hpcflow-new2 0.2.0a155__py3-none-any.whl → 0.2.0a156__py3-none-any.whl

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0a155"
+__version__ = "0.2.0a156"

hpcflow/sdk/app.py

@@ -822,12 +822,12 @@ class BaseApp(metaclass=Singleton):
             # load the file, modify, then dump to temp location:
             if builtin_path.suffix in (".yaml", ".yml"):
                 # use round-trip loader to preserve comments:
-                data = read_YAML_file(builtin_path, typ="rt")
+                data = read_YAML_file(builtin_path, typ="rt", variables=False)
                 data.pop("doc", None)
                 write_YAML_file(data, path, typ="rt")
 
             elif builtin_path.suffix in (".json", ".jsonc"):
-                data = read_JSON_file(builtin_path)
+                data = read_JSON_file(builtin_path, variables=False)
                 data.pop("doc", None)
                 write_JSON_file(data, path)
 

hpcflow/sdk/core/utils.py

@@ -387,22 +387,36 @@ def check_in_object_list(spec_name, spec_pos=1, obj_list_pos=2):
     return decorator
 
 
+@TimeIt.decorator
 def substitute_string_vars(string, variables: Dict[str, str] = None):
     variables = variables or {}
 
     def var_repl(match_obj):
-        var_name = match_obj.group(1)
+        kwargs = {}
+        var_name, kwargs_str = match_obj.groups()
+        if kwargs_str:
+            kwargs_lst = kwargs_str.split(",")
+            for i in kwargs_lst:
+                k, v = i.strip().split("=")
+                kwargs[k.strip()] = v.strip()
         try:
             out = str(variables[var_name])
         except KeyError:
-            raise MissingVariableSubstitutionError(
-                f"The variable {var_name!r} referenced in the string does not match any "
-                f"of the provided variables: {list(variables)!r}."
-            )
+            if "default" in kwargs:
+                out = kwargs["default"]
+                print(
+                    f"Using default value ({out!r}) for workflow template string "
+                    f"variable {var_name!r}."
+                )
+            else:
+                raise MissingVariableSubstitutionError(
+                    f"The variable {var_name!r} referenced in the string does not match "
+                    f"any of the provided variables: {list(variables)!r}."
+                )
         return out
 
     new_str = re.sub(
-        pattern=r"\<\<var:(.*?)\>\>",
+        pattern=r"\<\<var:(.*?)(?:\[(.*)\])?\>\>",
         repl=var_repl,
         string=string,
     )
@@ -412,7 +426,7 @@ def substitute_string_vars(string, variables: Dict[str, str] = None):
 @TimeIt.decorator
 def read_YAML_str(yaml_str, typ="safe", variables: Dict[str, str] = None):
     """Load a YAML string."""
-    if variables:
+    if variables is not False and "<<var:" in yaml_str:
         yaml_str = substitute_string_vars(yaml_str, variables=variables)
     yaml = YAML(typ=typ)
     return yaml.load(yaml_str)
@@ -432,7 +446,7 @@ def write_YAML_file(obj, path: PathLike, typ="safe"):
 
 
 def read_JSON_string(json_str: str, variables: Dict[str, str] = None):
-    if variables:
+    if variables is not False and "<<var:" in json_str:
         json_str = substitute_string_vars(json_str, variables=variables)
     return json.loads(json_str)
 

hpcflow/sdk/demo/cli.py

@@ -120,7 +120,7 @@ def get_demo_workflow_CLI(app):
             store=store,
             ts_fmt=ts_fmt,
             ts_name_fmt=ts_name_fmt,
-            variables=variables,
+            variables=dict(variables),
         )
         click.echo(wk.path)
 
@@ -164,7 +164,7 @@ def get_demo_workflow_CLI(app):
             store=store,
             ts_fmt=ts_fmt,
             ts_name_fmt=ts_name_fmt,
-            variables=variables,
+            variables=dict(variables),
             JS_parallelism=js_parallelism,
             wait=wait,
             add_to_known=add_to_known,

hpcflow/tests/unit/test_utils.py

@@ -515,3 +515,16 @@ def test_substitute_string_vars_raise_missing():
 
 def test_substitute_string_vars_non_str():
     assert substitute_string_vars("<<var:a>>", variables={"a": 2}) == "2"
+
+
+def test_substitute_string_vars_default_value():
+    assert substitute_string_vars("hello <<var:my_name[default=bill]>>!") == "hello bill!"
+
+
+def test_substitute_string_vars_default_value_with_specified():
+    assert (
+        substitute_string_vars(
+            "hello <<var:my_name[default=bill]>>!", variables={"my_name": "bob"}
+        )
+        == "hello bob!"
+    )

