pytest marks for programs

.github/workflows/CI.yml

@@ -142,11 +142,11 @@ jobs:
           #  pytest: ""
 
           # DOWNLOAD problem Mar 2026
-          #- conda-env: mace
-          #  python-version: "3.10"
-          #  label: MACE
-          #  runs-on: ubuntu-latest
-          #  pytest: ""
+          - conda-env: mace
+            python-version: "3.13"
+            label: MACE
+            runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: aimnet2
             python-version: 3.11
@@ -205,7 +205,7 @@ jobs:
       run: |
         # conda remove qcelemental --force
         # python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@next2026' --no-deps
-        conda install "conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3"
+        conda install "conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc4"
 
       # 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
@@ -254,7 +254,7 @@ jobs:
         python -c "import qcelemental as q;print(q.__file__, q.__version__)"
         python -c "import qcengine as q;print(q.__file__, q.__version__)"
         git describe
-        git log --oneline
+        # git log --oneline
 
     - name: Special Config - Windows Psi4
       if: "(((matrix.cfg.label == 'optimization-dispersion') || (matrix.cfg.label == 'Psi4-1.8')) && (matrix.cfg.runs-on == 'windows-latest'))"
@@ -286,12 +286,12 @@ jobs:
     - name: PyTest
       run: |
         # export MKL_CBWR=AVX
-        pytest -rws -v ${{ matrix.cfg.pytest }} --cov=qcengine --color=yes --cov-report=xml qcengine/
+        pytest -rws -v ${{ matrix.cfg.pytest }} --cov=qcengine --durations=20 --durations-min=40 --strict-markers --color=yes --cov-report=xml qcengine/
 
     - name: PyTest - Task_Config
       run: |
         rm -f qcengine.yaml
-        pytest -rws -v -k "test_config" --cov=qcengine --color=yes --cov-report=xml qcengine/
+        pytest -rws -v -k "test_config" --cov=qcengine --strict-markers --color=yes --cov-report=xml qcengine/
 
     - name: CodeCov
       uses: codecov/codecov-action@v4

devtools/conda-envs/adcc.yaml

@@ -6,12 +6,14 @@ channels:
 dependencies:
   - adcc>=0.15.7
   - psi4>=1.8.1
+  - libint=2.9.0=*_4
 
   # Core
   - python
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental>=0.50.0rc4
+  - qcmanybody>=0.7.0
   - pydantic=2
   - pydantic-settings
   - msgpack-python

devtools/conda-envs/aimnet2.yaml

@@ -9,7 +9,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2.0.0
   - pydantic-settings
 

devtools/conda-envs/mace.yaml

@@ -7,7 +7,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2.0.0
   - pydantic-settings
 

devtools/conda-envs/mrchem.yaml

@@ -12,7 +12,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic=2
   - pydantic-settings
   - setuptools <82.0  # for berny

devtools/conda-envs/nwchem-cf.yaml

@@ -9,7 +9,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2.0.0
   - networkx>=2.4.0
   - qcmanybody

devtools/conda-envs/nwchem.yaml

@@ -7,7 +7,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2.0.0
   - networkx>=2.4.0
   - pydantic-settings

devtools/conda-envs/openmm.yaml

@@ -18,7 +18,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic >=2
   - pydantic-settings
   # - pint <0.22  # needed for a while see #416

devtools/conda-envs/opt-disp-cf.yaml

@@ -7,6 +7,7 @@ dependencies:
   - rdkit
   # - rdkit<=2025.03.4  # Windows+psi4 error with 03.5  # sometimes fine, sometimes flaky even w/exactly same packages in env
   - mopac
+  - libint=2.9.0=*_4  # old (1.10=*_2) psi4 to release qcmb constraint to use new qcnb (0.7) with new qcel (rc4)
 
