Merge pull request #73 from NanoNLP/development

API updates
NLPatVCU · Jan 2, 2019 · ab5cce4 · ab5cce4
2 parents 79b5c8c + 1ccda7e
commit ab5cce4
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diff --git a/.gitignore b/.gitignore
@@ -64,7 +64,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/build/
+docs/source/medacy*
 
 # PyBuilder
 target/

diff --git a/README.md b/README.md
@@ -12,12 +12,13 @@ MedaCy is a text processing and learning framework built over [spaCy](https://sp
 - Customizable pipelines with detailed development instructions and documentation.
 - Allows the designing of replicable NLP systems for reproducing results and encouraging the distribution of models whilst still allowing for privacy.
 - Active community development spearheaded and maintained by [NLP@VCU](https://nlp.cs.vcu.edu/).
+- Detailed [API](https://medacy.readthedocs.io/en/latest/)
 
 ## :thought_balloon: Where to ask questions
 
 MedaCy is actively maintained by  [@AndriyMulyar](https://github.com/AndriyMulyar)
 and [@CoreySutphin](https://github.com/CoreySutphin). The best way to
-receive immediate responses to any questions is to raise an issue. See how to formulate a good issue or feature request in the [Contribution Guide](CONTRIBUTING.md).
+receive immediate responses to any questions is to raise an issue. Make sure to first consult the [API](https://medacy.readthedocs.io/en/latest/).  See how to formulate a good issue or feature request in the [Contribution Guide](CONTRIBUTING.md).
 
 ## :computer: Installation Instructions
 Medacy can be installed for general use or for pipeline development / research purposes.

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -42,11 +42,17 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.coverage',
+    'sphinx.ext.napoleon',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
 ]
 
+autodoc_default_options = {
+    'members': None,
+    'private-members': None
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

diff --git a/docs/source/medacy.model.rst b/docs/source/medacy.model.rst
@@ -1,27 +1,27 @@
-medacy\.model package
-=====================
+medacy.model package
+====================
 
 Submodules
 ----------
 
-medacy\.model\.feature\_extractor module
-----------------------------------------
+medacy.model.feature\_extractor module
+--------------------------------------
 
 .. automodule:: medacy.model.feature_extractor
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.model\.model module
----------------------------
+medacy.model.model module
+-------------------------
 
 .. automodule:: medacy.model.model
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.model\.stratified\_k\_fold module
------------------------------------------
+medacy.model.stratified\_k\_fold module
+---------------------------------------
 
 .. automodule:: medacy.model.stratified_k_fold
     :members:

diff --git a/docs/source/medacy.pipeline_components.annotation.rst b/docs/source/medacy.pipeline_components.annotation.rst
@@ -1,11 +1,11 @@
-medacy\.pipeline\_components\.annotation package
-================================================
+medacy.pipeline\_components.annotation package
+==============================================
 
 Submodules
 ----------
 
-medacy\.pipeline\_components\.annotation\.gold\_annotator\_component module
----------------------------------------------------------------------------
+medacy.pipeline\_components.annotation.gold\_annotator\_component module
+------------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.annotation.gold_annotator_component
     :members:

diff --git a/docs/source/medacy.pipeline_components.base.rst b/docs/source/medacy.pipeline_components.base.rst
@@ -1,11 +1,11 @@
-medacy\.pipeline\_components\.base package
-==========================================
+medacy.pipeline\_components.base package
+========================================
 
 Submodules
 ----------
 
-medacy\.pipeline\_components\.base\.base\_component module
-----------------------------------------------------------
+medacy.pipeline\_components.base.base\_component module
+-------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.base.base_component
     :members:

diff --git a/docs/source/medacy.pipeline_components.metamap.rst b/docs/source/medacy.pipeline_components.metamap.rst
@@ -1,41 +1,25 @@
-medacy\.pipeline\_components\.metamap package
-=============================================
+medacy.pipeline\_components.metamap package
+===========================================
 
 Submodules
 ----------
 
-medacy\.pipeline\_components\.metamap\.converter module
--------------------------------------------------------
-
-.. automodule:: medacy.pipeline_components.metamap.converter
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-medacy\.pipeline\_components\.metamap\.metamap module
------------------------------------------------------
+medacy.pipeline\_components.metamap.metamap module
+--------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.metamap.metamap
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.metamap\.metamap\_component module
-----------------------------------------------------------------
+medacy.pipeline\_components.metamap.metamap\_component module
+-------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.metamap.metamap_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.metamap\.unic2ascii module
---------------------------------------------------------
-
-.. automodule:: medacy.pipeline_components.metamap.unic2ascii
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 
 Module contents
 ---------------

diff --git a/docs/source/medacy.pipeline_components.rst b/docs/source/medacy.pipeline_components.rst
@@ -1,5 +1,5 @@
-medacy\.pipeline\_components package
-====================================
+medacy.pipeline\_components package
+===================================
 
