Release v0.64

docs/source/release_notes.rst

@@ -1,6 +1,36 @@
 Release Notes
 =============
 
+0.64 / 2026-03-04
+-----------------
+
+Some cleanup and some small bug fixes. Some old code and migrations were removed and some
+incorrect endpoints were fixed.
+
+One bigger change is the improved use of upserts (ON CONFLICT DO NOTHING) in postgres, particularly
+for the molecule table but also on specification tables. This should eliminate some deadlocks
+that were happening due to the use of advisory locks.
+
+Some bugs found during the development of the web app were fixed. These related to the "/me" endpoint which
+is not used by the PortalClient, but will be used by the web app. Also, we improved the performance
+of dataset listing, which was getting slow on our large instances.
+
+This release also introduces pydantic v2 in a few isolated areas (configuration files), with more
+coming the next version.
+
+Notable PRs:
+
+- (:pr:`977`) Adding & cleaning documentation
+- (:pr:`978`) Update server and compute config to use pydantic v2
+- (:pr:`980`) Remove pre-v0.50 database migrations
+- (:pr:`985`) Making dataset views should always include required record fields
+- (:pr:`988`) Improve errors for exporting to qcschema with missing data
+- (:pr:`991`, :pr:`992`) Fix /me endpoints and add tests
+- (:pr:`993`) Add owner/user to project listing
+- (:pr:`994`) Rework database locking to use upserts when possible
+- (:pr:`995`) Faster record count in dataset list
+
+
 0.63 / 2025-09-26
 -----------------
 

qcarchivetesting/conda-envs/fulltest_server.yaml

@@ -16,7 +16,7 @@ dependencies:
   - pydantic-settings
   - zstandard
   - apsw>=3.42
-  - qcelemental<0.70a0
+  - qcelemental>=0.30,<0.70a0
   - tabulate
   - tqdm
   - pandas

qcarchivetesting/conda-envs/fulltest_snowflake.yaml

@@ -16,7 +16,7 @@ dependencies:
   - pydantic-settings
   - zstandard
   - apsw>=3.42
-  - qcelemental<0.70a0
+  - qcelemental>=0.30,<0.70a0
   - tabulate
   - tqdm
   - pandas
@@ -47,7 +47,7 @@ dependencies:
   - scipy # TODO Required for geometric REMOVE EVENTUALLY
 
   # Worker codes below
-  - qcengine<0.70a0
+  - qcengine>=0.34,<0.70a0
   - psi4>=1.9.1
   - rdkit
 

qcarchivetesting/conda-envs/fulltest_testing.yaml

@@ -16,7 +16,7 @@ dependencies:
   - pydantic-settings
   - zstandard
   - apsw>=3.42
-  - qcelemental<0.70a0
+  - qcelemental>=0.30,<0.70a0
   - tabulate
   - tqdm
   - pandas

qcarchivetesting/conda-envs/fulltest_worker.yaml

@@ -14,7 +14,7 @@ dependencies:
   - pydantic-settings
   - zstandard
   - apsw>=3.42
-  - qcelemental<0.70a0
+  - qcelemental>=0.30,<0.70a0
   - tabulate
   - tqdm
   - pandas
@@ -28,7 +28,7 @@ dependencies:
   - parsl
 
   # Worker codes below
-  - qcengine<0.70a0
+  - qcengine>=0.34,<0.70a0
   - psi4>=1.9.1
   - rdkit
   - geometric

qcarchivetesting/pyproject.toml

@@ -13,7 +13,7 @@ description = "A distributed compute and database platform for quantum chemistry
 readme = "README.md"
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 4 - Beta",
@@ -23,7 +23,7 @@ classifiers = [
 ]
 dependencies = [
     "qcfractal",
-    "qcengine<0.70a0",
+    "qcengine>=0.34,<0.70a0",
     "pytest",
     "deepdiff",
 ]

qcfractal/pyproject.toml

@@ -13,7 +13,7 @@ description = "A distributed compute and database platform for quantum chemistry
 readme = "README.md"
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 4 - Beta",

qcfractal/qcfractal/alembic/versions/2026-02-27-83127ad1a00e_add_postgres_nulls_not_distinct_to_specs.py

@@ -6,6 +6,7 @@
 
 """
 
+import sqlalchemy as sa
 from alembic import op
 
 # revision identifiers, used by Alembic.
@@ -19,6 +20,122 @@ def upgrade():
     op.drop_constraint("ux_neb_specification_keys", "neb_specification", type_="unique")
     op.drop_constraint("ux_reaction_specification_keys", "reaction_specification", type_="unique")
 
+    # We need to find duplicates due to a NULL optimization_specification_id
+    # then update references and delete
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id
+                    ) AS canonical_id
+            FROM neb_specification
+            WHERE optimization_specification_id IS NULL
+        ),
+             dupes AS (
+                 SELECT id AS duplicate_id, canonical_id
+                 FROM ranked
+                 WHERE id <> canonical_id
+             )
+        UPDATE neb_record r
+        SET specification_id = d.canonical_id
+        FROM dupes d
+        WHERE r.specification_id = d.duplicate_id;
+    """))
+
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id
+                    ) AS canonical_id
+            FROM neb_specification
+            WHERE optimization_specification_id IS NULL
+        ),
+             dupes AS (
+                 SELECT id AS duplicate_id, canonical_id
+                 FROM ranked
+                 WHERE id <> canonical_id
+             )
+        UPDATE neb_dataset_specification rds
+        SET specification_id = d.canonical_id
+        FROM dupes d
+        WHERE rds.specification_id = d.duplicate_id;
+    """))
+
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id
+                    ) AS canonical_id
+            FROM neb_specification
+            WHERE optimization_specification_id IS NULL
+        )
+        DELETE FROM neb_specification r
+            USING ranked d
+        WHERE r.id = d.id
+          AND d.id <> d.canonical_id;
+    """))
+
+    # Now for reactions, which can have singlepoint or optimization specification ids be null
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id, optimization_specification_id
+                    ) AS canonical_id
+            FROM reaction_specification
+        ),
+             dupes AS (
+                 SELECT id AS duplicate_id, canonical_id
+                 FROM ranked
+                 WHERE id <> canonical_id
+             )
+        UPDATE reaction_record r
+        SET specification_id = d.canonical_id
+        FROM dupes d
+        WHERE r.specification_id = d.duplicate_id;
+    """))
+
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id, optimization_specification_id
+                    ) AS canonical_id
+            FROM reaction_specification
+        ),
+             dupes AS (
+                 SELECT id AS duplicate_id, canonical_id
+                 FROM ranked
+                 WHERE id <> canonical_id
+             )
+        UPDATE reaction_dataset_specification rds
+        SET specification_id = d.canonical_id
+        FROM dupes d
+        WHERE rds.specification_id = d.duplicate_id;
+    """))
+
+    op.execute(sa.text("""
+        WITH ranked AS (
+            SELECT
+                id,
+                MIN(id) OVER (
+                    PARTITION BY specification_hash, singlepoint_specification_id, optimization_specification_id
+                    ) AS canonical_id
+            FROM reaction_specification
+        )
+        DELETE FROM reaction_specification r
+            USING ranked d
+        WHERE r.id = d.id
+          AND d.id <> d.canonical_id;
+    """))
+
     op.create_unique_constraint(
         "ux_neb_specification_keys",
         "neb_specification",

qcfractalcompute/pyproject.toml

@@ -13,7 +13,7 @@ description = "A distributed compute and database platform for quantum chemistry
 readme = "README.md"
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 4 - Beta",
@@ -24,6 +24,7 @@ classifiers = [
 dependencies = [
     "qcportal",
     "parsl",
+    "qcengine>=0.34,<0.70a0",
 ]
 
 

qcportal/pyproject.toml

@@ -13,7 +13,7 @@ description = "A distributed compute and database platform for quantum chemistry
 readme = "README.md"
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 4 - Beta",
@@ -26,12 +26,11 @@ dependencies = [
     "msgpack",
     "requests",
     "pyyaml",
-    "pydantic>2.10",
+    "pydantic>=2.11",
     "pydantic-settings",
     "zstandard",
     "apsw>=3.42",
-    "qcelemental<0.70a0",
-    "pint", # Required for qcelemental. Doesn't install with py3.13. REMOVE EVENTUALLY
+    "qcelemental>=0.30,<0.70a0",
     "tabulate",
     "tqdm",
     "pandas",