[WIP] Upgrade to pydantic V2.

CHANGES.md

@@ -5,8 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [v0.1.0](https://github.com/CederGroupHub/WFacer/tree/0.0.1) (2023-09-22)
--   Upgraded to pymatgen==2023.09.10, and remove python==3.8 support.
--   Implemented support to generic structural calculation makers.
+- Upgraded to pymatgen==2023.09.10, and remove python==3.8 support.
+- Implemented support to generic structural calculation makers.
+- Upgraded to Pydantic 2.
 
 ## [v0.0.0](https://github.com/CederGroupHub/WFacer/tree/0.0.0) (2023-09-20)
 Initial relatively *stable* version of the code.

docs/src/example_scripts/semi_automation_BCC_AlLi/fit_model.py

@@ -5,15 +5,17 @@
 from jobflow import SETTINGS
 from monty.json import jsanitize
 from monty.serialization import loadfn
-from pydantic import parse_file_as, parse_obj_as
+from pydantic import parse_obj_as
 
 from WFacer.jobs import fit_calculations, parse_calculations, update_document
 from WFacer.schema import CeOutputsDocument
 
 
 # Execute this once all queue tasks has been completed and no job is lost.
 def __main__():
-    document = parse_file_as(CeOutputsDocument, "document.json")
+    with open("documents.json") as fin:
+        json_str = fin.read()
+    document = CeOutputsDocument.model_validate_json(json_str)
 
     iter_id = document.last_iter_id + 1
     project_name = document.project_name

docs/src/example_scripts/semi_automation_BCC_AlLi/generate.py

@@ -4,14 +4,15 @@
 from fireworks import LaunchPad
 from jobflow.managers.fireworks import flow_to_workflow
 from monty.serialization import dumpfn
-from pydantic import parse_file_as
 
 from WFacer.jobs import enumerate_structures, get_structure_calculation_flows
 from WFacer.schema import CeOutputsDocument
 
 
 def __main__():
-    document = parse_file_as(CeOutputsDocument, "document.json")
+    with open("documents.json") as fin:
+        json_str = fin.read()
+    document = CeOutputsDocument.model_validate_json(json_str)
 
     iter_id = document.last_iter_id + 1
     max_iter = document.ce_options["max_iter"]

pyproject.toml

@@ -23,12 +23,12 @@ dependencies = [
     "sparse-lm>=0.4.0",
     "sympy>=1.11.1",
     "jobflow>=0.1.9",
-    "atomate2>=0.0.11",
-    "emmet-core>=0.51.1",
+    "atomate2>=0.0.12",
+    "emmet-core>=0.71.1",
     "scikit-learn>=1.2.0",
     "scikit-optimize>=0.9.0",
     "scipy>=1.10.0, <=1.11.3",
-    "pydantic>=1.10.2,<2.0",
+    "pydantic>=2.0",
     "polytope>=0.2.3",
     "cvxpy>=1.2.1",
     "cvxopt"

requirements-optional.txt

@@ -1,3 +1,4 @@
 gurobipy==10.0.3
 pyscipopt==4.3.0
 fireworks==2.0.3
+ase==3.22.1

requirements.txt

@@ -1,18 +1,18 @@
 pyyaml==6.0.1
 joblib==1.3.2
-monty==2023.9.25
+monty==2023.11.3
 numpy==1.26.2
-pymatgen==2023.10.4
+pymatgen==2023.11.12
 smol==0.5.3
 sparse-lm==0.5.1
 sympy==1.12
-jobflow==0.1.13
-atomate2==0.0.11
-scikit-learn==1.3.1
-emmet-core==0.68.0
+jobflow==0.1.14
+atomate2==0.0.12
+scikit-learn==1.3.2
+emmet-core==0.72.21
 scikit-optimize==0.9.0
 scipy==1.11.3
-pydantic==1.10.12
+pydantic==2.5.0
 polytope==0.2.4
-cvxpy==1.3.2
+cvxpy==1.4.1
 cvxopt==1.3.2

tests/conftest.py

@@ -5,7 +5,6 @@
 from atomate2.forcefields.schemas import ForceFieldTaskDocument
 from emmet.core.tasks import TaskDoc  # emmet-core >= 0.60.0.
 from monty.serialization import loadfn
-from pydantic import parse_file_as
 from smol.cofe import ClusterExpansion
 from smol.moca import Ensemble
 
@@ -183,9 +182,10 @@ def single_wrangler_sin(single_ensemble_sin):
 
 @pytest.fixture(scope="package", params=["zns_taskdoc.json", "zns_ff_taskdoc.json"])
 def single_taskdoc(request):
+    with open(os.path.join(DATA_DIR, request.param)) as fin:
+        json_str = fin.read()
+    # In pydantic V2, we must change to using BaseModel.model_validate_json.
     if "ff" not in request.param:
-        return parse_file_as(TaskDoc, os.path.join(DATA_DIR, request.param))
+        return TaskDoc.model_validate_json(json_str)
     else:
-        return parse_file_as(
-            ForceFieldTaskDocument, os.path.join(DATA_DIR, request.param)
-        )
+        return ForceFieldTaskDocument.model_validate_json(json_str)