     # Mixed Tests
   - dftd3-python
@@ -15,7 +16,7 @@ dependencies:
   - geometric=1.0
   - optking
   - pymdi
-  - qcmanybody
+  - qcmanybody>=0.7.0
   - pyberny
   - setuptools <82.0  # for berny
 
@@ -24,7 +25,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental>=0.50.0rc4
   - pydantic=2
   - pydantic-settings
   - msgpack-python

devtools/conda-envs/opt-disp.yaml

@@ -27,7 +27,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - msgpack-python
 
     # Testing

devtools/conda-envs/psi-cf.yaml

@@ -9,7 +9,7 @@ dependencies:
   - numpy<2
   - libgcc<14.3  # until psi4 package itself conveys this
   - pydantic-settings
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
 
     # Core
   - python

devtools/conda-envs/psi-nightly.yaml

@@ -13,7 +13,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2.0.0
   - pydantic-settings
   - msgpack-python

devtools/conda-envs/torchani.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic>=2
   - pydantic-settings
 

devtools/conda-envs/xtb.yaml

@@ -10,7 +10,7 @@ dependencies:
   - pyyaml
   - py-cpuinfo
   - psutil
-  - conda-forge/label/qcelemental_dev::qcelemental=0.50.0rc3
+  - conda-forge/label/qcelemental_dev::qcelemental
   - pydantic >=2
   - pydantic-settings
 

docs/source/changelog.rst

@@ -32,6 +32,34 @@ Changelog
 .. - UNSOLVED (:issue:`397`) extras failed
 
 
+.. _`sec:cl0500rc3`:
+
+v0.50.0rc3 / 2026-04-02 (Prerelease)
+------------------------------------
+
+:docs:`v0.50.0rc3` for current. :docs:`v0.34.1` for QCSchema v1.
+
+New Features
+++++++++++++
+- (:pr:`499`) Testing - Program names are now pytest markers, so `pytest -m openmm`
+  thoroughly collects all tests involving that program. Note that the nearly
+  retired harnesses for Grimme programs have markers "classic-dftd3" and "classic-gcp".
+
+Enhancements
+++++++++++++
+- (:pr:`499`) QCElemental - Update encoding=json to mode=json in serialization
+  calls to match QCElemental v0.50.0rc4 changes.
+- (:pr:`499`) DFTD3, DFTD4 - Allow running in QCSchema v2 mode for WIP upstream versions.
+  Note that QCEngine-added input extras appear in `AtomicResult.input_data.specification.extras`,
+  formerly `AtomicResult.extras`, even routing through older (pre-v1.3, v4.1) programs.
+- (:pr:`499`) GCP, MP2D - Update model_copy and casting of energy for qcel rc3 and Pydantic v2.
+
+Bug Fixes
++++++++++
+- (:pr:`499`) Psi4 - Fix Psi4 detected but not registered error arising from parsing
+  of version and paths being obscured by QCSchema/Pydantic Warnings.
+
+
 .. _`sec:cl0500rc2`:
 
 v0.50.0rc2 / 2026-03-13 (Prerelease)

pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
     "pyyaml",
     "py-cpuinfo",
     "psutil",
-    "qcelemental>=0.50.0rc3,<0.70.0",
+    "qcelemental>=0.50.0rc4,<0.70.0",
     "pydantic >=2.11; python_version <'3.14'",
     "pydantic >=2.12; python_version >='3.14'",
     "pydantic-settings",
@@ -105,4 +105,41 @@ markers = [
     "long",
     """slow: marks tests as slow (deselect with '-m "not slow"')""",
     "smoke",
+    'addon: "tests require external non-required software"',
+
+    "adcc: tests using adcc software; skip if unavailable",
+    "aimnet2: tests using AIMNET2 software; skip if unavailable",
+    "berny: tests using pyberny software; skip if unavailable",
+    "cfour: tests using Cfour software; skip if unavailable",
+    "classic-dftd3: tests using DFTD3 executable software; skip if unavailable",
+    "classic-dftd3_321: tests using DFTD3 classic executable >=v3.2.1 software; skip if unavailable",
+    "s-dftd3: tests using modern simple-dftd3 software; skip if unavailable",
+    "dftd4: tests using DFTD4 software; skip if unavailable",
+    "dftd4_350: tests using DFTD4 >=3.5.0 software; skip if unavailable",
+    "gamess: tests using GAMESS-US software; skip if unavailable",
+    "mctc-gcp: tests using modern mctc-gcp software; skip if unavailable",
+    "classic-gcp: tests using GCP executable software; skip if unavailable",
+    "geometric: tests using geomeTRIC software; skip if unavailable",
+    "mace: tests using MACE software; skip if unavailable",
+    "mdi: tests using MDI software; skip if unavailable",
+    "molpro: tests using Molpro software; skip if unavailable",
+    "mopac: tests using Mopac software; skip if unavailable",
+    "mp2d: tests using MP2D software; skip if unavailable",
+    "mrchem: tests using MR-Chem software; skip if unavailable",
+    "nwchem: tests using NWChem Classic software; skip if unavailable",
+    "openmm: tests using OpenMM software; skip if unavailable",
+    "optking: tests using OptKing software; skip if unavailable",
+    "optking_v2: tests using OptKing QCSchema-v2-compatible software; skip if unavailable",
+    "psi4: tests using Psi4 software; skip if unavailable",
+    "qcdb: tests using QCDB software; skip if unavailable",
+    "qchem: tests using Q-Chem software; skip if unavailable",
+    "qcmanybody: tests using QCManyBody software; skip if unavailable",
+    "qcore: tests using Qcore (ret.) software; skip if unavailable",
+    "rdkit: tests using RDKIT software; skip if unavailable",
+    "terachem: tests using TeraChem software; skip if unavailable",
+    "terachem_pbs: tests using TeraChem through PBS software; skip if unavailable",
+    "torchani: tests using Torch-ANI software; skip if unavailable",
+    "torsiondrive: tests using TorsionDrive software; skip if unavailable",
+    "turbomole: tests using Turbomole software; skip if unavailable",
+    "xtb: tests using xTB software; skip if unavailable",
 ]

qcengine/programs/adcc.py

@@ -115,7 +115,7 @@ def compute(self, input_model: "AtomicInput", config: "TaskConfig") -> "AtomicRe
         except Exception as e:
             raise UnknownError(str(e))
 
-        input_data = input_model.model_dump(encoding="json")
+        input_data = input_model.model_dump(mode="json")
         output_data = {"input_data": input_data, "extras": {}, "molecule": mol}
         output_data["success"] = compute_success
 

qcengine/programs/dftd3.py

@@ -277,7 +277,7 @@ def parse_output(self, outfiles: Dict[str, str], input_model: "AtomicInput") ->
         # jobrec["molecule"]["real"] = list(jobrec["molecule"]["real"])
 
         retres = calcinfo[f"CURRENT {input_model.specification.driver.upper()}"]
-        if isinstance(retres, Decimal):
+        if isinstance(retres, (str, Decimal)):
             retres = float(retres)
         elif isinstance(retres, np.ndarray):
             retres = retres.ravel().tolist()

qcengine/programs/dftd_ng.py

@@ -104,20 +104,40 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
             level_hint = "d4"
             input_data["specification"]["keywords"]["level_hint"] = level_hint
 
-        # dftd4 speaks qcsk.v1
-        input_model_v1 = qcelemental.models.v2.AtomicInput(**input_data).convert_v(1)
+        if parse_version(self.get_version()) < parse_version("4.1.0"):
+            # dftd4 speaks qcsk.v1
+            input_model_v1 = qcelemental.models.v2.AtomicInput(**input_data).convert_v(1)
 
-        # Run the Harness
-        output_v1 = run_qcschema(input_model_v1)
+            # Run the Harness
+            output_v1 = run_qcschema(input_model_v1)
 
-        # d4 qcschema interface stores error in Result model
-        if not output_v1.success:
-            return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
+            # d4 qcschema interface stores error in Result model
+            if not output_v1.success:
+                return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
 
-        output = output_v1.convert_v(2, external_input_data=input_model)
+            # Unclear whether external_input_data should be input_model (user input in v2) or input_data
+            #   (user input + processing above with tweaks and hints). Former seems cleaner (and works)
+            #   but places "extras.info" differently in pre-/post-1.3.0 routes, so using latter.
+            output = output_v1.convert_v(2, external_input_data=input_data)
 
-        if "info" in output.extras:
-            qcvkey = output.extras["info"]["fctldash"].upper()
+        else:
+            # dftd4 >4.1 speaks qcsk.v1 or qcsk.v2
+            input_model_v2 = qcelemental.models.v2.AtomicInput(**input_data)
+
+            # Run the Harness
+            output_v2 = run_qcschema(input_model_v2)
+
+            # d4 qcschema interface stores error in Result model
+            # TODO
+            if not output_v2.success:
+                # return FailedOperation(input_data=input_data, error=output_v2.error.model_dump())
+                return output_v2
+
+            output = output_v2
+
+        if "info" in output.input_data.specification.extras:
+            # formerly output.extras["info"]
+            qcvkey = output.input_data.specification.extras["info"]["fctldash"].upper()
 
         calcinfo = {}
         energy = output.properties.return_energy
@@ -279,20 +299,40 @@ def compute(self, input_model: AtomicInput, config: TaskConfig) -> AtomicResult:
                     input_data["specification"]["keywords"]["params_tweaks"] = {**planinfo["dashparams"], "s9": 0.0}
                 input_data["specification"]["keywords"]["level_hint"] = level_hint
 
-        # sdftd3 speaks qcsk.v1
-        input_model_v1 = qcelemental.models.v2.AtomicInput(**input_data).convert_v(1)
+        if parse_version(self.get_version()) < parse_version("1.3.0"):
+            # sdftd3 speaks qcsk.v1
+            input_model_v1 = qcelemental.models.v2.AtomicInput(**input_data).convert_v(1)
+
+            # Run the Harness
+            output_v1 = run_qcschema(input_model_v1)
+
+            # d3 qcschema interface stores error in Result model
+            if not output_v1.success:
+                return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
+
+            # Unclear whether external_input_data should be input_model (user input in v2) or input_data
+            #   (user input + processing above with tweaks and hints). Former seems cleaner (and works)
+            #   but places "extras.info" differently in pre-/post-1.3.0 routes, so using latter.
+            output = output_v1.convert_v(2, external_input_data=input_data)
+
+        else:
+            # sdftd3 >1.3.0??? speaks qcsk.v1 or qcsk.v2
+            input_model_v2 = qcelemental.models.v2.AtomicInput(**input_data)
 
-        # Run the Harness
-        output_v1 = run_qcschema(input_model_v1)
+            # Run the Harness
+            output_v2 = run_qcschema(input_model_v2)
 
-        # d3 qcschema interface stores error in Result model
-        if not output_v1.success:
-            return FailedOperation(input_data=input_data, error=output_v1.error.model_dump())
+            # d3 qcschema interface stores error in Result model
+            # TODO
+            if not output_v2.success:
+                # return FailedOperation(input_data=input_data, error=output_v2.error.model_dump())
+                return output_v2
 
-        output = output_v1.convert_v(2, external_input_data=input_model)
+            output = output_v2
 
-        if "info" in output.extras:
-            qcvkey = output.extras["info"]["fctldash"].upper()
+        if "info" in output.input_data.specification.extras:
+            # formerly output.extras["info"]
+            qcvkey = output.input_data.specification.extras["info"]["fctldash"].upper()
 
         calcinfo = {}
         energy = output.properties.return_energy