Csse layout 550 error

.github/workflows/CI.yml

@@ -102,6 +102,13 @@ jobs:
             runs-on: windows-latest
             pytest: "-k 'not (hes2 or qchem)'"
 
+            # 3.13
+          #- conda-env: disp-win
+          #  python-version: 3.12
+          #  label: disp-win
+          #  runs-on: windows-latest
+          #  pytest: ""
+
           - conda-env: mace
             python-version: "3.10"
             label: MACE
@@ -158,7 +165,7 @@ jobs:
       #if: false
       run: |
         conda remove qcelemental --force
-        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_pyd2_warnings' --no-deps
+        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_layout_536a' --no-deps
 
       # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
       #       alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75

devtools/conda-envs/disp-win.yaml

@@ -0,0 +1,26 @@
+name: test
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - dftd3-python =1.2.0
+  - gcp-correction
+  - geometric
+  - optking
+  - pymdi
+
+    # Core
+  - python
+  - pyyaml
+  - py-cpuinfo
+  - psutil
+  - qcelemental
+  - pydantic=2
+  - pydantic-settings
+  - msgpack-python
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+

docs/source/changelog.rst

@@ -70,6 +70,11 @@ Misc.
 
 MUST (Unmerged)
 +++++++++++++++
+- When qcengine.compute() fails and forms a fop = FailedOperation (raise_error=T), with v2, `fop.input_data` will be an <>Input model (when possible; if the error was in forming the model, it'll still be a dict), not always a dict like v1.
+- When <executor>.compute() fails and collects the input for processing, with v2 it now uses the <>Input model passed to the executor, not the model-or-dict passed into compute().
+- The net result of the two above is that whereas fop.input_data in v1 was reliably a dict and its contents would reflect whether a model or dict was passed to qcengine.compute(), now in v2, fop.input_data is a model whenever possible (to mirror <>Result.input_data) regardless of model or dict passed to qcengine.compute(); the only case where it's a dict is if the error was in forming the model.
+- DFTD3 & DFTD4 (new intf) - intercept ``v1.AtomicResult`` with ``success=False`` and ``error`` fields set from QCSchema interfaces and return ``FailedOperation``s. Someday when upstream switches to v2, request packages return FaileOp directly and use ``input_error`` rather than ``input error``.
+- ``qcengine run`` learned new argument ``--return-version`` analogous to ``qcengine.compute(..., return_version=1|2)`` so CLI matches API capabilities. Note *not* ported to phasing-out ``qcengine run-procedure``.
 
 WIP (Unmerged)
 ++++++++++++++

qcengine/cli.py

@@ -73,6 +73,9 @@ def parse_args():
         "(ii) A file name, "
         "(iii) '-', indicating data will be read from STDIN.",
     )
+    run.add_argument(
+        "--return-version", default=-1, type=int, help="Schema version to return, if not the input version"
+    )
 
     run_procedure = subparsers.add_parser(
         "run-procedure",
@@ -214,7 +217,12 @@ def main(args=None):
     if command == "info":
         info_cli(args)
     elif command == "run":
-        ret = compute(data_arg_helper(args["data"]), args["program"], task_config=task_config)
+        ret = compute(
+            data_arg_helper(args["data"]),
+            args["program"],
+            task_config=task_config,
+            return_version=args["return_version"],
+        )
         print(ret.json())
     elif command == "run-procedure":
         ret = compute_procedure(data_arg_helper(args["data"]), args["procedure"], task_config=task_config)

qcengine/compute.py

@@ -70,6 +70,28 @@ def compute(
         AtomicResult, OptimizationResult, FailedOperation, etc., or Dict representation of any object type
         A QCSchema representation of the requested output, type depends on return_dict key.
 
+        .. _`table:compute_result`:
+
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | good_calc | raise_error | return_dict | output                                           |
+        +===========+=============+=============+==================================================+
+        | T         | F (def)     | F (def)     | ``AtomicResult`` object                          |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | T         | T           | F (def)     | ``AtomicResult`` object                          |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | T         | T           | T           | dict of ``AtomicResult``                         |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | T         | F (def)     | T           | dict of ``AtomicResult``                         |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | F         | F (def)     | F (def)     | ``FailedOperation`` object                       |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | F         | T           | F (def)     | raises ``InputError`` (type encoded in FailedOp) |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | F         | T           | T           | raises ``InputError`` (type encoded in FailedOp) |
+        +-----------+-------------+-------------+--------------------------------------------------+
+        | F         | F (def)     | T           | dict of ``FailedOperation``                      |
+        +-----------+-------------+-------------+--------------------------------------------------+
+
     .. versionadded:: 0.50.0
        input_data can newly be QCSchema v2 as well as longstanding v1.
        The compute_procedure is newly incorporated into compute.
@@ -113,12 +135,16 @@ def compute(
                     output_data = executor.compute(input_data, config)
                     break
                 except RandomError as e:
+                    if return_version >= 2:
+                        output_data = input_data
 
