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Refactor and small updates to OpenMM and OpenFF task documents #1087

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merged 18 commits into from
Sep 9, 2024
Merged

Refactor and small updates to OpenMM and OpenFF task documents #1087

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9b77213
Refine and organize the core schema for the openmm and openff atomate…
orionarcher Sep 5, 2024
45baaf0
Create a calculations task document to organize the outputs of openmm…
orionarcher Sep 5, 2024
721ec22
Create a benchmarking task document to be output by a benchmarking bu…
orionarcher Sep 5, 2024
4e298b0
Create a solvation task document to be output by a solvation builder.
orionarcher Sep 5, 2024
8e94763
Refactor the dependencies and CI for emmet-core to include MD-related…
orionarcher Sep 5, 2024
26cd281
Add testing for calc output from directory and related test files.
orionarcher Sep 5, 2024
3029fd4
Fix linting error in molecules api code.
orionarcher Sep 5, 2024
16f1b44
fixup! Refactor the dependencies and CI for emmet-core to include MD-…
orionarcher Sep 5, 2024
64d05dc
Respond to tsmathis review
orionarcher Sep 5, 2024
bb75a08
rm py3.9 reqs file
tsmathis Sep 5, 2024
2277660
re pip-compile
tsmathis Sep 5, 2024
5926ec1
Add docstring to calculations doc, clean up in line descriptions.
orionarcher Sep 5, 2024
d4c5214
pin dgl for ml reqs, re pip-compile
tsmathis Sep 5, 2024
8977964
Multiple WIP changes to change HexBytes to CompressedStr
orionarcher Sep 6, 2024
aa8d2bd
Delete classical_md folder
orionarcher Sep 9, 2024
2252a3c
Improve documentation of CompressedStr
orionarcher Sep 9, 2024
0aeacc9
Improve documentation of CompressedStr
orionarcher Sep 9, 2024
a1ede7c
Merge branch 'main' into md_core
orionarcher Sep 9, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/testing.yml
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Expand Up @@ -30,7 +30,7 @@ jobs:
python-version: ${{ matrix.python-version }}
channels: anaconda, conda-forge

- name: Install OpenBabel
- name: Install all conda requirements
shell: bash -l {0}
run: |
conda install openbabel openff-toolkit>=0.14.0 openff-interchange>=0.3.22 sqlite -y
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1 change: 0 additions & 1 deletion emmet-api/emmet/api/routes/molecules/summary/resources.py
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Expand Up @@ -13,7 +13,6 @@
ChargeSpinQuery,
HashQuery,
StringRepQuery,
DeprecationQuery,
)
from emmet.api.routes.materials.summary.query_operators import HasPropsQuery
from emmet.api.routes.molecules.summary.hint_scheme import SummaryHintScheme
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74 changes: 0 additions & 74 deletions emmet-core/emmet/core/classical_md.py
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1 change: 0 additions & 1 deletion emmet-core/emmet/core/classical_md/__init__.py
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6 changes: 0 additions & 6 deletions emmet-core/emmet/core/classical_md/openmm/__init__.py
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235 changes: 0 additions & 235 deletions emmet-core/emmet/core/classical_md/openmm/tasks.py
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5 changes: 5 additions & 0 deletions emmet-core/emmet/core/openff/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
from emmet.core.openff.tasks import (
MoleculeSpec,
ClassicalMDTaskDocument,
MDTaskDocument,
)
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