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Update Molecule.from_qcschema, notebook #1763

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merged 36 commits into from
Jan 24, 2024
Merged

Update Molecule.from_qcschema, notebook #1763

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1e02018
Update `Molecule.from_qcshema`, notebook
mattwthompson Nov 8, 2023
16b580d
Update some tests
mattwthompson Nov 8, 2023
a31c615
Update more tests
mattwthompson Nov 8, 2023
fa29737
Drop annotation
mattwthompson Nov 10, 2023
2496f60
Update tests
mattwthompson Nov 13, 2023
9a39d2d
Merge remote-tracking branch 'upstream/main' into new-qcarchive
mattwthompson Nov 13, 2023
aaea8d9
Update
mattwthompson Nov 15, 2023
97ee4f6
Separate QCArchive tests
mattwthompson Nov 15, 2023
5a23bd6
Work around QCPortal/OpenEye import bug
mattwthompson Nov 15, 2023
ab2ca20
Try using most recent record
mattwthompson Nov 15, 2023
5aa49b7
Install NGLview
mattwthompson Nov 15, 2023
16ff0ab
Re-run notebook
mattwthompson Nov 15, 2023
2b4c7e1
Fix doctests
mattwthompson Nov 15, 2023
eb88022
Update cookbook
mattwthompson Nov 15, 2023
2800c38
Expand linting to doc notebooks
mattwthompson Nov 15, 2023
abfe360
Fiddle with notebook setup
mattwthompson Nov 15, 2023
19ad9dc
Typo
mattwthompson Nov 15, 2023
24a8a4d
cleanups and changes to qcarchive interface notebook
j-wags Dec 2, 2023
514d3d0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 2, 2023
0b2cf14
Merge remote-tracking branch 'upstream/main' into new-qcarchive
mattwthompson Dec 2, 2023
013a900
initial update of from_qcschema
j-wags Jan 9, 2024
b58cc04
update docstrings, add/update tests, lint
j-wags Jan 9, 2024
518c08f
update qcarchive interface notebook
j-wags Jan 10, 2024
3a445fc
remove offline molecule test, remove unused code
j-wags Jan 12, 2024
61be960
Merge branch 'main' into new-qcarchive
j-wags Jan 12, 2024
2881eb3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 12, 2024
1d40923
fix tests and make mypy happy
j-wags Jan 12, 2024
8d97762
fix tests and make mypy happy
j-wags Jan 12, 2024
06b3a3e
try to make linters happy
j-wags Jan 12, 2024
65d93b3
don't lint docs notebooks
j-wags Jan 13, 2024
b733a54
Update releasehistory for api change
j-wags Jan 17, 2024
c6aa4c6
Merge remote-tracking branch 'upstream/new-qcarchive' into new-qcarchive
mattwthompson Jan 17, 2024
57754cf
Update docs/releasehistory.md
mattwthompson Jan 17, 2024
e8f3418
Lint notebooks in automation
mattwthompson Jan 17, 2024
5fd8e75
Apply suggestions from code review
j-wags Jan 18, 2024
d0bb1f5
fix docs for flake errors
j-wags Jan 18, 2024
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2 changes: 1 addition & 1 deletion devtools/conda-envs/beta_rc_env.yaml
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Expand Up @@ -37,7 +37,7 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- nglview
- mdtraj
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3 changes: 2 additions & 1 deletion devtools/conda-envs/openeye-examples.yaml
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Expand Up @@ -23,6 +23,7 @@ dependencies:
- openff-nagl-base ==0.3.0
- openff-nagl-models ==0.1.0
- typing_extensions
- nglview
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# Toolkit-specific
- openeye-toolkits
# Test-only/optional/dev/typing/examples
Expand All @@ -34,7 +35,7 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- mdtraj
- parmed =3
Expand Down
2 changes: 1 addition & 1 deletion devtools/conda-envs/openeye.yaml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- mdtraj
- nglview
Expand Down
3 changes: 2 additions & 1 deletion devtools/conda-envs/rdkit-examples.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ dependencies:
- openff-nagl-base ==0.3.0
- openff-nagl-models ==0.1.0
- typing_extensions
- nglview
# Toolkit-specific
# AmberTools 23 brings in ParmEd 4, which doesn't yet work with examples
# https://github.com/openforcefield/openff-toolkit/issues/1532
Expand All @@ -36,7 +37,7 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- nbval
- mdtraj
Expand Down
2 changes: 1 addition & 1 deletion devtools/conda-envs/rdkit.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,6 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- nglview
2 changes: 1 addition & 1 deletion devtools/conda-envs/test_env.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ dependencies:
- bson
- msgpack-python
- qcelemental
- qcportal >=0.15, <0.50.0a0
- qcportal >=0.50
- qcengine
- nglview
- mdtraj
Expand Down
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