 Subpackages
 -----------

diff --git a/docs/source/medacy.pipeline_components.tokenization.rst b/docs/source/medacy.pipeline_components.tokenization.rst
@@ -1,27 +1,27 @@
-medacy\.pipeline\_components\.tokenization package
-==================================================
+medacy.pipeline\_components.tokenization package
+================================================
 
 Submodules
 ----------
 
-medacy\.pipeline\_components\.tokenization\.character\_tokenizer module
------------------------------------------------------------------------
+medacy.pipeline\_components.tokenization.character\_tokenizer module
+--------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.tokenization.character_tokenizer
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.tokenization\.clinical\_tokenizer module
-----------------------------------------------------------------------
+medacy.pipeline\_components.tokenization.clinical\_tokenizer module
+-------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.tokenization.clinical_tokenizer
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.tokenization\.systematic\_review\_tokenizer module
---------------------------------------------------------------------------------
+medacy.pipeline\_components.tokenization.systematic\_review\_tokenizer module
+-----------------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.tokenization.systematic_review_tokenizer
     :members:

diff --git a/docs/source/medacy.pipeline_components.units.rst b/docs/source/medacy.pipeline_components.units.rst
@@ -1,59 +1,59 @@
-medacy\.pipeline\_components\.units package
-===========================================
+medacy.pipeline\_components.units package
+=========================================
 
 Submodules
 ----------
 
-medacy\.pipeline\_components\.units\.frequency\_unit\_component module
-----------------------------------------------------------------------
+medacy.pipeline\_components.units.frequency\_unit\_component module
+-------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.frequency_unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.mass\_unit\_component module
------------------------------------------------------------------
+medacy.pipeline\_components.units.mass\_unit\_component module
+--------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.mass_unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.measurement\_unit\_component module
-------------------------------------------------------------------------
+medacy.pipeline\_components.units.measurement\_unit\_component module
+---------------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.measurement_unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.route\_unit\_component module
-------------------------------------------------------------------
+medacy.pipeline\_components.units.route\_unit\_component module
+---------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.route_unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.time\_unit\_component module
------------------------------------------------------------------
+medacy.pipeline\_components.units.time\_unit\_component module
+--------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.time_unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.unit\_component module
------------------------------------------------------------
+medacy.pipeline\_components.units.unit\_component module
+--------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.unit_component
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipeline\_components\.units\.volume\_unit\_component module
--------------------------------------------------------------------
+medacy.pipeline\_components.units.volume\_unit\_component module
+----------------------------------------------------------------
 
 .. automodule:: medacy.pipeline_components.units.volume_unit_component
     :members:

diff --git a/docs/source/medacy.pipelines.base.rst b/docs/source/medacy.pipelines.base.rst
@@ -1,11 +1,11 @@
-medacy\.pipelines\.base package
-===============================
+medacy.pipelines.base package
+=============================
 
 Submodules
 ----------
 
-medacy\.pipelines\.base\.base\_pipeline module
-----------------------------------------------
+medacy.pipelines.base.base\_pipeline module
+-------------------------------------------
 
 .. automodule:: medacy.pipelines.base.base_pipeline
     :members:

diff --git a/docs/source/medacy.pipelines.rst b/docs/source/medacy.pipelines.rst
@@ -1,5 +1,5 @@
-medacy\.pipelines package
-=========================
+medacy.pipelines package
+========================
 
 Subpackages
 -----------
@@ -11,30 +11,38 @@ Subpackages
 Submodules
 ----------
 
-medacy\.pipelines\.clinical\_pipeline module
---------------------------------------------
+medacy.pipelines.clinical\_pipeline module
+------------------------------------------
 
 .. automodule:: medacy.pipelines.clinical_pipeline
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipelines\.fda\_nano\_drug\_label\_pipeline module
-----------------------------------------------------------
+medacy.pipelines.fda\_nano\_drug\_label\_pipeline module
+--------------------------------------------------------
 
 .. automodule:: medacy.pipelines.fda_nano_drug_label_pipeline
     :members:
     :undoc-members:
     :show-inheritance:
 
-medacy\.pipelines\.systematic\_review\_pipeline module
-------------------------------------------------------
+medacy.pipelines.systematic\_review\_pipeline module
+----------------------------------------------------
 
 .. automodule:: medacy.pipelines.systematic_review_pipeline
     :members:
     :undoc-members:
     :show-inheritance:
 
+medacy.pipelines.testing\_pipeline module
+-----------------------------------------
+
+.. automodule:: medacy.pipelines.testing_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

diff --git a/docs/source/medacy.rst b/docs/source/medacy.rst
@@ -6,9 +6,11 @@ Subpackages
 
 .. toctree::
 
+    medacy.data
     medacy.model
     medacy.pipeline_components
     medacy.pipelines
+    medacy.tests
     medacy.tools
 
 Module contents