QCSchema v2 and Py314 (#43)

* split computer for qcschema v1, v2

* separate computers and clean up

* update for 3-way schema_versions testing

* imitate qcel for v1/v2 imports

* fix computer and BsseEnum imports

* enable CI

* try CI again with qcel 0.50

* CI with qcengine v0.50rc1

* qcng

* min py310

* xtra dep

* networkx

* fix docs?

* fix docs 2?

* right py

* to griffe

* cleanup

* fix pyd ver

* fix docs

* full docs

* qcel rb2

* try py314

* changelog, all tests

* respond to copilot review

* more follow-up

* more updates

* finalize v0.6.0

Author: loriab

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         cfg:
           - label: Py-min
-            python-version: "3.8"
+            python-version: "3.10"
             runs-on: ubuntu-latest
             pytest: "-m 'not addon'"
 
@@ -34,6 +34,11 @@ jobs:
             runs-on: ubuntu-latest
             pytest: "-k '(not (he4 and (3b or 4b) and not sio)) or supersys'"
 
+          - label: Py-314
+            python-version: "3.14"
+            runs-on: ubuntu-latest
+            pytest: "-k '(not (he4 and (3b or 4b) and not sio)) or supersys'"
+
           - label: Demo
             python-version: "3.11"
             runs-on: ubuntu-latest
@@ -58,13 +63,16 @@ jobs:
           name: test
           channels:
             - conda-forge
+            - conda-forge/label/qcelemental_dev
+            - conda-forge/label/qcengine_dev
           dependencies:
             # Build
             - setuptools
             - setuptools-scm
             # Core
             - python
-            - qcelemental
+            - qcelemental >=0.50.0rc2
+            - qcengine >=0.50rc1  # TODO temp
             - pydantic
             # Testing
             - pytest
@@ -78,7 +86,8 @@ jobs:
             #- nwchem  # lands on different he4 soln
           EOF
           if [[ "${{ matrix.cfg.label }}" == "Py-min" ]]; then
-              sed -i "s;pydantic;pydantic=1;g" export.yaml
+            :
+              #sed -i "s;pydantic;pydantic=1;g" export.yaml
           fi
           if [[ "${{ matrix.cfg.label }}" == "Py-max" ]]; then
               sed -i "s;#- dummy1;- psi4;g" export.yaml
@@ -94,6 +103,11 @@ jobs:
               sed -i "s;#- dummy1;- psi4;g" export.yaml
               sed -i "s;#- dummy2;- pydantic-settings;g" export.yaml
           fi
+          if [[ "${{ matrix.cfg.label }}" == "Py-314" ]]; then
+              sed -i "s;#- nwchem;- nwchem;g" export.yaml
+              sed -i "s;#- dummy1;- msgpack-python;g" export.yaml
+              sed -i "s;#- dummy2;- networkx;g" export.yaml
+          fi
           # model sed for L/W
           #   sed -i "s;;;g" export.yaml
           # model sed for M
@@ -160,7 +174,7 @@ jobs:
             --color=yes --durations 50 --durations-min 20
 
     - name: CodeCov
-      uses: codecov/codecov-action@v4.0.1
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         slug: loriab/QCManyBody
@@ -190,23 +204,25 @@ jobs:
           name: test
           channels:
             - conda-forge
+            - conda-forge/label/qcelemental_dev
+            - conda-forge/label/qcengine_dev
           dependencies:
             # Build
             - setuptools
             - setuptools-scm
             # Core
             - python
-            - qcelemental
+            - qcelemental >=0.50.0rc2
             # Docs
             - numpydoc
             - docutils
-            - sphinx >=7.0.0,<8
+            - sphinx >=7.0.0
             - sphinxcontrib-napoleon
             - sphinx-rtd-theme
-            - autodoc-pydantic <2
+            - autodoc-pydantic >=2
             - sphinx-automodapi
             - sphinx-autodoc-typehints
-            - pydantic <2
+            - pydantic >=2
           EOF
           cat export.yaml
 

