Xenonpy embeddings #141
Xenonpy embeddings #141
Conversation
WalkthroughThe recent updates across various files introduce new functionalities and enhancements to the Changes
Sequence Diagram(s) (Beta)sequenceDiagram
participant User
participant Notebook
participant Core
participant Config
User->>Notebook: Run code cell
Notebook->>Notebook: Record ExecuteTime metadata
Notebook->>Core: Request feature vector computation
Core->>Config: Load embedding configurations
Config-->>Core: Return embedding settings
Core-->>Notebook: Provide feature vector
Notebook-->>User: Display feature vector
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Actionable comments posted: 2
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (1)
src/elementembeddings/data/element_representations/xenonpy_element_features.csvis excluded by!**/*.csv
Files selected for processing (4)
- examples/composition.ipynb (9 hunks)
- src/elementembeddings/core.py (1 hunks)
- src/elementembeddings/data/element_representations/README.md (1 hunks)
- src/elementembeddings/utils/config.py (2 hunks)
Files skipped from review due to trivial changes (1)
- src/elementembeddings/utils/config.py
Additional context used
LanguageTool
src/elementembeddings/data/element_representations/README.md
[style] ~3-~3: ‘A majority of’ might be wordy. Consider a shorter alternative.
Context: ...urce for which the files were obtained. A majority of these representations have been obtaine...
[uncategorized] ~29-~29: When ‘Materials-Agnostic’ is used as a modifier, it is usually spelled with a hyphen.
Context: ...wing paper describes the details of the Materials Agnostic Platform for Informatics and Exploratio...
Markdownlint
src/elementembeddings/data/element_representations/README.md
48-48: Expected: 0 or 2; Actual: 1
Trailing spaces
57-57: null
Lists should be surrounded by blank lines
139-139: null
Lists should be surrounded by blank lines
170-170: null
Files should end with a single newline character
Additional comments not posted (3)
examples/composition.ipynb (2)
64-69: The addition of a cell to print individual element feature vectors enhances the notebook's interactivity and educational value.
6-11: Ensure that the execution time metadata is accurate and consistent across all cells.Also applies to: 39-44, 64-69, 87-92, 111-116, 162-167, 174-188, 192-197, 224-229, 240-245, 270-275
Verification successful
The execution time metadata is present and consistent across multiple cells in the notebook. Each cell has both
start_timeandend_timefields, and the timestamps appear to be in a logical sequence.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the consistency of execution time metadata across all cells. # Test: Search for inconsistencies in execution time metadata. Expect: No inconsistencies. rg --type json $'\"ExecuteTime\":'Length of output: 33
Script:
#!/bin/bash # Description: Extract all cells and their metadata from the Jupyter notebook and verify the consistency of "ExecuteTime" metadata. # Extract all cells and their metadata jq '.cells[] | {cell_type, metadata}' examples/composition.ipynb > cells_metadata.json # Verify the consistency of "ExecuteTime" metadata jq 'select(.metadata.ExecuteTime != null) | .metadata.ExecuteTime' cells_metadata.jsonLength of output: 1254
src/elementembeddings/core.py (1)
61-62: The addition ofCrystallmandXenonPyto the supported embeddings enhances the flexibility and utility of theload_datafunction.
| ### XenonPy | ||
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| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](. |
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Add a complete URL for the XenonPy package to enhance the documentation.
- The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](.
+ The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](https://example.com/xenonpy).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.
| ### XenonPy | |
| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](. | |
| ### XenonPy | |
| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](https://example.com/xenonpy). |
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| ### XenonPy | ||
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| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](. |
There was a problem hiding this comment.
Ensure the file ends with a newline character for consistency and to adhere to POSIX standards.
+ 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.
| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](. | |
| The XenonPy embedding uses the 58 features which are commonly used in publications that use the [XenonPy package](. | |
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Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (4)
baseline/test_dimension_2d_plotter_pca.pngis excluded by!**/*.pngbaseline/test_dimension_2d_plotter_tsne.pngis excluded by!**/*.pngbaseline/test_dimension_2d_plotter_tsne_skipspecies.pngis excluded by!**/*.pngbaseline/test_dimension_3d_plotter_tsne_skipspecies.pngis excluded by!**/*.png
Files selected for processing (1)
- src/elementembeddings/tests/test_plotter.py (2 hunks)
Files skipped from review due to trivial changes (1)
- src/elementembeddings/tests/test_plotter.py
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #141 +/- ##
==========================================
- Coverage 92.56% 92.55% -0.02%
==========================================
Files 12 12
Lines 1049 1047 -2
==========================================
- Hits 971 969 -2
Misses 78 78 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
Outside diff range and nitpick comments (4)
src/elementembeddings/data/element_representations/README.md (4)
Line range hint
3-3: Consider revising "A majority of" to a more concise alternative like "Most".- A majority of these representations have been obtained from the following repositories: + Most of these representations have been obtained from the following repositories:Tools
Markdownlint
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: null
Lists should be surrounded by blank lines
Line range hint
29-29: Hyphenate "Materials Agnostic" when used as a modifier.- Materials Agnostic Platform for Informatics and Exploration + Materials-Agnostic Platform for Informatics and ExplorationTools
Markdownlint
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: null
Lists should be surrounded by blank lines
Line range hint
48-48: Remove trailing spaces to adhere to Markdown best practices.- <details> - <summary>Click to see the 22 properties</summary> + <details> + <summary>Click to see the 22 properties</summary> - * [Representation of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107) + * [Representation of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107)Also applies to: 172-172
Tools
Markdownlint
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: null
Lists should be surrounded by blank lines
Line range hint
57-57: Ensure lists are surrounded by blank lines for better readability and to comply with Markdown standards.- * Number; + + * Number; - * Number + + * Number - * [Representation of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107) + + * [Representation of materials by kernel mean embedding](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.108.134107)Also applies to: 139-139, 172-172
Tools
Markdownlint
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: null
Lists should be surrounded by blank lines
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (2)
- src/elementembeddings/data/element_representations/README.md (1 hunks)
- src/elementembeddings/tests/test_plotter.py (2 hunks)
Files skipped from review as they are similar to previous changes (1)
- src/elementembeddings/tests/test_plotter.py
Additional context used
LanguageTool
src/elementembeddings/data/element_representations/README.md
[style] ~3-~3: ‘A majority of’ might be wordy. Consider a shorter alternative.
Context: ...urce for which the files were obtained. A majority of these representations have been obtaine...
[uncategorized] ~29-~29: When ‘Materials-Agnostic’ is used as a modifier, it is usually spelled with a hyphen.
Context: ...wing paper describes the details of the Materials Agnostic Platform for Informatics and Exploratio...
Markdownlint
src/elementembeddings/data/element_representations/README.md
48-48: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
57-57: null
Lists should be surrounded by blank lines
139-139: null
Lists should be surrounded by blank lines
172-172: null
Lists should be surrounded by blank lines
Additional comments not posted (1)
src/elementembeddings/data/element_representations/README.md (1)
170-173: The addition of the XenonPy section is well-documented and includes relevant publications. Ensure the URL provided is correct and accessible.Tools
Markdownlint
172-172: Expected: 0 or 2; Actual: 1
Trailing spaces
172-172: null
Lists should be surrounded by blank lines
XenonPy descriptors
Description
This PR adds the 58 element descriptors which are commonly used in works based on the XenonPy package
Type of change
How Has This Been Tested?
Reviewers
Checklist:
Summary by CodeRabbit
New Features
CrystallmandXenonPyembeddings in the data loading function.Bug Fixes
Chores
"typing-extensions"to the list of dependencies in the setup configuration.