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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

unreleased

0.10.0 - 2024-09-12

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

0.8.1 - 2024-07-12

Added

  • release.py script.

Changed

  • Updated qcop and qcio. Reverts back to Structure.identifiers over Structure.ids. Adds 10x performance gain to xtb by solving their overthreading issue.

0.8.0 - 2024-07-10

Changed

  • 🚨 Updated qcio and qcop to use new Structure instead of Molecule

0.7.2 - 2024-06-13

Changed

  • Updated to qcio 0.9.3 which properly registers all concrete classes of ProgramOutput[InputType, ResultsType on output.py module for celery serializers.
  • Updated to qcop 0.6.2 which properly sets exc.program_output on all exception classes.
  • Updated all packages with poetry lock.
  • Updated syntax in examples scripts to be more comprehensive.

0.7.1 - 2024-06-10

Changed

  • Updated qcio 0.6.0 -> 0.6.1 to fix AdapterError subclasses not passing the .program_output argument correctly to parent classes so celery was failing to serialize this attribute on the exception object.
  • Updated all dependencies to the latest versions in poetry.lock. (poetry lock)

0.7.0 - 2024-04-23

Changed

  • Updated to qcop=^0.6.0 and qcio=^0.9.0 to use latest Generic data structures including ProgramOutput[InputType, ResultsType] as a replacement for all other output models.

0.6.9 - 2024-04-12

Changed

  • Updated qcop=^0.5.5 to capture exception.program_failure more comprehensively on adapter.compute(...) calls.
  • Updated qcop also has native xtb adapter now to avoid >1s overhead associated with qcengine.

0.6.8 - 2024-04-05

Changed

  • Updated celery from buggy 5.3.1 that would feed gradients to parallel_hessian in random orders causing the wrong gradients to be applied to the wrong atoms. Now using ^5.3.4 which fixes this issue.
  • Tightened many >= package dependencies to more tight ^ dependencies to avoid breaking changes in the future.
  • Changed tests for parallel_hessian and parallel_frequency_analysis to test for correctness of the results rather than just that the function runs without error. This would capture a future regression where celery returns results in the wrong order.
  • Updated all dependencies to the latest versions. (poetry update)

0.6.7 - 2024-03-29

Changed

    • Upgraded to qcop>=0.5.1 and qcio>=0.8.1 to fix QCElemental behavior that auto-rotates Molecules without user consent.

0.6.6 - 2024-03-26

Added

  • Documentation for a SLURM deploy of BigChem.
  • BIGCHEM_RESULT_EXPIRES environment variable to set the expiration time of results in the database.

Changed

  • Example scripts are all standalone runnable and don't require the .xyz files to be present in the directory.

Removed

  • version: 3.8 tag from docker-compose files as per new docs suggesting this is no longer necessary.

0.6.5 - 2024-03-16

Changed

  • Updated qcop from 0.4.8 to 0.5.0 which sets raise_exc=True by default on compute(...) function.
  • Updated black from 23.x.x -> 24.x.x.

0.6.4 - 2024-01-12

Changed

  • Updated qcop from 0.4.7 to 0.4.8 to fix the bug when geometric exceptions were raised.
  • Updated qcio from 0.7.1 to 0.8.0.

0.6.3 - 2023-09-27

Changed

  • Updated qcop from 0.4.6 to 0.4.7 to use latest qcparse encoding of TeraChem input files.

0.6.2 - 2023-09-26

Added

  • Added dftd3 conda package for psi4 to enable dispersion corrections. Updated other worker packages to latest versions.

0.6.1 - 2023-09-22

Changed

  • Updated qcop from 0.4.4 -> 0.4.6 to incorporate bugfix for collect_wfn=True on adapters that don't support it.

0.6.0 - 2023-09-20

Changed

  • Updated qcio to >=0.7.0 which renamed DualProgramArgs to SubProgramArgs.
  • Updated /docker/fire.yaml stack configuration to use the latest BigChem image.

Fixed

  • Fixed typo in multistep_opt algorithm where the loop was selecting programs [:1] instead of [1:] for the second and subsequent steps.

0.5.4 - 2023-09-08

Changed

  • Installing BigChem to /opt/ in docker container instead of /code/.
  • Updated qcio from >=0.5.0 to >=0.6.0.
  • Updated qcop from >=0.4.3 to >=0.5.0.

Added

  • Device configuration to /docker/terachem.yaml.
  • Test to ensure exception objects raised in workers have .program_failure object returned to the client.

0.5.3 - 2023-09-03

Changed

  • Moved qcengine and geometric to be optional dependencies so that client applications can install and use BigChem without these packages.

0.5.2 - 2023-09-02

Changed

  • Updated to qcop>=0.4.2 for patch fixing TeraChem input file runtime variable.
  • Updated all package dependencies.

0.5.1 - 2023-09-02

Added

  • Typos spell check to pre-commit and GitHub actions.

Removed

  • The energy kwarg for frequency_analysis task since the electronic energy is correctly passed to the underlying geomeTRIC function from the hessian calculation.
  • tcpb, pyberny

Changed

  • Updated to qcop v0.4.1 so that we can access exception.program_failure objects.
  • Settings can now accept extra types. This makes it possible to install BigChem inside other apps--like ChemCloud--and not have the Settings object raise an exception if there are values in a .env file or other secrets for the second application. BigChem's Settings object will pick them up too, but they are never accessed so it doesn't matter.

0.5.0 - 2023-08-31

Added

  • Multiple scripts to /examples/ directory to show basic utilization of BigChem.
  • docs/swarm-gpu.md write up covering GPU support in Docker Swarm.
  • TeraChem compose and swarm yaml specifications.
  • Quickstart documentation to README.md.
  • qcio and qcop as main data structures and QC program driver packages.

Changed

  • Dropped docker-compose from yaml filenames in /docker to make commands less verbose.
  • Modified docker-compose.yaml to work for both compose and swarm.
  • Removed support for Python 3.7 (reached end of life).
  • Updated worker container from micromamba:1.3-jammy -> micromamba:1.4-jammy.
  • Upgraded pydantic from v1 -> v2.

Removed

  • Removed support for QCElemental and QCEngine.
  • scripts/hacking directory with old, unused files.

0.4.0 - 2023-02-3

Added

  • multistep_opt algorithm and associated multistep_opt.py script to demonstrate how multiple QC packages can be used in unison to optimize a molecule.
  • result_to_input task to transform results from one process (like an optimization) into inputs for the next (perhaps a subsequent optimization step). This enables easy chaining together of multiple packages in multistep_opt.

Changed

  • Modified env.yaml to allow flexible versions for worker packages and created a new env.lock file for workers.
  • Updated tcpb>=0.13.0 to better return stdout data from a crashed TeraChem server.

0.3.0 - 2022-12-16

Added

  • Added extensive documentation to README.md to guide new users and developers.

Changed

  • Switched default worker environment from conda to micromamba to accelerate build times (dramatically!).
  • Created env.lock file for reproducible builds of micromamba/conda installs
  • Updated psi4==1.5 -> 1.7
  • Updated qcengine==0.21.0 -> 0.26.0
  • Updated qcelemental==0.24.0 -> 0.25.1
  • Switched geomeTRIC from personal patched version to new 1.0 release.

0.2.0 - 2022-07-19

Changed

  • Changed name from BigQC to BigChem to highlight that backend packages and routines may be related to any computational chemistry algorithm, not just quantum chemistry.

0.1.3 - 2022-06-20

Added

  • C_FORCE_ROOT=true environment variable to the worker image so the variable doesn't have to be passed to a container at instantiation.
  • Added :latest tag to build_worker.sh script.
  • Added push_worker.sh scripts so I don't forget to push the tag and the image as the latest tag to the docker repo.

0.1.2 - 2022-06-15

Changed

  • Wrapped qcng.compute and qcng.compute_procedure directly with bigqc.task rather than redefining each function
  • Simplified settings by removing get_settings function in favor of globally defined settings object. (No advantage to using a callable since we are not using dependency injection of a settings callable.)
  • Updated app name to bigqc from tasks in app.py.

0.1.1 - 2022-06-14

Added

  • docker-compose.web.yaml to specify middleware services for a deployment behind traefik reverse proxy.

Changed

  • Separated out dependencies only required for the worker.
  • Cleaned up root of project by moving files to docker directory
  • Cleaned up docker-compose.xstream.yaml stack specification

0.1.0 - 2022-06-14

Added

  • Initial release of core BigQC feature set. Tasks for compute (single point energy, gradient, hessian, and properties calculations) and compute_procedure (geometry optimization routine). Algorithms for distributed hessian and normal mode analysis with their associated tasks.