CITATION.cff

@@ -44,8 +44,8 @@ keywords:
   - mbe
   - schema
 license: BSD-3-Clause
-version: 0.5.2
-date-released: '2026-02-16'
+version: 0.6.0
+date-released: '2026-02-24'
 preferred-citation:
   type: article
   authors:

docs/api.rst

@@ -8,10 +8,10 @@ QCManyBody API
 .. automodapi:: qcmanybody.core
    :noindex:
 
-.. automodapi:: qcmanybody.computer
+.. automodapi:: qcmanybody.v2.computer
 
 .. automodapi:: qcmanybody.builder
 
 .. automodapi:: qcmanybody.utils
 
-.. automodapi:: qcmanybody.models
+.. automodapi:: qcmanybody.models.v2

docs/changelog.rst

@@ -2,12 +2,75 @@
 Changelog
 =========
 
+.. .. _`sec:cl0x0`:
+..
+.. v0.x.0 / 2026-MM-DD (Unreleased)
+.. ===================
+..
+.. :docs:`v0.x.0` for current. :docs:`v0.5.2` for QCSchema v1.
+..
+.. Breaking Changes
+.. ----------------
+..
+.. New Features
+.. ------------
+..
+.. Enhancements
+.. ------------
+..
+.. Bug Fixes
+.. ---------
+..
+.. Misc.
+.. -----
+..
+.. MUST (Unmerged)
+.. ---------------
+..
+.. WIP (Unmerged)
+.. --------------
+
+
+:docs:`dev` for latest.
+
+.. _`sec:cl060`:
+
+v0.6.0 / 2026-02-24
+===================
+
+:docs:`v0.6.0` for current. :docs:`v0.5.2` for QCSchema v1.
+
+v0.6.0 introduces QCSchema v2 compatibility and requires Pydantic v2.
+
+Breaking Changes
+----------------
+* :pr:`43` Deps -- require QCElemental `>=0.50.0rc2`. Package managers will not
+  solve for this version unless prereleases are allowed. No longer compatible
+  with pre-next QCElemental.
+* :pr:`43` Deps -- require Pydantic v2.
+* :pr:`43` Schema -- QCSchema v2 trial field renames updated:
+
+  * `component_results` → `cluster_results`
+  * `component_properties` → `cluster_properties`
+  * corresponding protocol name updates
+  * `ManyBodyResultProperties` → `ManyBodyProperties`
+
+New Features
+------------
+* :pr:`43` Schema -- add full QCSchema v2 compatibility, including QCManyBody schema and `Computer` interface.
+* :pr:`43` Deps -- allow Python 3.14+ insofar as supported by Pydantic.
+* :pr:`43` Models -- QCSchema v1 models are always importable (including on Python 3.14+), though instantiation will throw errors on 3.14+.
+* :pr:`43` Intf -- `Computer` reorganized into `v1/computer.py` and `v2/computer.py`.
+  The v1 version is used when accessed through ``qcmanybody.compter`` (and <3.14)
+* :pr:`43` Testing -- expand test matrix to run combinations of v1 and v2 input/output models.
+
+
 .. _`sec:cl052`:
 
 v0.5.2 / 2026-02-16
 ===================
 
-`Docs <https://MolSSI.github.io/QCManyBody/v0.5.2/>`_
+:docs:`v0.5.2` (Sphinx)
 
 Enhancements
 ------------
@@ -17,6 +80,8 @@ Enhancements
 v0.5.1 / 2025-06-14
 ===================
 
+:docs:`v0.5.1` (Mkdocs)
+
 Bug Fixes
 ---------
 

docs/conf.py

@@ -16,6 +16,8 @@
 import os
 import sys
 
+os.environ["SPHINX_BUILD"] = "1"
+
 sys.path.insert(0, os.path.abspath("../../"))
 import qcmanybody
 
@@ -70,6 +72,7 @@
 autodoc_pydantic_model_hide_paramlist = True
 autodoc_pydantic_model_show_config_summary = False
 autodoc_pydantic_field_swap_name_and_alias = True
+typehints_use_signature_return = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -213,6 +216,7 @@ def setup(app):
 extlinks = {
     "issue": ("https://github.com/MolSSI/QCManyBody/issues/%s", "GH#%s"),
     "pr": ("https://github.com/MolSSI/QCManyBody/pull/%s", "GH#%s"),
+    "docs": ("https://MolSSI.github.io/QCManyBody/%s", "Docs %s"),
 }
 
 
@@ -224,9 +228,9 @@ def setup(app):
     "numpy": ("https://numpy.org/doc/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
-    "qcelemental": ("https://molssi.github.io/QCElemental/dev/", None),
-    "qcengine": ("https://molssi.github.io/QCEngine/dev/", None),
-    "qcfractal": ("https://molssi.github.io/QCFractal/", None),
+    "qcelemental": ("https://molssi.github.io/QCElemental/next/", None),
+    "qcengine": ("https://molssi.github.io/QCEngine/next/", None),
+    "qcfractal": ("https://docs.qcarchive.molssi.org/", None),
 }
 
 # -- Options for todo extension ----------------------------------------------

docs/core-interface.rst

@@ -20,11 +20,11 @@ class.
 
 The first step is to create a molecule. This molecule is a
 `QCElemental molecule object <https://molssi.github.io/QCElemental/dev/model_molecule.html>`_, and must contain fragments.
-(see also: :ref:`molecule input <keywords:molecule>`)
+(see also: :ref:`molecule input <sec:keywords_molecule>`)
 
 .. code-block:: python
 
-    from qcelemental.models import Molecule
+    from qcelemental.models.v2 import Molecule
 
     # Create a molecule with 3 neon atoms, each as its own fragment
 
@@ -98,7 +98,7 @@ for a worked example or the below as a quick example of what ``run_calculation``
     basis = "def2-svp"
     program = "psi4"
 
-    mol = qcel.models.Molecule.from_data(p4_string)
+    mol = qcel.models.v2.Molecule.from_data(p4_string)
     mbc = qcmb.ManyBodyCore(
         molecule=mol,
         bsse_type=[bsse_type],
@@ -113,8 +113,8 @@ for a worked example or the below as a quick example of what ``run_calculation``
     calculation_results = {}
     for chem, label, imol in mbc.iterate_molecules():
         mc, real, bas = qcmb.utils.delabeler(label)
-        atin = qcel.models.AtomicInput(
-            molecule=imol, driver="energy", model={"method": method, "basis": basis}
+        atin = qcel.models.v2.AtomicInput(
+            molecule=imol, specification={"driver": "energy", "model": {"method": method, "basis": basis}}
         )
         atres = qcng.compute(atin, program, raise_error=True)
         calculation_results[label] = {

docs/high-level-interface.rst

@@ -6,20 +6,25 @@ The high-level interface takes advantage of :doc:`qcschema`
 data structures for input and output and defines an easy way to run
 the QC computations through QCEngine.
 The high-level interface uses the core-interface under the hood.
-See the :class:`~qcmanybody.models.ManyBodyInput` QCSchema class for the input options :class:`~qcmanybody.models.ManyBodyKeywords`.
+See the :class:`~qcmanybody.models.v2.ManyBodyInput` QCSchema class for the input options :class:`~qcmanybody.models.v2.ManyBodyKeywords`.
 Details on forming fragmented ``Molecule`` s are at
-:ref:`molecule input <keywords:molecule>`
+:ref:`molecule input <sec:keywords_molecule>`
 
-The high-level interface defines a :class:`~qcmanybody.computer.ManyBodyComputer` class in
-computer.py whose input is :class:`~qcmanybody.models.ManyBodyInput` schema and whose output is
-:class:`~qcmanybody.models.ManyBodyResult` schema.
-It provides :func:`qcmanybody.computer.ManyBodyComputer.from_manybodyinput()` to run through
+The high-level interface defines a :class:`~qcmanybody.v2.computer.ManyBodyComputer` class in
+computer.py whose input is :class:`~qcmanybody.models.v2.ManyBodyInput` schema and whose output is
+:class:`~qcmanybody.models.v2.ManyBodyResult` schema.
+It provides :func:`qcmanybody.v2.computer.ManyBodyComputer.from_manybodyinput()` to run through
 QCEngine.
 See ``test_highlevel_interface_example()`` in
 `test_example.py <https://github.com/MolSSI/QCManyBody/blob/main/qcmanybody/tests/test_examples.py>`_
 for a working example.
-The :class:`~qcmanybody.models.ManyBodyComputer` provides the missing link from the core interface
+The :class:`~qcmanybody.models.v2.ManyBodyComputer` provides the missing link from the core interface
 to run QC computations. A strategy that Psi4 uses is to define its own
 ``ManyBodyComputer`` (inheriting from the high-level interface) that
 runs QC computations the way Psi4 wants to while still using all the
 validation and structure provided by the QCSchema I/O classes.
+
+.. note:: QCManyBody import paths *without* QCSchema/Pydantic version specification (*i.e.*,
+   ``qcmanybody.models`` vs ``models.v1`` and ``models.v2`` and ``qcmanybody.computer`` vs. ``v1.computer`` and ``v2.computer)
+   are *always* pointing to v1 for continuity. This will be true until QCManyBody depends on QCElemental >=v0.70.0.
+   For technical constraints, these docs always reference v2 classes. See :docs:`v0.5.2` for QCSchema v1-based documentation.

docs/keywords.rst

@@ -5,6 +5,8 @@ Keywords and Options
 Required
 ========
 
+.. _`sec:keywords_molecule`:
+
 Molecule
 --------
 
@@ -16,7 +18,7 @@ Examples:
 
 .. code-block:: python
 
-    from qcelemental.models import Molecule
+    from qcelemental.models.v2 import Molecule
 
     # Molecule with 3 neon atoms, each as its own fragment
     ne3 = Molecule(symbols=["ne", "ne", "ne"],

docs/qcschema.rst

@@ -2,10 +2,15 @@
 QCSchema
 ========
 
+.. note:: QCManyBody import paths *without* QCSchema/Pydantic version specification (*i.e.*,
+   ``qcmanybody.models`` vs ``models.v1`` and ``models.v2`` and ``qcmanybody.computer`` vs. ``v1.computer`` and ``v2.computer)
+   are *always* pointing to v1 for continuity. This will be true until QCManyBody depends on QCElemental >=v0.70.0.
+   For technical constraints, these docs always reference v2 classes. See :docs:`v0.5.2` for QCSchema v1-based documentation.
+
 Inputs
 ======
 
-.. automodule:: qcmanybody.models.v1
+.. automodule:: qcmanybody.models.v2
    :members: BsseEnum, ManyBodyKeywords, ManyBodyProtocols, ManyBodySpecification, ManyBodyInput
    :undoc-members:
    :show-inheritance:
@@ -26,15 +31,15 @@ Properties/Outputs
 
     .. code-block:: python
 
-        python -c "import qcmanybody as qcmb;print(qcmb.models.MAX_NBODY)"
+        python -c "import qcmanybody as qcmb;print(qcmb.models.v2.MAX_NBODY)"
         #> 5
         export QCMANYBODY_MAX_NBODY=9  # explicitly enumerates octamer properties
-        python -c "import qcmanybody as qcmb;print(qcmb.models.MAX_NBODY)"
+        python -c "import qcmanybody as qcmb;print(qcmb.models.v2.MAX_NBODY)"
         #> 9
 
 
-.. automodule:: qcmanybody.models.v1
-   :members: ManyBodyResultProperties, ManyBodyResult
+.. automodule:: qcmanybody.models.v2
+   :members: ManyBodyProperties, ManyBodyResult
    :undoc-members:
    :show-inheritance:
    :noindex: