Update our Jupyter Notebooks#884
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Pull request overview
This PR updates several ARC utility Jupyter notebooks to reflect recent internal API/module changes (notably parser and xyz-perception utilities) and strips execution metadata/outputs to keep notebooks clean in version control.
Changes:
- Update notebook imports to current module paths (e.g.,
arc.parser.parser.parse_1d_scan_energies). - Replace removed/obsolete xyz parsing helpers with
arc.species.perceive.perceive_molecule_from_xyz. - Clear cell outputs and reset
execution_counttonullacross updated notebooks.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| ipython/Tools/Visualize 1D Torsion scan.ipynb | Updates parser import path and strips cell outputs/execution counts. |
| ipython/Tools/TS Guesses.ipynb | Removes legacy RMG DB setup, adjusts reaction-family call site, strips outputs/execution counts (but currently has API mismatches). |
| ipython/Tools/Plot xyz.ipynb | Switches from removed xyz-to-molecule utilities to perceive_molecule_from_xyz, strips outputs/execution counts. |
| ipython/Tools/Perceive_xyz_(xyz_to_smiles).ipynb | Updates xyz perception flow to use perceive_molecule_from_xyz, strips outputs/execution counts. |
| ipython/Tools/External symmetry and optical isomers.ipynb | Updates xyz perception import/usage and strips outputs/execution counts. |
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| " )\n", | ||
| "sched.job_dict = {'TS': {'tsg': {}}}" | ||
| ] | ||
| "source": "sched = Scheduler(project='TS_search_1',\n species_list=rxn.r_species + rxn.p_species,\n conformer_level='wb97xd/Def2TZVP',\n opt_level='wb97xd/Def2TZVP',\n sp_level='wb97xd/Def2TZVP',\n freq_level='wb97xd/Def2TZVP',\n ess_settings=None,\n testing=True,\n project_directory='/home/alon/Dropbox (MIT)/runs/TS_search_1',\n )\nsched.job_dict = {'TS': {'tsg': {}}}" |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #884 +/- ##
==========================================
+ Coverage 60.44% 63.04% +2.59%
==========================================
Files 103 113 +10
Lines 31156 37958 +6802
Branches 8121 9956 +1835
==========================================
+ Hits 18833 23931 +5098
- Misses 9980 11146 +1166
- Partials 2343 2881 +538
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|
LeenFahoum
requested changes
May 25, 2026
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This path seems user-specific, so the notebook may fail for other users. Could we make it more general/relative?
| " )\n", | ||
| "sched.job_dict = {'TS': {'tsg': {}}}" | ||
| ] | ||
| "source": "sched = Scheduler(project='TS_search_1',\n species_list=rxn.r_species + rxn.p_species,\n conformer_level='wb97xd/Def2TZVP',\n opt_level='wb97xd/Def2TZVP',\n sp_level='wb97xd/Def2TZVP',\n freq_level='wb97xd/Def2TZVP',\n ess_settings=None,\n testing=True,\n project_directory='/home/alon/Dropbox (MIT)/runs/TS_search_1',\n )\nsched.job_dict = {'TS': {'tsg': {}}}" |
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Small update needed here: conformer_level is no longer a valid Scheduler argument. It should be split into conformer_sp_level.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: LeenFahoum <140955217+LeenFahoum@users.noreply.github.com> Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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As spotted by @LeenFahoum, some imports were outs=dated in our Jupyter notebooks.
This PR updates them