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Fix/readme#131

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lmseidler merged 3 commits intofix/124from
fix/readme
Mar 5, 2026
Merged

Fix/readme#131
lmseidler merged 3 commits intofix/124from
fix/readme

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This pull request updates the README.md to 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:

  • Clarified the description of thermal contributions by removing the reference to "single-point Hessians" and simplifying the explanation for xtb Hessians.
  • Added "(CLI)" to the statement about xyz-format input files to clarify that this applies to the command-line interface.

Python API usage updates:

  • Updated import paths in the Python example to reflect recent module refactoring, including changes from ensembledata to ensemble, and from configuration to config.setup.
  • Changed the initialization of EnsembleData to use the read_input method instead of passing the input file at construction, aligning with the new API.
  • Revised parallelization setup to use ParallelConfig and updated the task management example to pass parallel_config and client to workflow steps.

Output and workflow clarification:

  • Clarified that results are output to JSON files and that molecule data in the ensemble is kept up-to-date, while simplifying the note about output file management.

Copilot AI review requested due to automatic review settings March 5, 2026 09:58
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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.json with 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

  • PartsConfig is 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., annotate config as PartsConfig).
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 references os.getcwd() earlier) but os is never imported in the snippet. Add import os (or avoid os usage) 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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Comment thread src/censo/assets/solvents.json
Comment thread src/censo/assets/solvents.json
Comment thread README.md Outdated
Comment thread README.md Outdated
Comment thread src/censo/assets/solvents.json
Comment thread src/censo/assets/solvents.json
Comment thread README.md Outdated
@lmseidler lmseidler added this to the v3.0.6 milestone Mar 5, 2026
@lmseidler lmseidler changed the base branch from main to fix/124 March 5, 2026 10:36
@lmseidler lmseidler merged commit d591e1c into fix/124 Mar 5, 2026
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lmseidler added a commit that referenced this pull request 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
@lmseidler lmseidler deleted the fix/readme branch March 6, 2026 11:35
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2 participants