Added 'main' to 'commonality' parameter in the 'filter' function #386
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WalkthroughThe changes update the Changes
Sequence Diagram(s)sequenceDiagram
participant U as User
participant F as ICSD24OxStatesFilter
participant DB as DataFrame
U->>F: Call filter(commonality)
F->>F: Check value of commonality parameter
alt commonality is "main"
F->>DB: Group by "element"
DB-->>F: Return max "species_proportion (%)"
else commonality is "low/medium/high"
F->>F: Apply standard threshold check
end
F-->>U: Return filtered DataFrame
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #386 +/- ##
===========================================
+ Coverage 76.09% 76.23% +0.14%
===========================================
Files 33 33
Lines 2786 2790 +4
===========================================
+ Hits 2120 2127 +7
+ Misses 666 663 -3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Actionable comments posted: 1
🧹 Nitpick comments (1)
smact/utils/oxidation.py (1)
45-47: Consider more explicit handling of the 'main' option.The use of
passmakes the code less clear about what happens whencommonality == "main". While the logic works because the actual handling is in the later conditional block, it would be more explicit to set a flag or variable here to indicate the special handling.- if commonality == "main": - pass - else: - commonality_threshold = commonality_map.get(commonality) + if commonality == "main": + commonality_threshold = None # Indicate special handling + else: + commonality_threshold = commonality_map.get(commonality)Also, this code path is flagged as not covered by tests. Consider adding test coverage for this new functionality.
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[warning] 46-46: smact/utils/oxidation.py#L46
Added line #L46 was not covered by tests
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smact/utils/oxidation.py(3 hunks)
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🪛 GitHub Check: codecov/patch
smact/utils/oxidation.py
[warning] 46-46: smact/utils/oxidation.py#L46
Added line #L46 was not covered by tests
[warning] 52-52: smact/utils/oxidation.py#L52
Added line #L52 was not covered by tests
[warning] 67-67: smact/utils/oxidation.py#L67
Added line #L67 was not covered by tests
⏰ Context from checks skipped due to timeout of 90000ms (4)
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- GitHub Check: test (3.12, macos-latest)
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🔇 Additional comments (5)
smact/utils/oxidation.py (5)
37-37: Documentation correctly updated for the new 'main' option.The docstring for the
commonalityparameter has been properly updated to include and explain the new "main" option, which clearly states that it "selects the species with the highest occurrence for a given element."
52-52: Error message correctly updated to include 'main' option.The error message has been properly updated to include "main" in the list of valid string options for the
commonalityparameter.Note: This line is flagged as not covered by tests. Consider adding tests for invalid parameter scenarios.
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🪛 GitHub Check: codecov/patch
[warning] 52-52: smact/utils/oxidation.py#L52
Added line #L52 was not covered by tests
93-93: Documentation correctly updated in get_species_list method.The docstring for the
commonalityparameter in theget_species_listmethod has been properly updated to include and explain the new "main" option.
170-170: Documentation correctly updated in write method.The docstring for the
commonalityparameter in thewritemethod has been properly updated to include and explain the new "main" option.
66-68: Consider handling potential issue with full dataset filtering.When using
commonality == "main", be aware that the implementation only selects rows with maximum "species_proportion (%)" per element, but doesn't retrieve the corresponding oxidation states. This could potentially lead to incorrect results as the complete row data isn't retained.- filtered_df = filtered_df.groupby("element")["species_proportion (%)"].max().reset_index() + # Keep all columns and select rows with maximum species_proportion for each element + filtered_df = filtered_df.loc[filtered_df.groupby("element")["species_proportion (%)"].idxmax()].reset_index(drop=True)Consider testing with real data to verify the current implementation produces the expected results.
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🪛 GitHub Check: codecov/patch
[warning] 67-67: smact/utils/oxidation.py#L67
Added line #L67 was not covered by tests
| if commonality == "main": | ||
| filtered_df = filtered_df.groupby("element")["species_proportion (%)"].max().reset_index() | ||
| else: | ||
| filtered_df = filtered_df[filtered_df["species_proportion (%)"] >= commonality_threshold].reset_index( | ||
| drop=True | ||
| ) |
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💡 Verification agent
🧩 Analysis chain
Implementation of 'main' option needs test coverage.
The implementation logic for the "main" option correctly selects the species with the highest occurrence for a given element by:
- Grouping the DataFrame by "element"
- Finding the maximum "species_proportion (%)" for each element
However, this code path is flagged as not covered by tests. Ensure comprehensive test coverage for this new functionality to verify it works as expected across different scenarios.
🏁 Script executed:
#!/bin/bash
# Search for tests related to the ICSD24OxStatesFilter.filter method with 'main' option
rg -A 10 -B 10 "commonality.*main" --glob "**/*.py" | grep -v "oxidation.py"Length of output: 82
Action Required: Add Test Coverage for 'main' Option in oxidation.py
The recent search confirms that no tests currently address the 'main' option in the smact/utils/oxidation.py file. Please add comprehensive tests to verify that when commonality is "main", the logic correctly groups by "element" and selects the maximum "species_proportion (%)" for each group.
- File:
smact/utils/oxidation.py(Lines 66-71) - Action: Create tests covering various scenarios for the 'main' branch to ensure the grouping and max selection behaviour work as expected.
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🪛 GitHub Check: codecov/patch
[warning] 67-67: smact/utils/oxidation.py#L67
Added line #L67 was not covered by tests
Pull Request Template
Description
''commonality'' parameter now has one more predefined option ''main''. "main" selects the species with the highest occurrence for a given element. It was brought to my attention that there is an interest in finding the common specie for a given element and current thresholds didn't allow to do it easily as one threshold value was applied to all elements. Doesn't require extra dependencies.
Fixes # (issue)
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
All tests finished successfuly.
Reviewers
@AntObi
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