[WIP] Add option to use pre-supplied embeddings within SMACT for the dopant_prediction module #260
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Warning Review failedThe pull request is closed. WalkthroughThe Changes
Sequence Diagram(s) (Beta)sequenceDiagram
participant User
participant Doper
participant DataLoader
participant SimilarityCalculator
User->>Doper: Initialize with embedding and use_probability
Doper->>DataLoader: Load embedding data
Doper->>SimilarityCalculator: Calculate species similarity/probability
User->>Doper: Call get_dopants
Doper->>Doper: Check use_probability flag
Doper->>SimilarityCalculator: Get similarity/probability scores
Doper->>User: Return dopant predictions
Poem
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #260 +/- ##
===========================================
+ Coverage 73.82% 74.45% +0.63%
===========================================
Files 24 24
Lines 2048 2083 +35
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+ Hits 1512 1551 +39
+ Misses 536 532 -4 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 6
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Files selected for processing (1)
- smact/dopant_prediction/doper.py (5 hunks)
Additional context used
Ruff
smact/dopant_prediction/doper.py
3-3:
typing.Callableimported but unused
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typing.Unionimported but unused
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smact.Elementimported but unused
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smact.element_dictionaryimported but unused
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groupbyfrom line 2 shadowed by loop variable
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smact/dopant_prediction/doper.py
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Additional comments not posted (2)
smact/dopant_prediction/doper.py (2)
47-50: Ensure proper error handling for mutually exclusive parameters.Tools
GitHub Check: codecov/patch
[warning] 48-48: smact/dopant_prediction/doper.py#L48
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344-347: Ensure that the headers into_tablemethod are correctly set based on theuse_probabilityflag.Tools
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smact/dopant_prediction/doper.py
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| import numpy as np | ||
| from pymatgen.util import plotting | ||
| from tabulate import tabulate | ||
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| import smact | ||
| from smact import Element, element_dictionary | ||
| from smact import Element, data_directory, element_dictionary |
There was a problem hiding this comment.
Remove unused imports to maintain clarity and reduce overhead.
- from smact import Element, element_dictionaryCommittable 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.
| from smact import Element, data_directory, element_dictionary | |
| from smact import data_directory |
Tools
Ruff
10-10:
smact.Elementimported but unused
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smact.element_dictionaryimported but unused
smact/dopant_prediction/doper.py
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| from itertools import groupby | ||
| from typing import Callable, List, Tuple, Type, Union | ||
| from typing import Callable, List, Optional, Tuple, Type, Union |
There was a problem hiding this comment.
Remove unused imports to clean up the code.
- from typing import Callable, UnionCommittable suggestion was skipped due low confidence.
Tools
Ruff
3-3:
typing.Callableimported but unused
3-3:
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smact/dopant_prediction/doper.py
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| if self.use_probability: | ||
| sum_prob += CM.sub_prob(cation, selected_site) | ||
| else: | ||
| sum_prob += CM.get_lambda(cation, selected_site) |
There was a problem hiding this comment.
Refactor the repeated logic for probability and lambda calculations into a helper function to improve code maintainability.
+ def calculate_value(self, CM, specie, selected_site):
+ if self.use_probability:
+ return CM.sub_prob(specie, selected_site)
+ else:
+ return CM.get_lambda(specie, selected_site)
- if self.use_probability:
- sum_prob += CM.sub_prob(cation, selected_site)
- else:
- sum_prob += CM.get_lambda(cation, selected_site)
+ sum_prob += self.calculate_value(CM, cation, selected_site)Also applies to: 197-204, 211-218, 228-235, 242-249
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.
| if self.use_probability: | |
| sum_prob += CM.sub_prob(cation, selected_site) | |
| else: | |
| sum_prob += CM.get_lambda(cation, selected_site) | |
| def calculate_value(self, CM, specie, selected_site): | |
| if self.use_probability: | |
| return CM.sub_prob(specie, selected_site) | |
| else: | |
| return CM.get_lambda(specie, selected_site) | |
| sum_prob += self.calculate_value(CM, cation, selected_site) |
Tools
GitHub Check: codecov/patch
[warning] 88-89: smact/dopant_prediction/doper.py#L88-L89
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| SKIPSSPECIES_COSINE_SIM_PATH = os.path.join( | ||
| data_directory, | ||
| "species_rep/skipspecies_20221028_319ion_dim200_cosine_similarity.json", | ||
| ) |
There was a problem hiding this comment.
Tip
Codebase Verification
The specified JSON file exists but is located at a different path than expected. Update the path in your code to reflect the correct location.
- Correct path:
smact/data/species_rep/skipspecies_20221028_319ion_dim200_cosine_similarity.json
Analysis chain
Ensure the path to the cosine similarity JSON is correct and accessible.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the existence of the cosine similarity JSON file.
# Test: Check if the file exists. Expect: File exists.
if [ -f "src/smact/data_directory/species_rep/skipspecies_20221028_319ion_dim200_cosine_similarity.json" ]; then
echo "File exists."
else
echo "File does not exist."
fi
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# Description: Search for the cosine similarity JSON file within the repository.
# Test: Use fd to locate the file. Expect: File path is found.
fd skipspecies_20221028_319ion_dim200_cosine_similarity.json
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| "Only one of filepath or embedding should be provided" | ||
| ) | ||
| if embedding and embedding != "skipspecies": | ||
| raise ValueError(f"Embedding {embedding} is not supported") |
There was a problem hiding this comment.
Tip
Codebase Verification
The search results indicate that there are no specific tests for embedding validation logic in the current test suite. The existing tests do not cover the scenario where an unsupported embedding raises a ValueError.
- smact/tests/test_doper.py: Contains a test for
dopant_prediction, but it does not seem to cover embedding validation. - Other test files and functions do not appear to be related to embedding validation.
To ensure comprehensive test coverage, please add a test case that specifically validates the embedding logic and raises a ValueError for unsupported embeddings.
Analysis chain
Add test coverage for the embedding validation logic.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the test coverage for embedding validation logic.
# Test: Search for tests related to embedding validation. Expect: Tests exist.
rg --type python $'def test_embedding_validation'
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#!/bin/bash
# Description: Verify the test coverage for embedding validation logic.
# Correct the rg command to search for test functions in Python files.
rg 'def test_' --glob '*.py'
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fd --type f --name '*test*.py'
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# Description: Verify the test coverage for embedding validation logic.
# Correct the fd command to search for test files.
fd --type f test
# Manually inspect the test functions found by rg to see if any might cover embedding validation.
rg 'def test_' --glob '*.py'
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GitHub Check: codecov/patch
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smact/dopant_prediction/doper.py
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| self.cation_mutator = CationMutator.from_json( | ||
| SKIPSSPECIES_COSINE_SIM_PATH | ||
| ) |
There was a problem hiding this comment.
Tip
Codebase Verification
The from_json method in the CationMutator class was not found, and no error handling was detected in the from_json method located in smact/structure_prediction/mutation.py. This indicates that the CationMutator.from_json method might not handle JSON path errors properly.
- Ensure that the
CationMutator.from_jsonmethod exists and is correctly implemented. - Verify that the method includes proper error handling for the provided JSON path.
Analysis chain
Ensure that the CationMutator.from_json method correctly handles the provided JSON path.
Scripts executed
The following scripts were executed for the analysis:
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#!/bin/bash
# Description: Verify the correct handling of JSON path in `CationMutator.from_json`.
# Test: Search for error handling in `CationMutator.from_json`. Expect: Proper error handling.
rg --type python $'CationMutator.from_json' | rg 'try'
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# Description: Verify the correct handling of JSON path in `CationMutator.from_json`.
# Test: Search for the `from_json` method in the `CationMutator` class and check for error handling.
ast-grep --lang python --pattern $'class CationMutator {
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def from_json($_, $_) {
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}
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}' | rg 'try'
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ast-grep --lang python --pattern $'class CationMutator:
def from_json($_, $_):
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ast-grep --lang python --pattern $'def from_json($_, $_):
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rg --type py 'def from_json'
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rg --type py 'def from_json' -A 20 | rg 'try'
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GitHub Check: codecov/patch
[warning] 54-54: smact/dopant_prediction/doper.py#L54
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Actionable comments posted: 2
Outside diff range and nitpick comments (1)
smact/dopant_prediction/doper.py (1)
Line range hint
100-100: Avoid shadowing the importgroupbywith a loop variable.- for groupby in zip(keys, dopants_list, groupby_list): + for group in zip(keys, dopants_list, groupby_list):Tools
GitHub Check: codecov/patch
[warning] 58-58: smact/dopant_prediction/doper.py#L58
Added line #L58 was not covered by tests
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (3)
- docs/conf.py (1 hunks)
- smact/dopant_prediction/doper.py (7 hunks)
- smact/tests/test_doper.py (2 hunks)
Files not reviewed due to errors (1)
- smact/tests/test_doper.py (no review received)
Files skipped from review due to trivial changes (1)
- docs/conf.py
Additional context used
Ruff
smact/tests/test_doper.py
4-4:
smactimported but unused
6-6:
smact.structure_prediction.mutationimported but unused
14-14: Local variable
num_dopantsis assigned to but never used
59-59: Local variable
testis assigned to but never usedsmact/dopant_prediction/doper.py
100-100: Import
groupbyfrom line 2 shadowed by loop variable
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smact/tests/test_doper.py
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Additional comments not posted (1)
smact/dopant_prediction/doper.py (1)
1-1: Remove unused import.- import smactLikely invalid or redundant comment.