{hpcflow_new2-0.2.0a155.dist-info → hpcflow_new2-0.2.0a156.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: hpcflow-new2
-Version: 0.2.0a155
+Version: 0.2.0a156
 Summary: Computational workflow management
 License: MIT
 Author: aplowman

{hpcflow_new2-0.2.0a155.dist-info → hpcflow_new2-0.2.0a156.dist-info}/RECORD

@@ -1,7 +1,7 @@
 hpcflow/__init__.py,sha256=WIETuRHeOp2SqUqHUzpjQ-lk9acbYv-6aWOhZPRdlhs,64
 hpcflow/__pyinstaller/__init__.py,sha256=YOzBlPSck6slucv6lJM9K80JtsJWxXRL00cv6tRj3oc,98
 hpcflow/__pyinstaller/hook-hpcflow.py,sha256=SeMopsPkhCyd9gqIrzwFNRj3ZlkUlUYl-74QYz61mo4,1089
-hpcflow/_version.py,sha256=9ZghWtddzXUBMsLgCa1JCPMvCkSmf2VMX7XqVVV1M6M,26
+hpcflow/_version.py,sha256=hIoMm5ojG_YRRzcmbye_3NpTvZ051KBnJaOd1DAInzU,26
 hpcflow/app.py,sha256=GQsMq_sjjXxMLLiIPF1ZvyapW_7IgsxALCCwMiqmC8I,1520
 hpcflow/cli.py,sha256=G2J3D9v6MnMWOWMMWK6UEKLn_6wnV9lT_qygEBBxg-I,66
 hpcflow/data/demo_data_manifest/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -34,7 +34,7 @@ hpcflow/data/workflows/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 hpcflow/data/workflows/workflow_1.yaml,sha256=lF7Re2SVc_5gQk5AwB0gXaq-n-T5ia4su3zNQ9oMRV0,220
 hpcflow/examples.ipynb,sha256=cLKp4QsxwwMXRanDnfWY9kqsV23q6G4raOpu6IZXnMw,28553
 hpcflow/sdk/__init__.py,sha256=QN1hUM9MdJ5yB3ou8q3ky530TdSd8BJi1V4XI2NmT4k,5643
-hpcflow/sdk/app.py,sha256=JxBI3hPXkSfNvd71OUQaA1QpYw2vvFqBl_0eB2-wE8Q,90382
+hpcflow/sdk/app.py,sha256=5HkZ7DUQPyg081WW2jVVg_Ene_-1C7MOB6CTlqPTnTk,90416
 hpcflow/sdk/cli.py,sha256=0ww5eqikpUcy-zNwpZiKgFs86lF1hymtDFXWau-E9UA,34624
 hpcflow/sdk/cli_common.py,sha256=5lYYuwlP1D9kmULEk4r5iCT30hrx8sCjd40pttIfvh4,4257
 hpcflow/sdk/config/__init__.py,sha256=qJrrxcAN4f1u_RyTtXgz-xlTLwNafE9v0VEMP1x6-bU,70
@@ -59,7 +59,7 @@ hpcflow/sdk/core/rule.py,sha256=chMn-Unu_4Mtc3T4z93OpmYcqOapqYAdBWuRSP8CBdg,4510
 hpcflow/sdk/core/task.py,sha256=qX_LECPBK2ZESsSTvl_DQFN8IwULorJXy7g5WBwHpaE,108874
 hpcflow/sdk/core/task_schema.py,sha256=T94-3KIoMaAlQc0Z51zqGDO46n6CUfE1Mwkvf9GVtXQ,31452
 hpcflow/sdk/core/test_utils.py,sha256=9VwdOi4oPZ-fPXvLgJNRnRjLy2G4-We9lrOkbrzCVcQ,9334
-hpcflow/sdk/core/utils.py,sha256=9VXHcM64DfuqvivAuc56g9S8EYEGUOU1TH-ZwfqDWH8,24403
+hpcflow/sdk/core/utils.py,sha256=vgFc0_UD-2HWanUINT_e4VOffglP_H7RIcpuN-7AoQs,25015
 hpcflow/sdk/core/validation.py,sha256=KBKiy5DdfGiGmMaB0HdKTY0V972u5dJzvkYkX0_KtCo,518
 hpcflow/sdk/core/workflow.py,sha256=139wrrGPZfNyNpcb0TP_1892yOvPByqczJuQ-N1k5Kw,100608
 hpcflow/sdk/core/zarr_io.py,sha256=V_Zm6uSiuaCbXyHFJUO74K1pAr4Zqrj3aLCBjohCwvs,5724
