Merge pull request #30 from dgasmith/stdout

Psi4: Ensures output always goes to stdout field

devtools/conda-envs/psi.yaml

@@ -9,7 +9,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - qcelemental >=0.2.2
+  - qcelemental >=0.2.6
   - pydantic >=0.18.1
 
     # Testing

devtools/conda-envs/rdkit.yaml

@@ -9,7 +9,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - qcelemental >=0.2.2
+  - qcelemental >=0.2.6
   - pydantic >=0.18.1
 
     # Testing

devtools/conda-envs/torchani.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - qcelemental >=0.2.2
+  - qcelemental >=0.2.6
   - pydantic >=0.18.1
 
     # Testing

docs/source/changelog.rst

@@ -21,6 +21,7 @@ Enhancements
 
 - (:pr:`24`) Improves load times dramatically by delaying imports and cpuutils.
 - (:pr:`25`) Code base linting.
+- (:pr:`30`) Ensures Psi4 output is already returned and Pydantic v0.20+ changes.
 
 v0.5.1 / 2019-01-29
 -------------------

qcengine/programs/psi4.py

@@ -29,10 +29,10 @@ def _parse_psi_version(version):
     input_data["nthreads"] = config.ncores
     input_data["memory"] = int(config.memory * 1024 * 1024 * 1024 * 0.95)  # Memory in bytes
     input_data["success"] = False
-    reset_schema = False
+    input_data["return_output"] = True
+
     if input_data["schema_name"] == "qcschema_input":
         input_data["schema_name"] = "qc_schema_input"
-        reset_schema = True
 
     scratch = config.scratch_directory
     if scratch is not None:
@@ -51,8 +51,9 @@ def _parse_psi_version(version):
     else:
         raise TypeError("Psi4 version '{}' not understood.".format(psi_version))
 
-    if reset_schema:
-        output_data["schema_name"] = "qcschema_input"
+    # Reset the schema if required
+    output_data["schema_name"] = "qcschema_output"
+
     # Dispatch errors, PSIO Errors are not recoverable for future runs
     if output_data["success"] is False:
 
@@ -61,9 +62,13 @@ def _parse_psi_version(version):
 
     # Move several pieces up a level
     if output_data["success"]:
-        output_data["provenance"]["memory"] = round(input_data["memory"] / (1024**3), 3)
-        output_data["provenance"]["nthreads"] = input_data["nthreads"]
-        del output_data["memory"], input_data["nthreads"]
+        output_data["provenance"]["memory"] = round(output_data.pop("memory") / (1024**3), 3)  # Move back to GB
+        output_data["provenance"]["nthreads"] = output_data.pop("nthreads")
+        output_data["stdout"] = output_data.pop("raw_output", None)
+
+        # Delete keys
+        output_data.pop("return_ouput", None)
+
         return Result(**output_data)
     return FailedOperation(
         success=output_data.pop("success", False), error=output_data.pop("error"), input_data=output_data)

qcengine/tests/test_compute.py

@@ -29,10 +29,11 @@ def test_psi4_task():
     json_data["keywords"] = {"scf_type": "df"}
     json_data["return_output"] = False
 
-    ret = dc.compute(json_data, "psi4", raise_error=True)
+    ret = dc.compute(json_data, "psi4", raise_error=True, capture_output=False)
 
     assert ret["driver"] == "energy"
     assert "provenance" in ret
+    assert "Final Energy" in ret["stdout"]
 
     for key in ["cpu", "hostname", "username", "wall_time"]:
         assert key in ret["provenance"]
@@ -42,22 +43,21 @@ def test_psi4_task():
 
 @addons.using_psi4
 def test_psi4_ref_switch():
-    inp = ResultInput(
-        **{
-            "molecule": {
-                "symbols": ["Li"],
-                "geometry": [0, 0, 0],
-                "molecular_multiplicity": 2
-            },
-            "driver": "energy",
-            "model": {
-                "method": "SCF",
-                "basis": "sto-3g"
-            },
-            "keywords": {
-                "scf_type": "df"
-            }
-        })
+    inp = ResultInput(**{
+        "molecule": {
+            "symbols": ["Li"],
+            "geometry": [0, 0, 0],
+            "molecular_multiplicity": 2
+        },
+        "driver": "energy",
+        "model": {
+            "method": "SCF",
+            "basis": "sto-3g"
+        },
+        "keywords": {
+            "scf_type": "df"
+        }
+    })
 
     ret = dc.compute(inp, "psi4", raise_error=True, return_dict=False)
 

qcengine/util.py

@@ -128,8 +128,10 @@ def handle_output_metadata(output_data, metadata, raise_error=False, return_dict
     else:
         output_fusion = output_data.dict()
 
-    output_fusion["stdout"] = metadata["stdout"]
-    output_fusion["stderr"] = metadata["stderr"]
+    # Do not override if computer generates
+    output_fusion["stdout"] = output_fusion.pop("stdout", metadata["stdout"])
+    output_fusion["stderr"] = output_fusion.pop("stderr", metadata["stderr"])
+
     if metadata["success"] is not True:
         output_fusion["success"] = False
         output_fusion["error"] = {"error_type": "meta_error", "error_message": metadata["error_message"]}
@@ -142,9 +144,8 @@ def handle_output_metadata(output_data, metadata, raise_error=False, return_dict
         raise ValueError(output_fusion["error"]["error_message"])
 
     # Fill out provenance datadata
-    wall_time = metadata["wall_time"]
     provenance_augments = config.get_provenance_augments()
-    provenance_augments["wall_time"] = wall_time
+    provenance_augments["wall_time"] = metadata["wall_time"]
     if "provenance" in output_fusion:
         output_fusion["provenance"].update(provenance_augments)
     else:

setup.py

@@ -24,7 +24,7 @@
             'pyyaml',
             'py-cpuinfo',
             'psutil',
-            'qcelemental>=0.2.2',
+            'qcelemental>=0.2.6',
             'pydantic>=0.18.0'
         ],
         entry_points={"console_scripts": [