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| import numpy as np | ||
| from pymatgen.util import plotting | ||
| from tabulate import tabulate | ||
|
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||
| import smact | ||
| from smact import Element, element_dictionary | ||
| from smact import data_directory |
There was a problem hiding this comment.
Remove unused imports.
- from smact import data_directory
- from smact.structure_prediction import mutation, utilitiesCommittable suggestion was skipped due low confidence.
| SKIPSSPECIES_COSINE_SIM_PATH | ||
| ) | ||
| elif filepath: | ||
| self.cation_mutator = mutation.CationMutator.from_json(filepath) |
There was a problem hiding this comment.
Tip
Codebase Verification
The specific lines in doper.py are not covered by tests.
self.cation_mutator = mutation.CationMutator.from_json(filepath)sum_prob += self._calculate_species_sim_prob(cation, selected_site)return self.cation_mutator.get_lambda(species1, species2)headers = ["Rank", "Dopant", "Host", "Probability", "Selectivity"]headers = ["Rank", "Dopant", "Host", "Similarity", "Selectivity"]
These lines were not found in the test files smact/tests/test_core.py, smact/tests/test_doper.py, and smact/tests/test_structure.py.
Analysis chain
Ensure these lines are covered by tests.
Also applies to: 88-88, 159-159, 352-353, 355-355
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify test coverage for specific lines in doper.py.
# Test: Check if lines 58, 88, 159, 352-353, 355 are covered by tests. Expect: Lines are covered.
rg --type python $'self.cation_mutator = mutation.CationMutator.from_json(filepath)' --files-with-matches
rg --type python $'sum_prob += self._calculate_species_sim_prob(cation, selected_site)' --files-with-matches
rg --type python $'return self.cation_mutator.get_lambda(species1, species2)' --files-with-matches
rg --type python $'headers = ["Rank", "Dopant", "Host", "Probability", "Selectivity"]' --files-with-matches
rg --type python $'headers = ["Rank", "Dopant", "Host", "Similarity", "Selectivity"]' --files-with-matches
Length of output: 688
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#!/bin/bash
# Description: Verify test coverage for specific lines in doper.py.
# Test: Check if lines 58, 88, 159, 352-353, 355 are covered by tests. Expect: Lines are covered.
rg --glob '*.py' 'self.cation_mutator = mutation.CationMutator.from_json(filepath)'
rg --glob '*.py' 'sum_prob += self._calculate_species_sim_prob(cation, selected_site)'
rg --glob '*.py' 'return self.cation_mutator.get_lambda(species1, species2)'
rg --glob '*.py' 'headers = ["Rank", "Dopant", "Host", "Probability", "Selectivity"]'
rg --glob '*.py' 'headers = ["Rank", "Dopant", "Host", "Similarity", "Selectivity"]'
Length of output: 428
Script:
#!/bin/bash
# Description: Verify test coverage for specific lines in doper.py.
# Find all test files
test_files=$(fd --glob '*test*.py')
# Check if the specific lines are covered in the test files
for test_file in $test_files; do
echo "Checking $test_file"
rg 'self.cation_mutator = mutation.CationMutator.from_json(filepath)' $test_file
rg 'sum_prob += self._calculate_species_sim_prob(cation, selected_site)' $test_file
rg 'return self.cation_mutator.get_lambda(species1, species2)' $test_file
rg 'headers = ["Rank", "Dopant", "Host", "Probability", "Selectivity"]' $test_file
rg 'headers = ["Rank", "Dopant", "Host", "Similarity", "Selectivity"]' $test_file
done
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GitHub Check: codecov/patch
[warning] 58-58: smact/dopant_prediction/doper.py#L58
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Description
Doperindoper.pyto accept using pre-loaded similaritiesType of change
How Has This Been Tested?
Test Configuration:
Reviewers
Checklist:
Summary by CodeRabbit
New Features
Doperclass to support an additionalembeddingparameter and ause_probabilityflag for more flexible dopant predictions.Documentation
"tabulate"module to the list of imported modules in the documentation configuration.Tests
DopantPredictionTestand added new test methods for dopant prediction and number formatting.