@@ -72,7 +72,7 @@ hpcflow/sdk/data/parameters_spec_schema.yaml,sha256=Wj7CvG7Ul1nZDtBca-oxeFH_aSZk
 hpcflow/sdk/data/task_schema_spec_schema.yaml,sha256=6NROg7x-493bdvRwvY4M71R7POT-tNnmROkEsnnoL4k,93
 hpcflow/sdk/data/workflow_spec_schema.yaml,sha256=LLUV6RsdgT2BQrEPNKLCUB5Uijt9wxT9Bac2PLyGha8,1797
 hpcflow/sdk/demo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-hpcflow/sdk/demo/cli.py,sha256=hMwViEXn_D7h4-G1VRMnw93ij7Gi0chM2SXQx4h7db8,5345
+hpcflow/sdk/demo/cli.py,sha256=0W0SLt3c0ZtK1o3o7Uhxl_6Y5x-DJ_gb38fWCgFbKqg,5357
 hpcflow/sdk/helper/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 hpcflow/sdk/helper/cli.py,sha256=QPVvhXEtY3n87ua_6eBh-osaQeEBgG7g7kUR4jghqtI,3491
 hpcflow/sdk/helper/helper.py,sha256=MkjYKHox1F4XOpy-20sCCDUTWUbQY84QpWZkcpSq9n8,8143
@@ -139,14 +139,14 @@ hpcflow/tests/unit/test_slurm.py,sha256=ewfNuXXUEEelAxcd7MBbAQ-RCvU8xBenHTAyfXYF
 hpcflow/tests/unit/test_submission.py,sha256=E8ku48TeCpAQlYDci30D-hf0YvzbT3jpm-emAaS02Is,15764
 hpcflow/tests/unit/test_task.py,sha256=94TwyjlhKMRRXTQjys2a1PiK7A-rCzhnvrkk4vRz39I,70000
 hpcflow/tests/unit/test_task_schema.py,sha256=7a7o42gQhrZPMXfH0a6sGzFCJnuFrbDEl9u3u_bFsgw,3624
-hpcflow/tests/unit/test_utils.py,sha256=le9bb-HvGSkbrntX5uUr6AePNYckKidgeY1FNqOPBUo,13092
+hpcflow/tests/unit/test_utils.py,sha256=aWfhGDJWGlBfk7yi0hcrPlcd159MX0V0MwsndureeP8,13466
 hpcflow/tests/unit/test_value_sequence.py,sha256=mEU_e5Bu0GzRjBGIgPbcu1MOcafd2bBn6Gz2b02U7jA,15258
 hpcflow/tests/unit/test_workflow.py,sha256=-zLw-vytXbD9vEGrAQ9ZYLuNqVdxSe9OG0LgSoneTiU,22855
 hpcflow/tests/unit/test_workflow_template.py,sha256=EItRqUyXpU2z_z1rvpRqa848YOkXiBRLMj3oF_m7Ybw,1328
 hpcflow/tests/workflows/test_jobscript.py,sha256=9sp1o0g72JZbv2QlOl5v7wCZEFjotxiIKGNUxVaFgaA,724
 hpcflow/tests/workflows/test_workflows.py,sha256=xai6FRtGqG4lStJk6KmsqPUSuvqs9FrsBOxMVALshIs,13400
 hpcflow/viz_demo.ipynb,sha256=1QdnVsk72vihv2L6hOGyk318uEa22ZSgGxQCa7hW2oo,6238
-hpcflow_new2-0.2.0a155.dist-info/METADATA,sha256=XorDCy_8N4QovthniLwGvSDwZPI4iUEMQQd3oL2hJRc,2516
-hpcflow_new2-0.2.0a155.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-hpcflow_new2-0.2.0a155.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
-hpcflow_new2-0.2.0a155.dist-info/RECORD,,
+hpcflow_new2-0.2.0a156.dist-info/METADATA,sha256=whrUKGf2XT9ab-U9YZVs4-iKE6HVoFuqBhsVOmOOKkU,2516
+hpcflow_new2-0.2.0a156.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+hpcflow_new2-0.2.0a156.dist-info/entry_points.txt,sha256=aoGtCnFdfPcXfBdu2zZyMOJoz6fPgdR0elqsgrE-USU,106
+hpcflow_new2-0.2.0a156.dist-info/RECORD,,