Merge pull request #10 from PMCC-BioinformaticsCore/release-v0.3.1

Release v0.3.1

.gitignore

@@ -4,4 +4,6 @@ __pycache__/
 **/**/DS_Store
 build/
 dist/
-illusional.wdlgen.egg-info
+venv/
+illusional.wdlgen.egg-info
+*.egg-info

.vscode/settings.json

@@ -0,0 +1,11 @@
+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "test_*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true
+}

setup.py

@@ -1,6 +1,6 @@
 from setuptools import setup
 
-__version__ = "v0.3.0"
+__version__ = "v0.3.1.2"
 
 DESCRIPTION = (
     "Contains classes and helpers to generate WDL without worrying about the syntax. "

tests/helpers.py

@@ -0,0 +1,13 @@
+
+
+
+def non_blank_lines_list(text: str) -> list[str]:
+    lines = text.splitlines()
+    lines = [ln for ln in lines if not ln == '']
+    return lines
+
+def non_blank_lines_str(text: str) -> str:
+    lines = text.splitlines()
+    lines = [ln for ln in lines if not ln == '']
+    outstr = '\n'.join(lines)
+    return outstr

tests/test_task_generation.py

@@ -13,6 +13,8 @@
     ParameterMeta,
 )
 
+from tests.helpers import non_blank_lines_list
+
 
 class TestTaskGeneration(unittest.TestCase):
     def test_simple_task(self):
@@ -44,7 +46,7 @@ def test_readme(self):
         w.imports.append(Workflow.WorkflowImport("tool_file", ""))
         w.inputs.append(Input(WdlType.parse_type("String"), "inputGreeting"))
 
-        inputs_map = {"taskGreeting": "inputGreeting"}
+        inputs_map = {'taskGreeting': {'value': 'inputGreeting'}}
         w.calls.append(
             WorkflowCall("Q.namspaced_task_identifier", "task_alias", inputs_map)
         )
@@ -234,15 +236,18 @@ def test_commandinp_array_inp(self):
 class TestWorkflowGeneration(unittest.TestCase):
     def test_hello_workflow(self):
         # https://github.com/openwdl/wdl/#specifying-inputs-and-using-declarations
-        w = Workflow("test")
+        w = Workflow('test')
 
         w.calls.append(WorkflowCall(TestTaskGeneration.test_hello_tasks().name))
-
+        inputs_details={
+            'salutation': {'value': 'Greetings'},
+            'name': {'value': 'Michael'}
+        }
         w.calls.append(
             WorkflowCall(
                 TestTaskGeneration.test_hello_tasks().name,
-                alias="hello2",
-                inputs_map={"salutation": '"Greetings"', "name": '"Michael"'},
+                alias='hello2',
+                inputs_details=inputs_details,
             )
         )
 
@@ -255,8 +260,8 @@ def test_call_scatter(self):
             "i",
             "integers",
             [
-                WorkflowCall(Task("task1").name, inputs_map={"num": "i"}),
-                WorkflowCall(Task("task2").name, inputs_map={"num": "task1.output"}),
+                WorkflowCall(Task('task1').name, inputs_details={'num': {'value': 'i'}}),
+                WorkflowCall(Task('task2').name, inputs_details={'num': {'value': 'task1.output'}}),
             ],
         )
 
@@ -267,19 +272,23 @@ def test_call_scatter(self):
 
 class TestWorkflowParameterMetaGeneration(unittest.TestCase):
     def test_parameter_meta_scalar(self):
-        w = Task("param_meta_scalar", parameter_meta=ParameterMeta(test=42))
+        task = Task("param_meta_scalar", parameter_meta=ParameterMeta(test=42))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
 
         expected = """\
 task param_meta_scalar {
   parameter_meta {
     test: 42
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_parameter_meta_bool(self):
-        w = Task("param_meta_scalar", parameter_meta=ParameterMeta(pos=True, neg=False))
+        task = Task("param_meta_scalar", parameter_meta=ParameterMeta(pos=True, neg=False))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
 
         expected = """\
 task param_meta_scalar {
@@ -288,96 +297,104 @@ def test_parameter_meta_bool(self):
     neg: false
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_parameter_meta_string(self):
-        w = Task(
-            "param_meta_string", parameter_meta=ParameterMeta(other="string value")
-        )
+        task = Task("param_meta_string", parameter_meta=ParameterMeta(other="string value"))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
+
 
         expected = """\
 task param_meta_string {
   parameter_meta {
     other: "string value"
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_parameter_meta_obj(self):
-        w = Task(
+        task = Task(
             "param_meta_obj",
             parameter_meta=ParameterMeta(
                 obj_value=ParameterMeta.ParamMetaAttribute(
                     help="This is help text", scalar=96
                 )
             ),
         )
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
 
         expected = """\
 task param_meta_obj {
   parameter_meta {
     obj_value: {help: "This is help text", scalar: 96}
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_parameter_meta_dict(self):
-        w = Task(
+        task = Task(
             "param_meta_obj",
             parameter_meta=ParameterMeta(
                 obj_value={
                     "help": "This is help text", "scalar": 96
                 }
             ),
         )
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
 
         expected = """\
 task param_meta_obj {
   parameter_meta {
     obj_value: {help: "This is help text", scalar: 96}
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
 
 class TestWorkflowMetaGeneration(unittest.TestCase):
     def test_meta_scalar(self):
-        w = Task("meta_scalar", meta=Meta(arbitrary_scalar=42))
-
+        task = Task("meta_scalar", meta=Meta(arbitrary_scalar=42))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
         expected = """\
 task meta_scalar {
   meta {
     arbitrary_scalar: 42
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_meta_bool(self):
-        w = Task("meta_scalar", meta=Meta(pos=True, neg=False))
-
+        task = Task("meta_scalar", meta=Meta(pos=True, neg=False))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
         expected = """\
 task meta_scalar {
   meta {
     pos: true
     neg: false
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)
 
     def test_meta_string(self):
-        w = Task("meta_string", meta=Meta(author="illusional"))
-
+        task = Task("meta_string", meta=Meta(author="illusional"))
+        task_str = task.get_string()
+        task_lines = non_blank_lines_list(task_str)
         expected = """\
 task meta_string {
   meta {
     author: "illusional"
   }
 }"""
-        derived_workflow_only = "".join(w.get_string().splitlines(keepends=True)[2:])
-        self.assertEqual(expected, derived_workflow_only)
+        task_str = '\n'.join(task_lines[1:])
+        self.assertEqual(expected, task_str)