Feature/add gh actions

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+exclude = .git,__pycache__, docs/source/conf.py, old, build, dist, tests

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: Python Package
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 
+          if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

.gitignore

@@ -7,3 +7,5 @@ venv/
 docs/build/
 odmlib/build/
 dist/
+.tox/
+.idea/

odmlib/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.5"

odmlib/ct_1_1_1/model.py

@@ -3,7 +3,9 @@
 import odmlib.ns_registry as NS
 
 
-NS.NamespaceRegistry(prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True)
+NS.NamespaceRegistry(
+    prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True
+)
 NS.NamespaceRegistry(prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
 NS.NamespaceRegistry(prefix="xs", uri="http://www.w3.org/2001/XMLSchema-instance")
 NS.NamespaceRegistry(prefix="xml", uri="http://www.w3.org/XML/1998/namespace")
@@ -62,8 +64,12 @@ class EnumeratedItem(OE.ODMElement):
     CodedValue = T.String(required=True)
     ExtCodeID = T.String(required=True, namespace="nciodm")
     CDISCSynonym = T.ODMListObject(element_class=CDISCSynonym, namespace="nciodm")
-    CDISCDefinition = T.ODMObject(required=True, element_class=CDISCDefinition, namespace="nciodm")
-    PreferredTerm = T.ODMObject(required=True, element_class=PreferredTerm, namespace="nciodm")
+    CDISCDefinition = T.ODMObject(
+        required=True, element_class=CDISCDefinition, namespace="nciodm"
+    )
+    PreferredTerm = T.ODMObject(
+        required=True, element_class=PreferredTerm, namespace="nciodm"
+    )
 
 
 class CodeList(OE.ODMElement):
@@ -74,9 +80,15 @@ class CodeList(OE.ODMElement):
     CodeListExtensible = T.ValueSetString(required=True, namespace="nciodm")
     Description = T.ODMObject(element_class=Description)
     EnumeratedItem = T.ODMListObject(element_class=EnumeratedItem)
-    CDISCSubmissionValue = T.ODMObject(required=True, element_class=CDISCSubmissionValue, namespace="nciodm")
-    CDISCSynonym = T.ODMObject(required=True, element_class=CDISCSynonym, namespace="nciodm")
-    PreferredTerm = T.ODMObject(required=True, element_class=PreferredTerm, namespace="nciodm")
+    CDISCSubmissionValue = T.ODMObject(
+        required=True, element_class=CDISCSubmissionValue, namespace="nciodm"
+    )
+    CDISCSynonym = T.ODMObject(
+        required=True, element_class=CDISCSynonym, namespace="nciodm"
+    )
+    PreferredTerm = T.ODMObject(
+        required=True, element_class=PreferredTerm, namespace="nciodm"
+    )
 
 
 class MetaDataVersion(OE.ODMElement):

odmlib/dataset_1_0_1/model.py

@@ -1,10 +1,11 @@
-import odmlib.odm_1_3_2.model as ODM
 import odmlib.odm_element as OE
 import odmlib.typed as T
 import odmlib.ns_registry as NS
 
 
-NS.NamespaceRegistry(prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True)
+NS.NamespaceRegistry(
+    prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True
+)
 NS.NamespaceRegistry(prefix="xs", uri="http://www.w3.org/2001/XMLSchema-instance")
 NS.NamespaceRegistry(prefix="xml", uri="http://www.w3.org/XML/1998/namespace")
 NS.NamespaceRegistry(prefix="data", uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
@@ -50,7 +51,9 @@ class ODM(OE.ODMElement):
     PriorFileOID = T.OIDRef(required=False)
     AsOfDateTime = T.DateTimeString(required=False)
     ODMVersion = T.ValueSetString(required=False)
-    DatasetXMLVersion = T.ExtendedValidValues(required=True, valid_values=["1.0.0", "1.0.1"])
+    DatasetXMLVersion = T.ExtendedValidValues(
+        required=True, valid_values=["1.0.0", "1.0.1"]
+    )
     Originator = T.String(required=False)
     SourceSystem = T.String(required=False)
     SourceSystemVersion = T.String(required=False)

odmlib/define_2_0/model.py

@@ -52,7 +52,9 @@ class ItemRef(ODM.ItemRef):
     MethodOID = ODM.ItemRef.MethodOID
     Role = ODM.ItemRef.Role
     RoleCodeListOID = ODM.ItemRef.RoleCodeListOID
-    WhereClauseRef = T.ODMListObject(required=True, element_class=WhereClauseRef, namespace="def")
+    WhereClauseRef = T.ODMListObject(
+        required=True, element_class=WhereClauseRef, namespace="def"
+    )
 
 
 class title(OE.ODMElement):
@@ -213,7 +215,9 @@ class AnnotatedCRF(OE.ODMElement):
 
 class SupplementalDoc(OE.ODMElement):
     namespace = "def"
-    DocumentRef = T.ODMListObject(required=True, element_class=DocumentRef, namespace="def")
+    DocumentRef = T.ODMListObject(
+        required=True, element_class=DocumentRef, namespace="def"
+    )
 
 
 class WhereClauseDef(OE.ODMElement):