update documentation

Author: khillion

.gitignore

@@ -1,2 +1,3 @@
 test/__pycache__
 cwlgen/__pycache__
+doc/build/

README.md

@@ -17,7 +17,7 @@ The library works for both Python 2.7.12+ and 3.6.0.
 You can install python-cwlgen using pip with the following command:
 
 ```bash
-pip install git+https://github.com/common-workflow-language/python-cwlgen.git#egg=python-cwlgen
+pip install cwlgen
 ```
 
 ## How it works ?

doc/source/changelogs.rst

@@ -0,0 +1,29 @@
+.. python-cwlgen - Python library for manipulation and generation of CWL tools.
+
+.. _changelogs:
+
+**********
+Changelogs
+**********
+
+Summary of developments of Python-cwlgen library.
+
+v0.2
+====
+
+v0.2.0
+------
+
+* Add import feature for what is covered so far by the library
+* Change attribute names of object to correspond exactly to CWL Tool fields
+
+v0.1
+====
+
+v0.1.1
+------
+
+This is the first release of Python-cwlgen:
+
+* Basic model of CWL Tool
+* export feature to STDOUT or output file

doc/source/classes.rst

@@ -18,6 +18,7 @@ CommandLineTool
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 .. _in_out:
 
@@ -31,6 +32,7 @@ CommandInputParameter
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 CommandOutputParameter
 """"""""""""""""""""""
@@ -39,6 +41,7 @@ CommandOutputParameter
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 CommandLineBinding
 """"""""""""""""""
@@ -47,6 +50,7 @@ CommandLineBinding
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 CommandOutputBinding
 """"""""""""""""""""
@@ -55,6 +59,7 @@ CommandOutputBinding
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 .. _requirements:
 
@@ -68,6 +73,7 @@ Requirement
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 InlineJavascriptReq
 """""""""""""""""""
@@ -76,6 +82,7 @@ InlineJavascriptReq
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
 
 DockerRequirement
 """""""""""""""""
@@ -84,3 +91,52 @@ DockerRequirement
    :members:
    :private-members:
    :special-members:
+   :exclude-members: __weakref__
+
+Import CWL
+==========
+
+CWLToolParser
+"""""""""""""
+
+.. autoclass:: cwlgen.import_cwl.CWLToolParser
+   :members:
+   :private-members:
+   :special-members:
+   :exclude-members: __weakref__
+
+InputsParser
+""""""""""""
+
+.. autoclass:: cwlgen.import_cwl.InputsParser
+   :members:
+   :private-members:
+   :special-members:
+   :exclude-members: __weakref__
+
+InputBindingParser
+""""""""""""""""""
+
+.. autoclass:: cwlgen.import_cwl.InputBindingParser
+   :members:
+   :private-members:
+   :special-members:
+   :exclude-members: __weakref__
+
+OutputsParser
+"""""""""""""
+
+.. autoclass:: cwlgen.import_cwl.OutputsParser
+   :members:
+   :private-members:
+   :special-members:
+   :exclude-members: __weakref__
+
+OutputBindingParser
+"""""""""""""""""""
+
+.. autoclass:: cwlgen.import_cwl.OutputBindingParser
+   :members:
+   :private-members:
+   :special-members:
+   :exclude-members: __weakref__

doc/source/index.rst

@@ -20,6 +20,7 @@ Python-cwlgen API documentation
    :maxdepth: 2
 
    classes
+   changelogs
 
 ..
   Indices and tables

doc/source/installation.rst

@@ -24,9 +24,22 @@ Installation procedure
 Pip
 ---
 
-You can use pip to install directly for the git repository::
+You can use pip to install the latest version from pypi:
 
-    pip install git+https://github.com/common-workflow-language/python-cwlgen.git#egg=python-cwlgen
+.. code-block:: bash
+
+    pip install cwlgen
+
+Manually
+--------
+
+Clone the repository and install cwlgen with the following command:
+
+.. code-block:: bash
+
+    git clone https://github.com/common-workflow-language/python-cwlgen.git
+    cd python-cwlgen
+    pip install .
 
 .. _uninstallation:
 
@@ -36,6 +49,13 @@ Uninstallation procedure
 Pip
 ---
 
-You can remove python-cwlgen with the following command::
+You can remove python-cwlgen with the following command:
+
+.. code-block:: bash
 
     pip uninstall python-cwlgen
+
+.. Note::
+    This will not uninstall dependencies. To do so you can make use of `pip-autoremove`_.
+
+.. _pip-autoremove: https://github.com/invl/pip-autoremove