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Add NoBatch mode#602

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mattwthompson merged 4 commits intomainfrom
add-nobatch
Jan 29, 2025
Merged

Add NoBatch mode#602
mattwthompson merged 4 commits intomainfrom
add-nobatch

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@lilyminium
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@lilyminium lilyminium commented Jan 20, 2025

Description

Fixes #601

  • Adds a mode that just creates batches that increment sequentially
  • Refactors tests slightly to use fixtures and take place in a temporary directory -- running an EvaluatorServer creates a persistent stored_data directory

Status

  • Ready to go

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codecov bot commented Jan 20, 2025

Codecov Report

Attention: Patch coverage is 88.23529% with 2 lines in your changes missing coverage. Please review.

Project coverage is 87.30%. Comparing base (3b38655) to head (375f272).
Report is 22 commits behind head on main.

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This was referenced Jan 21, 2025
Comment on lines +460 to +461
elif batch_mode == BatchMode.NoBatch:
batches = self._no_batch(submission, force_field_id)
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Could you add a test that covers these lines?

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Sure -- added a test for _prepare_batches.

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PS This code path should be used in the tests in #604 and #608.

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LGTM

@mattwthompson mattwthompson merged commit 36fdda5 into main Jan 29, 2025
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@mattwthompson mattwthompson added this to the 0.4.11 milestone Jan 29, 2025
lilyminium added a commit that referenced this pull request Mar 3, 2025
* add nobatch

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
lilyminium added a commit that referenced this pull request Mar 25, 2025
* add equilibration code

* add some preliminary docs

* add some docstrings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* switch greaterthan -> greaterthanorequalto

* add updates for equilibrated properties

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix equilibration_properties

* Add easy way to create new substances for real numbers of mols (#611)

* add easy way to create new substances

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add new conditions and tests (#614)

* add new conditions and tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add NoBatch mode (#602)

* add nobatch

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Migrate `tmpdir` fixture to new `tmp_path` (#615)

* [pre-commit.ci] pre-commit autoupdate (#617)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 24.10.0 → 25.1.0](psf/black@24.10.0...25.1.0)
- [github.com/PyCQA/isort: 5.13.2 → 6.0.0](PyCQA/isort@5.13.2...6.0.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add AttributeClass initialization (#606)

* add failing test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add __init__ method

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Strip out `openmm.CMMotionRemover` force internally (#622)

* Automatically strip out `openmm.CMMotionRemover` force internally

* More consistently strip force

* Fix relative tolerance (#604)

* add nobatch

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add fix

* add helper test functions

* add test data

* Revert "add fix"

This reverts commit 3d9f043.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Revert "Revert "add fix""

This reverts commit 79a8bea.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>

* allow boxes to be retrieved, read, and short-circuit the graph

* add data

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove additional raise

* disallow merging

* rm doc stub for now

* Update openff/evaluator/workflow/workflow.py

* Update openff/evaluator/properties/density.py

* remove unused imports

* fix imports

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Matt Thompson <matt.thompson@openforcefield.org>
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
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Add NoBatch mode

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