                     if x == config.retries:
                         raise e
                     else:
                         metadata["retries"] += 1
                 except:
+                    if return_version >= 2:
+                        output_data = input_data
                     raise
 
     return handle_output_metadata(

qcengine/procedures/berny.py

@@ -5,7 +5,8 @@
 from typing import Any, ClassVar, Dict, Union
 
 import numpy as np
-from qcelemental.models.v2 import FailedOperation, OptimizationInput, OptimizationResult
+from qcelemental.models.v1 import OptimizationResult
+from qcelemental.models.v2 import FailedOperation, OptimizationInput
 from qcelemental.util import which_import
 
 import qcengine
@@ -94,5 +95,6 @@ def compute(
                     "stdout": log_stream.getvalue(),  # collect logged messages
                 }
             )
-            return OptimizationResult(**output_data)
+            output_data = OptimizationResult(**output_data)
+            return output_data.convert_v(2)
         return FailedOperation(input_data=input_data, error=error)

qcengine/procedures/geometric.py

@@ -1,6 +1,7 @@
 from typing import Any, ClassVar, Dict, Union
 
-from qcelemental.models.v2 import OptimizationInput, OptimizationResult
+from qcelemental.models.v1 import OptimizationResult
+from qcelemental.models.v2 import OptimizationInput
 from qcelemental.util import safe_version, which_import
 
 from .model import ProcedureHarness
@@ -65,5 +66,6 @@ def compute(self, input_model: "OptimizationInput", config: "TaskConfig") -> "Op
         output_data["input_specification"]["extras"].pop("_qcengine_local_config", None)
         if output_data["success"]:
             output_data = OptimizationResult(**output_data)
+            output_data = output_data.convert_v(2)
 
         return output_data

qcengine/procedures/model.py

@@ -71,9 +71,15 @@ def _build_model(
             # remember these are user-provided dictionaries, so they'll have the mandatory fields,
             #   like driver, not the helpful discriminator fields like schema_version.
 
-            # for now, the two dictionaries look the same, so cast to the one we want
-            # note that this prevents correctly identifying the user schema version when dict passed in, so either as_v1/None or as_v2 will fail
-            mdl = model_wrapper(data, v1_model)
+            schver = data.get("schema_version")
+            if schver == 1:
+                mdl = model_wrapper(data, v1_model)
+            elif schver == 2:
+                mdl = model_wrapper(data, v2_model)
+            else:
+                # for now, the two dictionaries look the same, so cast to the one we want
+                # note that this prevents correctly identifying the user schema version when dict passed in, so either as_v1/None or as_v2 will fail
+                mdl = model_wrapper(data, v1_model)
 
         input_schema_version = mdl.schema_version
         if return_input_schema_version:

qcengine/procedures/optking.py

@@ -1,6 +1,7 @@
 from typing import Any, ClassVar, Dict, Union
 
-from qcelemental.models.v2 import OptimizationInput, OptimizationResult
+from qcelemental.models.v1 import OptimizationResult
+from qcelemental.models.v2 import OptimizationInput
 from qcelemental.util import safe_version, which_import
 
 from .model import ProcedureHarness
@@ -55,5 +56,6 @@ def compute(self, input_model: "OptimizationInput", config: "TaskConfig") -> "Op
         output_data["input_specification"]["extras"].pop("_qcengine_local_config", None)
         if output_data["success"]:
             output_data = OptimizationResult(**output_data)
+            output_data = output_data.convert_v(2)
 
         return output_data

qcengine/programs/dftd_ng.py

@@ -10,7 +10,7 @@
 from typing import Any, ClassVar, Dict
 
 import qcelemental
-from qcelemental.models.v2 import AtomicInput, AtomicResult
+from qcelemental.models.v2 import AtomicInput, AtomicResult, FailedOperation
 from qcelemental.util import parse_version, safe_version, which_import
 
 from ..config import TaskConfig
@@ -109,6 +109,11 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
 
