share v0.30 changes among v1 and v2 models

Author: loriab

.github/workflows/CI.yaml

@@ -6,11 +6,13 @@ on:
       - master
       - next2024
       - next2025
+      - next2026
   pull_request:
     branches:
       - master
       - next2024
       - next2025
+      - next2026
   schedule:
     - cron: "9 16 * * 1"
 

README.md

@@ -3,7 +3,7 @@
 [![Build Status](https://github.com/MolSSI/QCElemental/workflows/CI/badge.svg?branch=master)](https://github.com/MolSSI/QCElemental/actions?query=workflow%3ACI)
 [![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCElemental.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCElemental)
 [![Documentation Status](https://img.shields.io/github/actions/workflow/status/MolSSI/QCElemental/CI.yaml?label=docs&logo=readthedocs&logoColor=white)](https://molssi.github.io/QCElemental/)
-[![Chat on Slack](https://img.shields.io/badge/chat-on_slack-green.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/enQtNDIzNTQ2OTExODk0LTE3MWI0YzBjNzVhNzczNDM0ZTA5MmQ1ODcxYTc0YTA1ZDQ2MTk1NDhlMjhjMmQ0YWYwOGMzYzJkZTM2NDlmOGM)
+[![Chat on Slack](https://img.shields.io/badge/chat-on_slack-green.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/zt-3calopudd-2rtUC~XN1tj1Zn9MHkV6GQ)
 ![python](https://img.shields.io/badge/python-3.8+-blue.svg)
 
 **Documentation:** [GitHub Pages](https://molssi.github.io/QCElemental/)

pyproject.toml

@@ -12,7 +12,8 @@ issues = "https://github.com/MolSSI/QCElemental/issues"
 name = "qcelemental"
 #version = "0.30.0"
 dynamic = ["version"]
-requires-python = ">=3.8"
+# pydantic.v1 not available for py >=3.14
+requires-python = ">=3.8,<3.14"
 description = "Core data structures for Quantum Chemistry."
 authors = [
   { name="The QCArchive Development Team", email="qcarchive@molssi.org" },
@@ -49,10 +50,10 @@ standard = [
 ]
 viz = [
     "nglview",  # !py38  # insufficient on pypi as also need `dot`. python-graphviz sufficient in conda.
-    "setuptools; python_version>='3.12'",  # nglview needs pkg_resources
+    "setuptools >=68.0.0; python_version>='3.12'",  # nglview needs pkg_resources
+                # setuptools is needed temporarily to avoid pkg_resources error with ngl_view. remove from here after next nglview release beyond v1.3.4
     "ipykernel <6.0",
 ]
-# pydantic.v1 not available for py >=3.14
 align = [
     "networkx <3.0", 
     "scipy",

qcelemental/models/v2/molecule.py

@@ -987,7 +987,11 @@ def from_data(
                 raise TypeError("Input type not understood, please supply the 'dtype' kwarg.")
 
         if dtype in ["string", "psi4", "xyz", "xyz+"]:
-            mol_dict = from_string(data, dtype if dtype != "string" else None)
+            subkwargs = {}
+            for key in ["verbose"]:
+                if key in kwargs:
+                    subkwargs[key] = kwargs.pop(key)
+            mol_dict = from_string(data, dtype if dtype != "string" else None, **subkwargs)
             assert isinstance(mol_dict, dict)
             input_dict = to_schema(mol_dict["qm"], dtype=3, np_out=True)
             input_dict = _filter_defaults(input_dict)
@@ -1454,21 +1458,21 @@ def align(
             amol.nuclear_repulsion_energy(),
             "Q: concern_mol-->returned_mol NRE uncorrupted",
             atol=1.0e-4,
-            quiet=(verbose > 1),
+            quiet=(verbose < 1),
         )
         if mols_align:
             assert compare_values(
                 ref_mol.nuclear_repulsion_energy(),
                 amol.nuclear_repulsion_energy(),
                 "Q: concern_mol-->returned_mol NRE matches ref_mol",
                 atol=1.0e-4,
-                quiet=(verbose > 1),
+                quiet=(verbose < 1),
             )
             assert compare(
                 True,
                 np.allclose(ref_mol.geometry, amol.geometry, atol=4),
                 "Q: concern_mol-->returned_mol geometry matches ref_mol",
-                quiet=(verbose > 1),
+                quiet=(verbose < 1),
             )
 
         return amol, {"rmsd": rmsd, "mill": solution}
@@ -1588,17 +1592,17 @@ def scramble(
             solution = data["mill"]
 
             assert compare(
-                True, np.allclose(solution.shift, perturbation.shift, atol=1.0e-6), "shifts equiv", quiet=(verbose > 1)
+                True, np.allclose(solution.shift, perturbation.shift, atol=1.0e-6), "shifts equiv", quiet=(verbose < 1)
             )
             if not do_resort:
                 assert compare(
                     True,
                     np.allclose(solution.rotation.T, perturbation.rotation),
                     "rotations transpose",
-                    quiet=(verbose > 1),
+                    quiet=(verbose < 1),
                 )
             if solution.mirror:
-                assert compare(True, do_mirror, "mirror allowed", quiet=(verbose > 1))
+                assert compare(True, do_mirror, "mirror allowed", quiet=(verbose < 1))
 
         return cmol, {"rmsd": rmsd, "mill": perturbation}
 

qcelemental/tests/test_molecule.py

@@ -1031,7 +1031,7 @@ def test_molecular_weight(Molecule, mol_string, args, formula, formula_dict, mol
 
 
 @pytest.mark.parametrize("verbose", [1, 5])
-def test_molecule_verbose(capsys, verbose):
+def test_molecule_verbose(Molecule, capsys, verbose):
     Molecule.from_data("""0 3\nNe 0 0 0\n--\nNe 2 2 2\n""", verbose=verbose)
     captured = capsys.readouterr()
     if verbose > 1:
@@ -1042,9 +1042,9 @@ def test_molecule_verbose(capsys, verbose):
 
 
 @pytest.mark.parametrize("verbose", [1, 2])
-def test_molecule_verbose_368(capsys, verbose):
+def test_molecule_verbose_368(Molecule, capsys, verbose):
     with pytest.raises(qcel.ValidationError) as e:
-        qcel.models.Molecule(
+        Molecule(
             symbols=["C", "C", "Pd", "C", "H", "H", "H", "H", "H"],
             geometry=[
                 [-39.98282536, -71.86061537, 15.18016997],