script_and_execute"]:
         for notebook in notebooks:
             print("Convert notebook:", notebook)
             input_file = os.path.join(notebook_dir, notebook)
-            output_file = os.path.join(
-                output_dir, notebook.replace(".ipynb", ".py"))
+            output_file = os.path.join(output_dir, notebook.replace(".ipynb", ".py"))
 
             call = [
-                jupyter_executable, "nbconvert",
+                jupyter_executable,
+                "nbconvert",
                 "--output-dir='%s'" % output_dir,
-                "--to", "script",
+                "--to",
+                "script",
                 input_file,
             ]
             subprocess.check_call(call)
@@ -108,7 +118,7 @@ def is_executable(filepath):
 
             if args.command == "to_script_and_execute":
                 subprocess.check_call(
-                    [sys.executable, notebook.replace(".ipynb", ".py")],
-                    cwd=output_dir)
+                    [sys.executable, notebook.replace(".ipynb", ".py")], cwd=output_dir
+                )
     else:
         raise ValueError("Command not recognized")