         # Run the Harness
         output = run_qcschema(input_model)
+
+        # d4 qcschema interface stores error in Result model
+        if not output.success:
+            return FailedOperation(input_data=input_data, error=output.error.model_dump())
+
         output = output.convert_v(2)
 
         if "info" in output.extras:
@@ -278,6 +283,11 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
 
         # Run the Harness
         output = run_qcschema(input_model)
+
+        # d3 qcschema interface stores error in Result model
+        if not output.success:
+            return FailedOperation(input_data=input_data, error=output.error.model_dump())
+
         output = output.convert_v(2)
 
         if "info" in output.extras:

qcengine/programs/model.py

@@ -76,19 +76,27 @@ def build_input_model(
         # Note: Someday when the multiple QCSchema versions QCEngine supports are all within the
         #  Pydantic v2 API base class, this can use discriminated unions instead of logic.
 
-        if isinstance(data, qcelemental.models.v1.AtomicInput):
-            mdl = model_wrapper(data, qcelemental.models.v1.AtomicInput)
-        elif isinstance(data, qcelemental.models.v2.AtomicInput):
-            mdl = model_wrapper(data, qcelemental.models.v2.AtomicInput)
+        v1_model = getattr(qcelemental.models.v1, "AtomicInput")
+        v2_model = getattr(qcelemental.models.v2, "AtomicInput")
+
+        if isinstance(data, v1_model):
+            mdl = model_wrapper(data, v1_model)
+        elif isinstance(data, v2_model):
+            mdl = model_wrapper(data, v2_model)
         elif isinstance(data, dict):
             # remember these are user-provided dictionaries, so they'll have the mandatory fields,
             #   like driver, not the helpful discriminator fields like schema_version.
 
-            # for now, the two dictionaries look the same, so cast to the one we want
-            # note that this prevents correctly identifying the user schema version when dict passed in, so either as_v1/None or as_v2 will fail
-            mdl = model_wrapper(
-                data, qcelemental.models.v1.AtomicInput
-            )  # TODO v2  # TODO kill off excuse_as_v2, now fix 2->-1 in schema_versions
+            schver = data.get("schema_version")
+            if schver == 1:
+                mdl = model_wrapper(data, v1_model)
+            elif schver == 2:
+                mdl = model_wrapper(data, v2_model)
+            else:
+                # for now, the two dictionaries look the same, so cast to the one we want
+                # note that this prevents correctly identifying the user schema version when dict passed in, so either as_v1/None or as_v2 will fail
+                # TODO v2  # TODO kill off excuse_as_v2, now fix 2->-1 in schema_versions
+                mdl = model_wrapper(data, v1_model)
 
         input_schema_version = mdl.schema_version
         if return_input_schema_version:

qcengine/programs/psi4.py

@@ -7,7 +7,8 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, ClassVar, Dict
 
-from qcelemental.models.v2 import AtomicResult, BasisSet
+from qcelemental.models.v1 import AtomicResult as AtomicResult
+from qcelemental.models.v2 import BasisSet
 from qcelemental.util import deserialize, parse_version, safe_version, which, which_import
 
 from ..exceptions import InputError, RandomError, ResourceError, UnknownError
@@ -306,4 +307,5 @@ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicRe
         # Delete keys
         output_data.pop("return_output", None)
 
-        return AtomicResult(**output_data)
+        atres = AtomicResult(**output_data)
+        return atres.convert_v(2)

qcengine/programs/tests/test_molpro.py

@@ -15,7 +15,9 @@ def test_molpro_output_parser(test_case):
     data = molpro_info.get_test_data(test_case)
     inp = qcel.models.v1.AtomicInput.parse_raw(data["input.json"])
 
-    output = qcng.get_program("molpro", check=False).parse_output(data, inp).dict()
+    output = qcng.get_program("molpro", check=False).parse_output(data, inp)
+    # only qcng.compute() handles schema versions. above returns v2, so need to convert
+    output = output.convert_v(1).dict()
     output.pop("provenance", None)
     output.pop("schema_version", None)
 

qcengine/programs/tests/test_programs.py

@@ -255,22 +255,36 @@ def test_mopac_task(schema_versions, request):
     assert "== MOPAC DONE ==" in ret.stdout
 
 
-def test_random_failure_no_retries(failure_engine, schema_versions, request):
+def test_random_failure_no_retries_input(failure_engine, schema_versions, request):
     _, retver, _ = schema_versions
 
     failure_engine.iter_modes = ["input_error"]
     ret = qcng.compute(failure_engine.get_job(), failure_engine.name, raise_error=False, return_version=retver)
     ret = checkver_and_convert(ret, request.node.name, "post", vercheck=False)
 
     assert ret.error.error_type == "input_error"
-    assert "retries" not in ret.input_data["provenance"].keys()
+    provenance_keys = (
+        ret.input_data.provenance.model_dump().keys()
+        if ("_v2" in request.node.name)
+        else ret.input_data["provenance"].keys()
+    )
+    assert "retries" not in provenance_keys
+
+
+def test_random_failure_no_retries_random(failure_engine, schema_versions, request):
+    _, retver, _ = schema_versions
 
     failure_engine.iter_modes = ["random_error"]
     ret = qcng.compute(failure_engine.get_job(), failure_engine.name, raise_error=False, return_version=retver)
     ret = checkver_and_convert(ret, request.node.name, "post", vercheck=False)
 
     assert ret.error.error_type == "random_error"
-    assert "retries" not in ret.input_data["provenance"].keys()
+    provenance_keys = (
+        ret.input_data.provenance.model_dump().keys()
+        if ("_v2" in request.node.name)
+        else ret.input_data["provenance"].keys()
+    )
+    assert "retries" not in provenance_keys
 
 
 def test_random_failure_with_retries(failure_engine, schema_versions, request):
@@ -286,7 +300,10 @@ def test_random_failure_with_retries(failure_engine, schema_versions, request):
     )
     ret = checkver_and_convert(ret, request.node.name, "post", vercheck=False)
 
-    assert ret.input_data["provenance"]["retries"] == 2
+    retries = (
+        ret.input_data.provenance.retries if ("_v2" in request.node.name) else ret.input_data["provenance"]["retries"]
+    )
+    assert retries == 2
     assert ret.error.error_type == "random_error"
 
     failure_engine.iter_modes = ["random_error", "input_error"]
@@ -299,7 +316,10 @@ def test_random_failure_with_retries(failure_engine, schema_versions, request):
     )
     ret = checkver_and_convert(ret, request.node.name, "post", vercheck=False)
 
-    assert ret.input_data["provenance"]["retries"] == 1
+    retries = (
+        ret.input_data.provenance.retries if ("_v2" in request.node.name) else ret.input_data["provenance"]["retries"]
+    )
+    assert retries == 1
     assert ret.error.error_type == "input_error"
 
 

qcengine/programs/tests/test_qchem.py

@@ -29,7 +29,9 @@ def test_qchem_output_parser(test_case):
     inp = qcel.models.v1.AtomicInput.parse_raw(data["input.json"])
 
     outfiles = qcel.util.deserialize(data["outfiles.msgpack"], "msgpack-ext")
-    output = qcng.get_program("qchem", check=False).parse_output(outfiles, inp).dict()
+    output = qcng.get_program("qchem", check=False).parse_output(outfiles, inp)
+    # only qcng.compute() handles schema versions. above returns v2, so need to convert
+    output = output.convert_v(1).dict()
     output.pop("provenance", None)
 
     output_ref = qcel.models.v1.AtomicResult.parse_raw(data["output.json"]).dict()
@@ -129,7 +131,9 @@ def test_qchem_logfile_parser(test_case):
     data = qchem_logonly_info.get_test_data(test_case)
     outfiles = {"dispatch.out": data["qchem.out"]}
     with pytest.warns(Warning):
-        output = qcng.get_program("qchem", check=False).parse_logfile(outfiles).dict()
+        output = qcng.get_program("qchem", check=False).parse_logfile(outfiles)
+    # only qcng.compute() handles schema versions. above returns v2, so need to convert
+    output = output.convert_v(1).dict()
     output["stdout"] = None
 
     output_ref = qcel.models.v1.AtomicResult.parse_raw(data["output.json"]).dict()
@@ -152,7 +156,9 @@ def test_qchem_logfile_parser_qcscr(test_case):
     outfiles = qcel.util.deserialize(data["outfiles.msgpack"], "msgpack-ext")
 
     with pytest.warns(Warning):
-        output = qcng.get_program("qchem", check=False).parse_logfile(outfiles).dict()
+        output = qcng.get_program("qchem", check=False).parse_logfile(outfiles)
+    # only qcng.compute() handles schema versions. above returns v2, so need to convert
+    output = output.convert_v(1).dict()
     output["stdout"] = None
 
     output_ref = qcel.models.v1.AtomicResult.parse_raw(data["output.json"]).dict()