Merge pull request #234 from deepakunni3/prepare-for-pypi-release

Prepare for pypi release

.gitignore

@@ -6,6 +6,7 @@ target/
 test-*
 metamodel/metamodel.py-PREV
 tests/test_scripts/temp/
+biolink/*-PREV
 
 # Jekyll
 Gemfile.lock

Makefile

@@ -15,7 +15,7 @@ imgflags?=--noimages
 all: install tests build
 
 # Build the biolink model python library
-python: biolinkmodel/datamodel.py
+python: biolink/model.py
 docs: docs/index.md
 json-schema: json-schema/biolink-model.json
 
@@ -43,7 +43,7 @@ env.lock:
 # ~~~~~~~~~~~~~~~~~~~~
 # Python
 # ~~~~~~~~~~~~~~~~~~~~
-biolinkmodel/datamodel.py: biolink-model.yaml env.lock
+biolink/model.py: biolink-model.yaml env.lock
 	pipenv run gen-py-classes $< > tmp.py && pipenv run python tmp.py &&  (pipenv run comparefiles tmp.py $@ && cp $@ $@-PREV && cp tmp.py $@); rm tmp.py
 
 

README.md

@@ -90,8 +90,8 @@ The yaml definition is currently used to derive:
     - these can be compiled down to Solr XML schemas
     - these are also intermediate targets used within the BBOP/AmiGO framework
  - [JSON Schema](json-schema)
- - [Python dataclasses](biolinkmodel/datamodel.py)
- - [marshmallow schema definitions](biolinkmodel/schema.py)
+ - [Python dataclasses](biolink/model.py)
+ - [marshmallow schema definitions](biolink/schema.py)
     - can be used to serialize/deserialize python object model to JSON and YAML
  - [Java code gen](java)
     - [Jackson annotations](https://github.com/FasterXML/jackson-annotations) used be default

biolink-model.ttl

@@ -171,30 +171,30 @@
         "rdfs",
         "skos",
         "xsd" ;
-    :generation_date "2019-06-27 17:08"^^xsd:dateTime ;
+    :generation_date "2019-06-27 20:42"^^xsd:dateTime ;
     :id <https://w3id.org/biolink/biolink-model> ;
     :imports <biolinkml:types> ;
     :metamodel_version "1.3.5" ;
-    :prefixes [ :prefix_prefix "SIO" ;
-            :prefix_reference <http://semanticscience.org/resource/SIO_> ],
-        [ :prefix_prefix "biolink" ;
-            :prefix_reference <https://w3id.org/biolink/vocab/> ],
+    :prefixes [ :prefix_prefix "xsd" ;
+            :prefix_reference xsd: ],
         [ :prefix_prefix "OBAN" ;
             :prefix_reference <http://purl.org/oban/> ],
-        [ :prefix_prefix "UMLSSG" ;
-            :prefix_reference <https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/GROUP/> ],
-        [ :prefix_prefix "biolinkml" ;
-            :prefix_reference <https://w3id.org/biolink/biolinkml/> ],
-        [ :prefix_prefix "xsd" ;
-            :prefix_reference xsd: ],
+        [ :prefix_prefix "biolink" ;
+            :prefix_reference <https://w3id.org/biolink/vocab/> ],
         [ :prefix_prefix "meta" ;
             :prefix_reference : ],
-        [ :prefix_prefix "UMLSSC" ;
-            :prefix_reference <https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/TUI/> ],
         [ :prefix_prefix "metatype" ;
             :prefix_reference metatype: ],
         [ :prefix_prefix "UMLSST" ;
             :prefix_reference <https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/STY/> ],
+        [ :prefix_prefix "UMLSSC" ;
+            :prefix_reference <https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/TUI/> ],
+        [ :prefix_prefix "SIO" ;
+            :prefix_reference <http://semanticscience.org/resource/SIO_> ],
+        [ :prefix_prefix "UMLSSG" ;
+            :prefix_reference <https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/GROUP/> ],
+        [ :prefix_prefix "biolinkml" ;
+            :prefix_reference <https://w3id.org/biolink/biolinkml/> ],
         [ :prefix_prefix "wgs" ;
             :prefix_reference <http://www.w3.org/2003/01/geo/wgs84_pos> ] ;
     :slots <https://w3id.org/biolink/vocab/actively_involved_in>,
@@ -456,7 +456,7 @@
         <https://w3id.org/biolink/vocab/variant_to_thing_association_subject>,
         <https://w3id.org/biolink/vocab/xenologous_to> ;
     :source_file "biolink-model.yaml" ;
-    :source_file_date "Thu Jun 27 17:01:19 2019"^^xsd:dateTime ;
+    :source_file_date "Thu Jun 27 16:58:59 2019"^^xsd:dateTime ;
     :source_file_size 107043 ;
     :subsets <https://w3id.org/biolink/vocab/testing>,
         <https://w3id.org/biolink/vocab/translator_minimal> ;
@@ -3788,11 +3788,11 @@
     :inherited true ;
     :is_a <https://w3id.org/biolink/vocab/regulates_entity_to_entity> ;
     :local_names [ a :LocalName ;
-            skos:altLabel "activity directly positively regulates activity of" ;
-            :local_name_source "ro" ],
-        [ a :LocalName ;
             skos:altLabel "positively regulates" ;
-            :local_name_source "translator" ] ;
+            :local_name_source "translator" ],
+        [ a :LocalName ;
+            skos:altLabel "activity directly positively regulates activity of" ;
+            :local_name_source "ro" ] ;
     :mixins <https://w3id.org/biolink/vocab/positively_regulates> ;
     :multivalued true ;
     :owner <https://w3id.org/biolink/vocab/positively_regulates_entity_to_entity> ;
@@ -8131,11 +8131,11 @@
     :domain <https://w3id.org/biolink/vocab/Association> ;
     :is_a <https://w3id.org/biolink/vocab/association_slot> ;
     :local_names [ a :LocalName ;
-            skos:altLabel "node with outgoing relationship" ;
-            :local_name_source "neo4j" ],
-        [ a :LocalName ;
             skos:altLabel "annotation subject" ;
-            :local_name_source "ga4gh" ] ;
+            :local_name_source "ga4gh" ],
+        [ a :LocalName ;
+            skos:altLabel "node with outgoing relationship" ;
+            :local_name_source "neo4j" ] ;
     :owner <https://w3id.org/biolink/vocab/Association> ;
     :range <https://w3id.org/biolink/vocab/iri_type> ;
     :required true ;

biolinkmodel/__init__.py → biolink/__init__.py

@@ -10,4 +10,4 @@
 BIOLINK_MODEL_JSON = os.path.join(basedir, 'biolink-model.json')
 BIOLINK_MODEL_JSON_SCHEMA = os.path.join(basedir, 'json-schema', 'biolink-model.json')
 BIOLINK_MODEL_JAVA = os.path.join(basedir, 'java')
-BIOLINK_MODEL_PYTHON = os.path.join(basedir, 'biolinkmodel', 'biolink-model.py')
+BIOLINK_MODEL_PYTHON = os.path.join(basedir, 'biolink', 'model.py')

biolinkmodel/datamodel.py → biolink/model.py

@@ -1,5 +1,5 @@
 # Auto generated from biolink-model.yaml by pythongen.py version: 0.2.0
-# Generation date: 2019-06-27 17:07
+# Generation date: 2019-06-27 17:41
 # Schema: biolink_model
 #
 # id: https://w3id.org/biolink/biolink-model

context.jsonld

@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.0.2\nGeneration date: 2019-06-27 17:08\nSchema: biolink_model\n\nid: https://w3id.org/biolink/biolink-model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n",
+   "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.0.2\nGeneration date: 2019-06-27 20:42\nSchema: biolink_model\n\nid: https://w3id.org/biolink/biolink-model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n",
    "@context": {
       "_comments": null,
       "type": "@type",

setup.cfg

@@ -1,5 +1,7 @@
 [metadata]
-name = biolink-model
+name = biolink_model
+description = 'A high level datamodel of biological entities and associations'
+version = 1.2.0
 url = https://github.com/biolink/biolink-model
 author = Harold Solbrig
 author-email = [email protected]
@@ -8,15 +10,21 @@ home-page = https://biolink.github.io/biolink-model/docs/
 license = CC0 1.0 Universal
 python-requires = >=3.7
 classifier =
-    Development Status :: 4 - Beta
     Environment :: Console
     Intended Audience :: Developers
     Intended Audience :: Science/Research
     Intended Audience :: Healthcare Industry
+    Topic :: Scientific/Engineering :: Bio-informatics
     License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
     Programming Language :: Python :: 3 :: Only
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
 keywords =
-    biolink
-    model
+    BioLink
+    Datamodel
+    NCATS
+    NCATS-Translator
+
+[files]
+packages =
+    biolink

tests/test_biolink_model.py

@@ -3,7 +3,7 @@
 
 from biolinkml.utils.schemaloader import SchemaLoader
 
-from biolinkmodel import BIOLINK_MODEL_YAML
+from biolink import BIOLINK_MODEL_YAML
 
 
 class BiolinkModelTestCase(unittest.TestCase):

tests/test_pythongen.py

@@ -3,7 +3,7 @@
 
 from biolinkml.generators.pythongen import PythonGenerator
 
-from biolinkmodel import BIOLINK_MODEL_YAML
+from biolink import BIOLINK_MODEL_YAML
 
 
 class PythonGenTestCase(unittest.TestCase):