Merge pull request #18 from suecharo/fix-docs

Fix docs

Author: giannisdoukas

README.md

@@ -16,12 +16,12 @@ from ipython2cwl.iotypes import CWLFilePathInput, CWLFilePathOutput
 import csv
 input_filename: 'CWLFilePathInput' = 'data.csv'
 with open(input_filename) as f:
-  csv_reader = csv.reader(f)
-  data = [line for line in csv_reader]
+    csv_reader = csv.reader(f)
+    data = [line for line in csv_reader]
 number_of_lines = len(data)
 result_file: 'CWLFilePathOutput' = 'number_of_lines.txt'
 with open(result_file, 'w') as f:
-  f.write(str(number_of_lines))
+    f.write(str(number_of_lines))
 ```
 
 IPython2CWL is based on [repo2docker](https://github.com/jupyter/repo2docker), the same tool
@@ -37,7 +37,7 @@ pip install ipython2cwl
 ```
 
 ### Example
- 
+
 ```
 jupyter repo2cwl https://github.com/giannisdoukas/cwl-annotated-jupyter-notebook.git -o .
 ```

docs/index.rst

@@ -21,12 +21,12 @@ IPython2CWL is a tool for converting `IPython <https://ipython.org/>`_ Jupyter N
     import csv
     input_filename: 'CWLFilePathInput' = 'data.csv'
     with open(input_filename) as f:
-      csv_reader = csv.reader(f)
-      data = [line for line in csv_reader]
+        csv_reader = csv.reader(f)
+        data = [line for line in csv_reader]
     number_of_lines = len(data)
     result_file: 'CWLFilePathOutput' = 'number_of_lines.txt'
     with open(result_file, 'w') as f:
-      f.write(str(number_of_lines))
+        f.write(str(number_of_lines))
 
 
 ------------------------------------------------------------------------------------------
@@ -79,4 +79,3 @@ WHAT IF I WANT TO VALIDATE THAT THE GENERATED SCRIPTS ARE CORRECT?
 
 All the generated scripts are stored in the docker image under the directory :code:`/app/cwl/bin`. You can see the list
 of the files by running :code:`docker run [IMAGE_ID] find /app/cwl/bin/ -type f`.
-

ipython2cwl/iotypes.py

@@ -65,13 +65,13 @@ class CWLBooleanInput(_CWLInput):
 
 class CWLStringInput(str, _CWLInput):
     """Use that hint to annotate that a variable is a string input. You can use the typing annotation
-        as a string by importing it. At the generated script a command line argument with the name of the variable
-        will be created and the assignment of value will be generalised.
+    as a string by importing it. At the generated script a command line argument with the name of the variable
+    will be created and the assignment of value will be generalised.
 
-        >>> dataset1: CWLBooleanInput = 'this is a message input'
-        >>> dataset2: 'CWLBooleanInput' = 'yet another message input'
+    >>> dataset1: CWLStringInput = 'this is a message input'
+    >>> dataset2: 'CWLStringInput' = 'yet another message input'
 
-        """
+    """
     pass
 
 
@@ -80,8 +80,8 @@ class CWLIntInput(_CWLInput):
     as a string by importing it. At the generated script a command line argument with the name of the variable
     will be created and the assignment of value will be generalised.
 
-    >>> dataset1: CWLBooleanInput = 1
-    >>> dataset2: 'CWLBooleanInput' = 2
+    >>> dataset1: CWLIntInput = 1
+    >>> dataset2: 'CWLIntInput' = 2
 
     """
     pass
@@ -95,7 +95,7 @@ class CWLFilePathOutput(str, _CWLOutput):
     """Use that hint to annotate that a variable is a string-path to an output file. You can use the typing annotation
     as a string by importing it. The generated file will be mapped as a CWL output.
 
-    >>> filename: CWLBooleanInput = 'data.csv'
+    >>> filename: CWLFilePathOutput = 'data.csv'
 
     """
     pass
@@ -111,7 +111,7 @@ def dump(cls, dumper: Callable, filename, *args, **kwargs):
 
         >>> import pandas
         >>> d: CWLDumpable.dump(d.to_csv, "dumpable.csv", sep="\\t", index=False) = pandas.DataFrame(
-        ...     [[1,2,3], [4,5,6], [7,8,9]]
+        ...     [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
         ... )
 
         In that example the converter will add at the end of the script the following line:
@@ -132,14 +132,11 @@ class CWLDumpableFile(CWLDumpable):
 
     >>> data: CWLDumpableFile = "this is text data"
 
-
     the converter will append at the end of the script the following lines:
 
-
     >>> with open('data', 'w') as f:
     ...     f.write(data)
 
-
     and at the CWL, the data, will be mapped as a output.
     """
     pass
@@ -165,14 +162,14 @@ class CWLPNGPlot(CWLDumpable):
     be called.
 
     >>> import matplotlib.pyplot as plt
-    >>> data = [1,2,3]
-    >>> new_data: 'CWLPNGPlot' = plt.plot(data)
+    >>> data = [1, 2, 3]
+    >>> new_data: CWLPNGPlot = plt.plot(data)
 
     the converter will tranform these lines to
 
     >>> import matplotlib.pyplot as plt
-    >>> data = [1,2,3]
-    >>> new_data: 'CWLPNGPlot' = plt.plot(data)
+    >>> data = [1, 2, 3]
+    >>> new_data: CWLPNGPlot = plt.plot(data)
     >>> plt.savefig('new_data.png')
 
 
@@ -181,9 +178,9 @@ class CWLPNGPlot(CWLDumpable):
     To do that in your notebook you have to create a new figure before the plot command or use the CWLPNGFigure.
 
     >>> import matplotlib.pyplot as plt
-    >>> data = [1,2,3]
+    >>> data = [1, 2, 3]
     >>> plt.figure()
-    >>> new_data: 'CWLPNGPlot' = plt.plot(data)
+    >>> new_data: CWLPNGPlot = plt.plot(data)
     """
     pass
 
@@ -194,14 +191,13 @@ class CWLPNGFigure(CWLDumpable):
 
     >>> import matplotlib.pyplot as plt
     >>> data = [1,2,3]
-    >>> new_data: 'CWLPNGPlot' = plt.plot(data)
+    >>> new_data: CWLPNGFigure = plt.plot(data)
 
     the converter will tranform these lines to
 
     >>> import matplotlib.pyplot as plt
-    >>> data = [1,2,3]
+    >>> data = [1, 2, 3]
     >>> plt.figure()
-    >>> new_data: 'CWLPNGPlot' = plt.plot(data)
+    >>> new_data: CWLPNGFigure = plt.plot(data)
     >>> plt.savefig('new_data.png')
-
     """