Merge pull request #62 from mtzgroup/feature-crest-terachemopt-new-te…

…rachem-binary

.github/workflows/basic-code-quality.yaml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install ruff
         run: pip install ruff
       - name: ruff
@@ -26,50 +26,22 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install poetry
         run: pip install poetry
       - name: Install repo
         run: poetry install --no-interaction --no-ansi
       - name: mypy
         run: mypy .
 
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-      - name: Install black
-        run: pip install black
-      - name: Check code formatting with black
-        run: black --check .
-
-  isort:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-      - name: Install poetry
-        run: pip install poetry
-      - name: Install repo
-        run: poetry install --no-interaction --no-ansi
-      - name: Check import formatting with isort
-        run: isort --check-only --diff .
-
   detect-secrets:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install detect secrets
         run: pip install detect-secrets
       - name: Look for secrets

.github/workflows/publish-to-pypi.yaml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install poetry
         run: |

.github/workflows/tests.yaml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Set up Python
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install poetry
         run: pip install poetry
       - name: Install repo

.pre-commit-config.yaml

@@ -15,18 +15,10 @@ repos:
         exclude: poetry.lock
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.278"
+    rev: "v0.5.7"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.4.1
     hooks:
@@ -40,7 +32,7 @@ repos:
             types-paramiko,
           ]
   - repo: https://github.com/crate-ci/typos
-    rev: v1.16.10
+    rev: v1.24.5
     hooks:
       - id: typos
   - repo: local

CHANGELOG.md

@@ -6,6 +6,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Changed
+
+- 🚨 Bumped minimum python version from 3.8 -> 3.9.
+- Updated all conda dependencies in `env.lock`.
+- Removed Intel's `openmp` from `env.yaml` since they seem to have removed their channel. Replaced it with `llvm-openmp`.
+- Updated to `qcelemental 0.28.0` as this is required for `psi4 1.9`.
+- Upgraded all python package dependencies.
+- Dropped `black` and `isort` in favor of `ruff`.
+- Updated typing syntax to python 3.9.
+- Updated base image from `mambaorg/micromamba:1.4-jammy` -> `mambaorg/micromamba:1.5-jammy`.
+
+### Added
+
+- Support for CREST conformer searches (interface support via new `qcop`. Binary via conda).
+
 ## [0.9.0] - 2024-07-19
 
 ### Changed

bigchem/algos.py

@@ -1,6 +1,6 @@
 """Top level functions for parallelized BigChem algorithms"""
 
-from typing import List, Union
+from typing import Union
 
 from qcio import (
     CalcType,
@@ -83,8 +83,8 @@ def parallel_frequency_analysis(
 def multistep_opt(
     structure: Structure,
     calctype: CalcType,
-    programs: List[str],
-    program_args: List[Union[ProgramArgs, ProgramArgsSub]],
+    programs: list[str],
+    program_args: list[Union[ProgramArgs, ProgramArgsSub]],
     **kwargs,
 ) -> Signature:
     """Use multiple steps to sequentially optimize a structure

bigchem/config.py

@@ -1,5 +1,7 @@
 """Settings and Configuration for workers. Read more: https://pydantic-docs.helpmanual.io/usage/settings/"""
 
+from __future__ import annotations
+
 from pathlib import Path
 from typing import Optional
 

bigchem/tasks.py

@@ -1,5 +1,5 @@
 from itertools import zip_longest
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 from qcio import (
@@ -15,6 +15,7 @@
     SinglePointResults,
     StructuredInputs,
 )
+
 from qcop import compute as qcop_compute
 
 from .app import bigchem
@@ -85,7 +86,7 @@ def output_to_input(
 
 @bigchem.task
 def assemble_hessian(
-    gradients: List[ProgramOutput[ProgramInput, SinglePointResults]], dh: float
+    gradients: list[ProgramOutput[ProgramInput, SinglePointResults]], dh: float
 ) -> ProgramOutput[ProgramInput, SinglePointResults]:
     """Assemble hessian from an array of gradient computations
 
@@ -178,7 +179,7 @@ def add(x, y):
 
 
 @bigchem.task
-def task_sum(values: List[Union[float, int]], extra: int = 0) -> Union[float, int]:
+def task_sum(values: list[Union[float, int]], extra: int = 0) -> Union[float, int]:
     """Sum all the values in a list
 
     NOTE: Used for design testing as a summation at the end of add (a chord)

bigchem/utils.py

@@ -1,6 +1,5 @@
 """Helper functions not for end users"""
 
-from typing import List
 
 import numpy as np
 from qcio import CalcType, ProgramInput
@@ -10,7 +9,7 @@
 
 def _gradient_inputs(
     prog_input: ProgramInput, dh: float = settings.bigchem_default_hessian_dh
-) -> List[ProgramInput]:
+) -> list[ProgramInput]:
     """Create ProgramInput gradient calculations for a numerical hessian
 
     Params: