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Pull request overview
This PR updates end-user documentation and significantly expands the built-in solvent name mapping data used by CENSO’s solvation-model integrations.
Changes:
- Refines README wording and updates the Python API example/import paths.
- Reworks the README parallelization example (currently not aligned with the repository’s actual public API).
- Expands
solvents.jsonwith many additional solvent aliases and model mappings (CPCM/SMD/COSMO*/etc.).
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.
| File | Description |
|---|---|
src/censo/assets/solvents.json |
Large expansion of solvent alias/model mapping data; currently introduces duplicate JSON keys in several entries. |
README.md |
Documentation tweaks plus a modernized Python example; currently references non-existent parallelization APIs and mismatched workflow function signatures. |
Comments suppressed due to low confidence (3)
README.md:15
- The PR description focuses on README updates, but this PR also includes a large update to
src/censo/assets/solvents.json. Please update the PR description/title to reflect the solvent mapping change, or split this into a separate PR to keep scope clear.
- **Geometry Optimization** using:
- ORCA (native optimizer)
- xtb (ANCOPT)
- **Thermal contributions** using xtb Hessians
- **Solvent Models**:
README.md:154
PartsConfigis imported in the snippet but not used. Either remove the import to keep the example minimal, or show how it is used/typed (e.g., annotateconfigasPartsConfig).
from censo.properties import nmr
from censo.config import PartsConfig
from censo.config.parallel_config import ParallelConfig
README.md:172
- This example uses
os.cpu_count()(and referencesos.getcwd()earlier) butosis never imported in the snippet. Addimport os(or avoidosusage) so the example runs as written.
# Configure parallelization
parallel_config = ParallelConfig(ncores=os.cpu_count(), ompmin=4)
# ompmin denotes the minimum number of OMP threads assigned to each task
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lmseidler
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Mar 6, 2026
* try to complete solvent mapping (primarily cpcm, smd, cosmors) * some missing mappings * pre-commit fix * Update readme with newest API (#131) * updated readme for new api * some changes * fix dask stuff * some fixes * fix cosmo/dcosmors mappings * completed cosmors mappings + removed invalid ones * fix unlinked mappings
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This pull request updates the
README.mdto clarify usage instructions and modernize the Python API integration examples. The changes primarily improve documentation accuracy and update code references to match recent refactoring in the codebase.Documentation improvements:
Python API usage updates:
ensembledatatoensemble, and fromconfigurationtoconfig.setup.EnsembleDatato use theread_inputmethod instead of passing the input file at construction, aligning with the new API.ParallelConfigand updated the task management example to passparallel_configandclientto workflow steps.Output and workflow clarification: