Conversation
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 Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
There was a problem hiding this comment.
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. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
| "print(f'Considering the following reaction:\\n\\n{rxn.label}\\n\\nReaction family: {rxn.family.label}')" | ||
| ] | ||
| "outputs": [], | ||
| "source": "r_species, p_species = list(), list()\nfor r_smiles in [r1_smiles, r2_smiles]:\n if r_smiles is not None:\n r_species.append(generate_species_from_smiles(r_smiles))\nfor p_smiles in [p1_smiles, p2_smiles]:\n if p_smiles is not None:\n p_species.append(generate_species_from_smiles(p_smiles))\n\nrxn = ARCReaction(r_species=r_species, p_species=p_species)\nrxn.ts_species = ARCSpecies(label='TS', is_ts=True)\nrxn.determine_family()\n\nprint(f'Considering the following reaction:\\n\\n{rxn.label}\\n\\nReaction family: {rxn.family.label}')" |
| " )\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 60.40% 60.37% -0.04%
==========================================
Files 103 103
Lines 31156 31156
Branches 8121 8121
==========================================
- Hits 18821 18811 -10
- Misses 9989 9998 +9
- Partials 2346 2347 +1
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
As spotted by @LeenFahoum, some imports were outs=dated in our Jupyter notebooks.
This PR updates them