Magpie data updates

[AntObi]

Pull Request Template

Description

• Access new properties for the Element class

Type of change

• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

Test Configuration:

• Python version: 3.10
• Operating System: macOS

Reviewers

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings

Summary by CodeRabbit

• New Features
  • Introduced new attributes to the Element class, including Mendeleev number, atomic weight, melting temperature, and number of valence electrons.
  • Added a function to retrieve element data from the Magpie dataset based on atomic symbols.

[coderabbitai]

Walkthrough

The recent changes introduce new attributes to the Element class in the smact module, such as mendeleev, AtomicWeight, MeltingT, and num_valence. Additionally, a new function lookup_element_magpie_data has been added to smact/data_loader.py for retrieving element data from the Magpie representation. These changes enhance the ability to access and utilise detailed elemental properties within the smact module.

Changes

Files	Change Summary
smact/init.py	Introduced new attributes to the Element class: mendeleev, AtomicWeight, MeltingT, and num_valence, enhancing the available elemental properties.
smact/data_loader.py	Added lookup_element_magpie_data function to fetch element data from Magpie representation and import pandas as pd for handling data.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Element
    participant DataLoader
    participant MagpieCSV
    
    User ->> Element: Create Element instance
    Element ->> DataLoader: Call lookup_element_magpie_data(symbol)
    DataLoader ->> MagpieCSV: Load CSV data
    MagpieCSV -->> DataLoader: Return element data
    DataLoader -->> Element: Populate attributes with data
    Element -->> User: Return Element instance with attributes

Loading

Poem

In the realm of code so bright,
Elements gain new attributes' light,
With mendeleev, weight so clear,
Melting points and valence near.
Data Loader's magic spell,
From Magpie's depths, new tales to tell.
🐇✨ Code evolves, a wondrous sight!

---

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[codecov]

Codecov Report

Attention: Patch coverage is 96.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 74.90%. Comparing base (7d89173) to head (b563be1).
Report is 65 commits behind head on develop.

Files with missing lines	Patch %	Lines
smact/data_loader.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #289      +/-   ##
===========================================
+ Coverage    74.65%   74.90%   +0.25%     
===========================================
  Files           24       24              
  Lines         2099     2124      +25     
===========================================
+ Hits          1567     1591      +24     
- Misses         532      533       +1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[coderabbitai]

Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 7d89173 and 0f3355f.

Files ignored due to path filters (1)

• smact/data/magpie.csv is excluded by !**/*.csv

Files selected for processing (2)

• smact/init.py (3 hunks)
• smact/data_loader.py (2 hunks)

Additional context used

Ruff

smact/data_loader.py

868-868: Loop control variable index not used within loop body

Rename unused index to _index

(B007)

GitHub Check: codecov/patch

smact/data_loader.py

[warning] 901-901: smact/data_loader.py#L901
Added line #L901 was not covered by tests

Additional comments not posted (8)

smact/__init__.py (6)

76-76: Attribute mendeleev correctly added.

The attribute mendeleev has been correctly integrated and initialized in the Element class.

---

78-78: Attribute AtomicWeight correctly added.

The attribute AtomicWeight has been correctly integrated and initialized in the Element class.

---

80-80: Attribute MeltingT correctly added.

The attribute MeltingT has been correctly integrated and initialized in the Element class.

---

82-82: Attribute num_valence correctly added.

The attribute num_valence has been correctly integrated and initialized in the Element class.

---

153-163: New attributes correctly initialized in __init__ method.

The new attributes mendeleev, AtomicWeight, MeltingT, and num_valence are correctly initialized using magpie_data. The fallback to None if magpie_data is not available is appropriate.

---

199-202: Attributes correctly set in __init__ method.

The new attributes mendeleev, AtomicWeight, MeltingT, and num_valence are correctly set in the __init__ method. Ensure that there are corresponding tests for these attributes.

smact/data_loader.py (2)

16-16: pandas import correctly added.

The pandas library is correctly imported to facilitate data handling in the new function lookup_element_magpie_data.

---

832-899: Function lookup_element_magpie_data correctly implemented.

The function lookup_element_magpie_data effectively retrieves element data from a CSV file and returns a dictionary containing various properties for the specified atomic symbol. The use of pandas is appropriate for data handling.

Tools

Ruff

868-868: Loop control variable index not used within loop body

Rename unused index to _index

(B007)

[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 0f3355f and b563be1.

Files selected for processing (1)

• smact/data_loader.py (2 hunks)

Files skipped from review as they are similar to previous changes (1)

• smact/data_loader.py