Nvalence_modification #290
Conversation
WalkthroughThe updates introduce a new attribute Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Element
participant DataLoader
User->>Element: Create Element instance with symbol
Element->>DataLoader: lookup_element_valence_data(symbol)
DataLoader-->>Element: Return valence electron count
Element-->>User: num_valence_modified set
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Actionable comments posted: 2
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files ignored due to path filters (1)
smact/data/element_valence_modified.csvis excluded by!**/*.csv
Files selected for processing (2)
- smact/init.py (3 hunks)
- smact/data_loader.py (1 hunks)
Additional comments not posted (1)
smact/__init__.py (1)
84-85: New attribute added to the Element class.The addition of
num_valence_modifiedto theElementclass has been noted. This attribute is intended to provide a modified definition of valence electrons, which could be useful for specific chemical modelling scenarios.
smact/__init__.py
Outdated
| valence_data = data_loader.lookup_element_valence_data(symbol) | ||
| if valence_data: | ||
| num_valence_modified = valence_data["NValence"] | ||
|
|
There was a problem hiding this comment.
Review of data retrieval and attribute setting for num_valence_modified.
The data retrieval process using data_loader.lookup_element_valence_data(symbol) and the subsequent setting of num_valence_modified are correctly implemented. However, consider adding error handling for cases where valence_data might return None, which could happen if the element symbol is not found in the dataset.
- num_valence_modified = valence_data["NValence"]
+ num_valence_modified = valence_data["NValence"] if valence_data else NoneAlso applies to: 209-209
| _element_valence_data = None | ||
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| def lookup_element_valence_data(symbol: str, copy: bool = True): | ||
| """ | ||
| Retrieve valence electron data. | ||
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| For d-block elements, the s and d electrons contribute to NValence. | ||
| For p-block elements, the s and p electrons contribute to NValence. | ||
| For s- and f-block elements, NValence is calculated from the Noble Gas electron configuration | ||
| i.e. | ||
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| Args: | ||
| symbol : the atomic symbol of the element to look up. | ||
| copy: if True (default), return a copy of the data dictionary, | ||
| rather than a reference to a cached object -- only use | ||
| copy=False in performance-sensitive code and where you are | ||
| certain the dictionary will not be modified! | ||
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| Returns: | ||
| NValence (int): the number of valence electrons | ||
| Returns None if the element was not found among the external | ||
| data. | ||
| """ | ||
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| global _element_valence_data | ||
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| if _element_valence_data is None: | ||
| _element_valence_data = {} | ||
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| df = pd.read_csv( | ||
| os.path.join(data_directory, "element_valence_modified.csv") | ||
| ) | ||
| for _index, row in df.iterrows(): | ||
| key = row.iloc[0] | ||
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| dataset = {"NValence": int(row.iloc[1])} | ||
| _element_valence_data[key] = dataset | ||
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| if symbol in _element_valence_data: | ||
| return _element_valence_data[symbol] | ||
| else: | ||
| if _print_warnings: | ||
| print( | ||
| "WARNING: Valence data for element {} not " | ||
| "found.".format(symbol) | ||
| ) | ||
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| return None |
There was a problem hiding this comment.
Review of new function lookup_element_valence_data.
The function lookup_element_valence_data is well-documented and correctly implemented with caching mechanics. However, consider improving the error message to provide more context about why the data might be missing, such as a missing or malformed CSV file.
- print(
- "WARNING: Valence data for element {} not "
- "found.".format(symbol)
- )
+ print(f"WARNING: Valence data for element {symbol} not found. Check if 'element_valence_modified.csv' is present and correctly formatted.")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.
| _element_valence_data = None | |
| def lookup_element_valence_data(symbol: str, copy: bool = True): | |
| """ | |
| Retrieve valence electron data. | |
| For d-block elements, the s and d electrons contribute to NValence. | |
| For p-block elements, the s and p electrons contribute to NValence. | |
| For s- and f-block elements, NValence is calculated from the Noble Gas electron configuration | |
| i.e. | |
| Args: | |
| symbol : the atomic symbol of the element to look up. | |
| copy: if True (default), return a copy of the data dictionary, | |
| rather than a reference to a cached object -- only use | |
| copy=False in performance-sensitive code and where you are | |
| certain the dictionary will not be modified! | |
| Returns: | |
| NValence (int): the number of valence electrons | |
| Returns None if the element was not found among the external | |
| data. | |
| """ | |
| global _element_valence_data | |
| if _element_valence_data is None: | |
| _element_valence_data = {} | |
| df = pd.read_csv( | |
| os.path.join(data_directory, "element_valence_modified.csv") | |
| ) | |
| for _index, row in df.iterrows(): | |
| key = row.iloc[0] | |
| dataset = {"NValence": int(row.iloc[1])} | |
| _element_valence_data[key] = dataset | |
| if symbol in _element_valence_data: | |
| return _element_valence_data[symbol] | |
| else: | |
| if _print_warnings: | |
| print( | |
| "WARNING: Valence data for element {} not " | |
| "found.".format(symbol) | |
| ) | |
| return None | |
| print(f"WARNING: Valence data for element {symbol} not found. Check if 'element_valence_modified.csv' is present and correctly formatted.") |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #290 +/- ##
===========================================
+ Coverage 74.90% 75.07% +0.16%
===========================================
Files 24 24
Lines 2124 2142 +18
===========================================
+ Hits 1591 1608 +17
- Misses 533 534 +1 ☔ View full report in Codecov by Sentry. |
There was a problem hiding this comment.
Actionable comments posted: 1
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- smact/init.py (3 hunks)
Additional context used
Ruff
smact/__init__.py
168-171: Use ternary operator
num_valence_modified = valence_data["NValence"] if valence_data else Noneinstead ofif-else-blockReplace
if-else-block withnum_valence_modified = valence_data["NValence"] if valence_data else None(SIM108)
Additional comments not posted (1)
smact/__init__.py (1)
84-85: Addition ofnum_valence_modifiedattribute.The new attribute
num_valence_modifiedhas been added to theElementclass to represent the number of valence electrons based on a modified definition. This is a non-breaking change that introduces new functionality as described in the PR.
| valence_data = data_loader.lookup_element_valence_data(symbol) | ||
| if valence_data: | ||
| num_valence_modified = valence_data["NValence"] | ||
| else: | ||
| num_valence_modified = None |
There was a problem hiding this comment.
Refactor data retrieval and setting for num_valence_modified.
The data retrieval process using data_loader.lookup_element_valence_data(symbol) and the subsequent setting of num_valence_modified are correctly implemented. However, consider using the ternary operator for cleaner code as suggested by static analysis.
- if valence_data:
- num_valence_modified = valence_data["NValence"]
- else:
- num_valence_modified = None
+ num_valence_modified = valence_data["NValence"] if valence_data else NoneCommittable 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.
| valence_data = data_loader.lookup_element_valence_data(symbol) | |
| if valence_data: | |
| num_valence_modified = valence_data["NValence"] | |
| else: | |
| num_valence_modified = None | |
| valence_data = data_loader.lookup_element_valence_data(symbol) | |
| num_valence_modified = valence_data["NValence"] if valence_data else None |
Tools
Ruff
168-171: Use ternary operator
num_valence_modified = valence_data["NValence"] if valence_data else Noneinstead ofif-else-blockReplace
if-else-block withnum_valence_modified = valence_data["NValence"] if valence_data else None(SIM108)
New NValence data
Description
Type of change
New feature (non-breaking change which adds functionality)
This change requires a documentation update
How Has This Been Tested?
num_valence_modifiedis accessibleTest Configuration:
Reviewers
N/A
Checklist:
Summary by CodeRabbit
num_valence_modifiedto theElementclass to indicate the number of valence electrons using a modified definition.