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- Add ORCIDs for 9 authors (12/13 now have ORCIDs) - Update date to 29 March 2026 - Add missing DOI for Nduma2025crystalyse bib entry - Condense Software Design section, remove API-level detail - Trim Research Impact section, remove uncited claims - Minor clarity edits to Summary
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WalkthroughUpdated documentation and publication metadata: README expanded with v4 wording (acronym, screenshot, mixed‑valence note, ICSD 2024 oxidation data, new property_prediction module and ROOST predictor), a package‑structure Mermaid diagram, and many shell commands fenced; JOSS manuscript and BibTeX updated with new entries and DOIs. Changes
Sequence Diagram(s)(Skipped — changes are documentation and metadata only; no new multi‑component control flow introduced.) Estimated code review effort🎯 2 (Simple) | ⏱️ ~10 minutes Suggested labels
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@CompRhys Could you please review this PR and confirm you're happy to be listed as a co-author on the JOSS paper? |
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@README.md`:
- Line 85: Update the package diagram label in README.md where the string core
--> init["init.py — Element, Species, neutral_ratios"] appears: change the label
to use Python package convention by replacing "init.py" with "__init__.py" so it
reads core --> init["__init__.py — Element, Species, neutral_ratios"] to avoid
misleading contributors; locate the diagram/string and perform the literal text
replacement.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Repository UI
Review profile: CHILL
Plan: Pro
Run ID: e19a42d1-5302-452e-a79d-2dc511bcd0c8
⛔ Files ignored due to path filters (3)
SMACT.pngis excluded by!**/*.pngSMACT_v4.pngis excluded by!**/*.pngjoss/paper.pdfis excluded by!**/*.pdf
📒 Files selected for processing (3)
README.mdjoss/paper.bibjoss/paper.md
| SMACT --> IO["🟢 io"] | ||
| SMACT --> UT["utils"] | ||
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| core --> init["init.py — Element, Species, neutral_ratios"] |
There was a problem hiding this comment.
Use __init__.py in the package diagram label.
Line 85 currently says init.py, which is misleading for Python package structure and may confuse new contributors.
Suggested doc fix
- core --> init["init.py — Element, Species, neutral_ratios"]
+ core --> init["__init__.py — Element, Species, neutral_ratios"]📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| core --> init["init.py — Element, Species, neutral_ratios"] | |
| core --> init["__init__.py — Element, Species, neutral_ratios"] |
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@README.md` at line 85, Update the package diagram label in README.md where
the string core --> init["init.py — Element, Species, neutral_ratios"] appears:
change the label to use Python package convention by replacing "init.py" with
"__init__.py" so it reads core --> init["__init__.py — Element, Species,
neutral_ratios"] to avoid misleading contributors; locate the diagram/string and
perform the literal text replacement.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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Coverage 89.31% 89.31%
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Files 49 49
Lines 4988 4988
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Hits 4455 4455
Misses 533 533 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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I have no objections to being listed as an author if the bugfix I contributed is sufficient in scope. The manuscript looks good and I don't see anything that needs corrections from my position. |
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@aronwalsh Do you think it's ready to submit for JOSS review? |
- Add GNoME (DeepMind) and MatterGen (Microsoft) to Research Impact section - Add Merchant2023 and Zeni2025 references to bibliography - Update date to 13 April 2026 - Minor text improvements throughout - Recompile PDF Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Actionable comments posted: 1
🧹 Nitpick comments (1)
joss/paper.md (1)
77-77: Consider evidencing or softening the quantitative performance claim.Line 77 makes a precise throughput claim without a benchmark reference in-text. Either cite measured evidence or make the statement less absolute.
Proposed wording tweak
-The library is designed for desktop-scale computation, with data caching and multiprocessing support that enables screening of millions of compositions in minutes. +The library is designed for desktop-scale computation, with data caching and multiprocessing support that enables high-throughput screening of large composition spaces.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@joss/paper.md` at line 77, The sentence asserting throughput ("enables screening of millions of compositions in minutes") is an unreferenced quantitative claim; either add a citation to benchmark data or soften the wording. Update the SMACT v4 description sentence (the one starting "SMACT v4 meets these needs...") to either include a reference to measured benchmark results (e.g., "see benchmark" or cite a figure/table) or rephrase to a qualified claim such as "can enable screening of millions of compositions in minutes on typical desktop hardware in our tests" or "can screen millions of compositions in minutes, depending on hardware and settings." Ensure the modified sentence clearly links to the benchmark or uses the softened wording.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@joss/paper.md`:
- Line 128: The sentence listing funders is missing the definite article before
the council name; update the sentence in the paragraph containing "Engineering
and Physical Sciences Research Council (UKRI), the Royal Society..." to read
"the Engineering and Physical Sciences Research Council (UKRI)" so it becomes
"...including the Engineering and Physical Sciences Research Council (UKRI), the
Royal Society, the Leverhulme Trust, and the European Research Council."
---
Nitpick comments:
In `@joss/paper.md`:
- Line 77: The sentence asserting throughput ("enables screening of millions of
compositions in minutes") is an unreferenced quantitative claim; either add a
citation to benchmark data or soften the wording. Update the SMACT v4
description sentence (the one starting "SMACT v4 meets these needs...") to
either include a reference to measured benchmark results (e.g., "see benchmark"
or cite a figure/table) or rephrase to a qualified claim such as "can enable
screening of millions of compositions in minutes on typical desktop hardware in
our tests" or "can screen millions of compositions in minutes, depending on
hardware and settings." Ensure the modified sentence clearly links to the
benchmark or uses the softened wording.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Repository UI
Review profile: CHILL
Plan: Pro
Run ID: 61864adb-8164-4234-a4bc-d5aedbc27752
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joss/paper.pdfis excluded by!**/*.pdf
📒 Files selected for processing (2)
joss/paper.bibjoss/paper.md
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| # Acknowledgements | ||
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| We acknowledge contributions from all members of the Materials Design Group at Imperial College London who have provided feedback, testing, and feature requests. We thank the JOSS editors and reviewers of the original 2019 paper. This work was supported by multiple funders over the years, including Engineering and Physical Sciences Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the European Research Council. |
There was a problem hiding this comment.
Minor grammar fix in funder sentence.
Line 128 reads more naturally with “the” before the council name.
Suggested edit
-We acknowledge contributions from all members of the Materials Design Group at Imperial College London who have provided feedback, testing, and feature requests. We thank the JOSS editors and reviewers of the original 2019 paper. This work was supported by multiple funders over the years, including Engineering and Physical Sciences Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the European Research Council.
+We acknowledge contributions from all members of the Materials Design Group at Imperial College London who have provided feedback, testing, and feature requests. We thank the JOSS editors and reviewers of the original 2019 paper. This work was supported by multiple funders over the years, including the Engineering and Physical Sciences Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the European Research Council.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| We acknowledge contributions from all members of the Materials Design Group at Imperial College London who have provided feedback, testing, and feature requests. We thank the JOSS editors and reviewers of the original 2019 paper. This work was supported by multiple funders over the years, including Engineering and Physical Sciences Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the European Research Council. | |
| We acknowledge contributions from all members of the Materials Design Group at Imperial College London who have provided feedback, testing, and feature requests. We thank the JOSS editors and reviewers of the original 2019 paper. This work was supported by multiple funders over the years, including the Engineering and Physical Sciences Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the European Research Council. |
🧰 Tools
🪛 LanguageTool
[uncategorized] ~128-~128: Possible missing article found.
Context: ...tiple funders over the years, including Engineering and Physical Sciences Research Council ...
(AI_HYDRA_LEO_MISSING_THE)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@joss/paper.md` at line 128, The sentence listing funders is missing the
definite article before the council name; update the sentence in the paragraph
containing "Engineering and Physical Sciences Research Council (UKRI), the Royal
Society..." to read "the Engineering and Physical Sciences Research Council
(UKRI)" so it becomes "...including the Engineering and Physical Sciences
Research Council (UKRI), the Royal Society, the Leverhulme Trust, and the
European Research Council."
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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This looks very good to me. I had a final check with coauthors and made some light tweaks. |
4 participants
Summary
joss/paper.mdandjoss/paper.bib) describing SMACT v4Changes
joss/paper.md— JOSS manuscript with summary, statement of need, state of the field, new features, and author contributionsjoss/paper.bib— bibliographyjoss/paper.pdf— rendered PDF for reviewTest plan
docker run --rm --volume $(pwd)/joss:/data openjournals/inara -o pdf paper.mdSummary by CodeRabbit