Merge pull request #120 from NLPatVCU/development

Version v0.1.0
NLPatVCU · Mar 29, 2019 · 0f0ced0 · 0f0ced0
2 parents 3c1c616 + 24c4604
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diff --git a/README.md b/README.md
@@ -34,7 +34,7 @@ Medacy can be installed for general use or for pipeline development / research p
 After installing medaCy and [medaCy's clinical model](examples/models/clinical_notes_model.md), simply run:
 
 ```python
-from medacy.model import Model
+from medacy.ner.model import Model
 
 model = Model.load_external('medacy_model_clinical_notes')
 annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.")

diff --git a/docs/source/medacy.model.feature_extractor.rst b/docs/source/medacy.model.feature_extractor.rst
diff --git a/docs/source/medacy.model.rst b/docs/source/medacy.model.rst
diff --git a/docs/source/medacy.model.model.rst → docs/source/medacy.ner.model.model.rst b/docs/source/medacy.model.model.rst → docs/source/medacy.ner.model.model.rst
@@ -1,7 +1,7 @@
-medacy.model.model module
+medacy.ner.model.model module
 =========================
 
-.. automodule:: medacy.model.model
+.. automodule:: medacy.ner.model.model
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/source/medacy.ner.model.rst b/docs/source/medacy.ner.model.rst
@@ -0,0 +1,7 @@
+medacy.ner.model package
+====================
+
+.. toctree::
+
+    medacy.ner.model.model
+    medacy.ner.model.stratified_k_fold
diff --git a/...source/medacy.model.stratified_k_fold.rst → ...ce/medacy.ner.model.stratified_k_fold.rst b/...source/medacy.model.stratified_k_fold.rst → ...ce/medacy.ner.model.stratified_k_fold.rst
@@ -1,7 +1,7 @@
-medacy.model.stratified\_k\_fold module
+medacy.ner.model.stratified\_k\_fold module
 =======================================
 
-.. automodule:: medacy.model.stratified_k_fold
+.. automodule:: medacy.ner.model.stratified_k_fold
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/source/medacy.ner.pipelines.base.base_pipeline.rst b/docs/source/medacy.ner.pipelines.base.base_pipeline.rst
@@ -0,0 +1,7 @@
+medacy.ner.pipelines.base.base\_pipeline module
+===========================================
+
+.. automodule:: medacy.ner.pipelines.base.base_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/medacy.ner.pipelines.base.rst b/docs/source/medacy.ner.pipelines.base.rst
@@ -0,0 +1,6 @@
+medacy.ner.pipelines.base package
+=============================
+
+.. toctree::
+
+    medacy.ner.pipelines.base.base_pipeline
diff --git a/docs/source/medacy.ner.pipelines.clinical_pipeline.rst b/docs/source/medacy.ner.pipelines.clinical_pipeline.rst
@@ -0,0 +1,7 @@
+medacy.ner.pipelines.clinical\_pipeline module
+==========================================
+
+.. automodule:: medacy.ner.pipelines.clinical_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/medacy.ner.pipelines.drug_event_pipeline.rst b/docs/source/medacy.ner.pipelines.drug_event_pipeline.rst
@@ -0,0 +1,7 @@
+medacy.ner.pipelines.drug\_event\_pipeline module
+=============================================
+
+.. automodule:: medacy.ner.pipelines.drug_event_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst b/docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst
@@ -0,0 +1,7 @@
+medacy.ner.pipelines.fda\_nano\_drug\_label\_pipeline module
+========================================================
+
+.. automodule:: medacy.ner.pipelines.fda_nano_drug_label_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/medacy.ner.pipelines.rst b/docs/source/medacy.ner.pipelines.rst
@@ -0,0 +1,11 @@
+medacy.ner.pipelines package
+========================
+
+.. toctree::
+
+    medacy.ner.pipelines.base
+    medacy.ner.pipelines.clinical_pipeline
+    medacy.ner.pipelines.drug_event_pipeline
+    medacy.ner.pipelines.fda_nano_drug_label_pipeline
+    medacy.ner.pipelines.systematic_review_pipeline
+    medacy.ner.pipelines.testing_pipeline
diff --git a/docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst b/docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst
@@ -0,0 +1,7 @@
+medacy.ner.pipelines.systematic\_review\_pipeline module
+====================================================
+
+.. automodule:: medacy.ner.pipelines.systematic_review_pipeline
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/...rce/medacy.pipelines.testing_pipeline.rst → ...medacy.ner.pipelines.testing_pipeline.rst b/...rce/medacy.pipelines.testing_pipeline.rst → ...medacy.ner.pipelines.testing_pipeline.rst
@@ -1,7 +1,7 @@
-medacy.pipelines.testing\_pipeline module
+medacy.ner.pipelines.testing\_pipeline module
 =========================================
 
-.. automodule:: medacy.pipelines.testing_pipeline
+.. automodule:: medacy.ner.pipelines.testing_pipeline
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/source/medacy.ner.rst b/docs/source/medacy.ner.rst
@@ -0,0 +1,7 @@
+medacy.ner package
+====================
+
+.. toctree::
+
+    medacy.ner.model
+    medacy.ner.pipelines
diff --git a/...ce/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst b/...ce/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst
@@ -0,0 +1,7 @@
+medacy.pipeline_components.feature_extraction.feature\_extractor module
+======================================
+
+.. automodule:: medacy.pipeline_components.feature_extraction.discrete_feature_extractor
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/medacy.pipeline_components.feature_extraction.rst b/docs/source/medacy.pipeline_components.feature_extraction.rst
@@ -0,0 +1,6 @@
+medacy.pipeline\_components.feature\_extraction package
+========================================
+
+.. toctree::
+
+    medacy.pipeline_components.feature_extraction.discrete_feature_extractor
diff --git a/docs/source/medacy.pipeline_components.rst b/docs/source/medacy.pipeline_components.rst
@@ -9,3 +9,4 @@ medacy.pipeline\_components package
     medacy.pipeline_components.metamap
     medacy.pipeline_components.tokenization
     medacy.pipeline_components.units
+    medacy.pipeline_components.feature_extraction
diff --git a/docs/source/medacy.pipelines.base.base_pipeline.rst b/docs/source/medacy.pipelines.base.base_pipeline.rst
diff --git a/docs/source/medacy.pipelines.base.rst b/docs/source/medacy.pipelines.base.rst
diff --git a/docs/source/medacy.pipelines.clinical_pipeline.rst b/docs/source/medacy.pipelines.clinical_pipeline.rst
diff --git a/docs/source/medacy.pipelines.drug_event_pipeline.rst b/docs/source/medacy.pipelines.drug_event_pipeline.rst
diff --git a/docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst b/docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst
diff --git a/docs/source/medacy.pipelines.rst b/docs/source/medacy.pipelines.rst
diff --git a/docs/source/medacy.pipelines.systematic_review_pipeline.rst b/docs/source/medacy.pipelines.systematic_review_pipeline.rst
diff --git a/docs/source/medacy.relation.rst b/docs/source/medacy.relation.rst
@@ -0,0 +1,4 @@
+medacy.relation package
+====================
+
+.. toctree::
diff --git a/docs/source/medacy.rst b/docs/source/medacy.rst
@@ -4,7 +4,7 @@ medacy package
 .. toctree::
 
     medacy.data
-    medacy.model
+    medacy.ner
+    medacy.relation
     medacy.pipeline_components
-    medacy.pipelines
     medacy.tools
diff --git a/examples/guide/data_management.md b/examples/guide/data_management.md
@@ -157,7 +157,7 @@ Once you have a trained or imported a model, pass in a Dataset object for bulk p
 
 ```python
 from medacy.data import Dataset
-from medacy.model import Model
+from medacy.ner.model import Model
 
 dataset = Dataset('/home/medacy/data')
 model = Model.load_external('medacy_model_clinical_notes')

diff --git a/examples/guide/model_training.md b/examples/guide/model_training.md
@@ -66,7 +66,7 @@ The previously mentioned components make up a medaCy model. In summary training
 import os
 from medacy.data import Dataset
 from medacy.pipelines import ClinicalPipeline
-from medacy.model import Model
+from medacy.ner import Model
 
 entities = ['Drug', 'Strength']
 
@@ -91,7 +91,7 @@ The `ClinicalPipeline` source looks like this:
 import spacy, sklearn_crfsuite
 from .base import BasePipeline
 from ..pipeline_components import ClinicalTokenizer
-from medacy.model.feature_extractor import FeatureExtractor
+from medacy.pipeline_components.feature_extractor import FeatureExtractor
 
 from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, UnitComponent, MetaMap
 

diff --git a/examples/guide/model_utilization.md b/examples/guide/model_utilization.md
@@ -9,7 +9,7 @@ Once a CRF model has been trained and saved to disk, it can be loaded again for
 
 ```python
 from medacy.pipelines import ClinicalPipeline
-from medacy.model import Model
+from medacy.ner import Model
 
 pipeline = ClinicalPipeline(metamap=None, entities=['Drug'])
 model = Model(pipeline)
@@ -30,7 +30,7 @@ Once a model has been [packaged](packaging_a_medacy_model.md) and installed it c
 
 ```python
 import medacy_model_clinical_notes #import the python package wrapping the model
-from medacy.model import Model
+from medacy.ner import Model
 
 model = Model.load_external('medacy_model_clinical_notes')
 

diff --git a/examples/scripts/training_predicting.py b/examples/scripts/training_predicting.py
@@ -4,7 +4,7 @@
 # it's own directory along the models build log and model/pipeline parameters to keep results easily referencable during run time.
 # Once a sufficent model is produced, consider wrapping it up into a medaCy compatible model as defined the example guide.
 
-from medacy.model import Model
+from medacy.ner import Model
 from medacy.pipelines import SystematicReviewPipeline
 from medacy.data import Dataset
 from medacy.pipeline_components import MetaMap

diff --git a/medacy/__init__.py b/medacy/__init__.py
@@ -1,2 +1,2 @@
-__version__ = '0.0.9'
+__version__ = '0.1.0'
 __authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes"