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Compute layer (development trunk)#87

Merged
mattwthompson merged 15 commits into
mainfrom
compute-layer
Jul 21, 2026
Merged

Compute layer (development trunk)#87
mattwthompson merged 15 commits into
mainfrom
compute-layer

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@mattwthompson

@mattwthompson mattwthompson commented Jun 3, 2026

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Closes #37
Closes #93

* Make `LiquidConfig` in place of `DensityConfig`

* Set up config for gas simulations

* Fix tragic typo

* Add property-to-compute prep module

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

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

* Add example prepping compute configs

* Lint

* Refactor apps to use `BulkLiquid`, start adding tests

* Fix typing

* Fix Python 3.12 support

* Update test environments

* Add prose to example

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

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

* Add other property-to-compute functions

* Do not assume "value" is density

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

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

* Lint

* Only use density when target is density

* Set up better deduplication of liquid simulations, code cleanup

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

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

* Improve deduplication logic, tests

* Re-run notebook

---------

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

codecov-commenter commented Jul 16, 2026

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Codecov Report

❌ Patch coverage is 43.51852% with 183 lines in your changes missing coverage. Please review.
✅ Project coverage is 69.26%. Comparing base (7cbea6a) to head (be9c3f7).

Files with missing lines Patch % Lines
dimsim/compute/apps.py 54.49% 76 Missing ⚠️
dimsim/compute/workflow.py 0.00% 58 Missing ⚠️
dimsim/compute/prep.py 63.15% 14 Missing ⚠️
dimsim/compute/fetch.py 0.00% 12 Missing ⚠️
dimsim/compute/jobs.py 0.00% 11 Missing ⚠️
dimsim/compute/configs.py 0.00% 10 Missing ⚠️
dimsim/configs/gas.py 88.88% 1 Missing ⚠️
dimsim/configs/liquid.py 90.90% 1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (7cbea6a) and HEAD (be9c3f7). Click for more details.

HEAD has 56 uploads less than BASE
Flag BASE (7cbea6a) HEAD (be9c3f7)
64 8
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #87      +/-   ##
==========================================
- Coverage   75.78%   69.26%   -6.52%     
==========================================
  Files          10       19       +9     
  Lines        1280     1604     +324     
==========================================
+ Hits          970     1111     +141     
- Misses        310      493     +183     

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@mattwthompson

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Merging this ~as-is not on the basis of it being complete but on the basis that this is effectively the new main branch

@mattwthompson
mattwthompson marked this pull request as ready for review July 21, 2026 19:45
@mattwthompson
mattwthompson merged commit 1f6b807 into main Jul 21, 2026
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Add production configs Use openff-packmol for initial coordinates?

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