[FIX] read annotation into NIMADs

[jdkent]

Closes #913

Changes proposed in this pull request:

• initialize variable
• use the correct syntax for reading annotation
• add metadata attribute to analysis

Summary by Sourcery

Bug Fixes:

• Fixes an issue where annotations were not being read into NiMADS objects.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request fixes an issue where the _annotations variable was not initialized in the Studyset class, leading to errors when reading annotations. It also adds a metadata attribute to the Analysis class to store metadata associated with the analysis. The annotation reading syntax in the example was also corrected.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Initialized the _annotations attribute in the Studyset class and corrected the syntax for reading annotations during Studyset initialization.	Initialized self._annotations = [] in the Studyset class's __init__ method. Modified the Studyset initialization to correctly pass the annotations.	nimare/nimads.py examples/01_datasets/05_plot_nimads.py
Added a metadata attribute to the Analysis class.	Added self.metadata = source.get("metadata", {}) or {} to the Analysis class's __init__ method.	nimare/nimads.py

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#913	Annotations should be successfully read into NiMARE from NiMADS data.	✅

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[sourcery-ai]

Hey @jdkent - I've reviewed your changes - here's some feedback:

Overall Comments:

• It looks like you're initializing self._annotations in the Studyset class constructor regardless of whether annotations are provided; consider removing the conditional logic.
• Consider adding a test case that specifically covers the metadata attribute in the Analysis class.

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[sourcery-ai]

suggestion (bug_risk): Evaluate the use of 'or {}' with metadata initialization.

The expression source.get("metadata", {}) already provides a default empty dict when the key is missing, so the additional 'or {}' will override any false-y but valid metadata value. Consider whether this behavior is intentional or if an explicit test for None might be more appropriate.

Suggested implementation:

        tmp = source.get("metadata")
        self.metadata = {} if tmp is None else tmp

Review any other parts of the code that may depend on metadata being always a dictionary to ensure this change doesn't impact expected false-y values.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.23%. Comparing base (3e5becf) to head (6a32b0e).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #914   +/-   ##
=======================================
  Coverage   88.23%   88.23%           
=======================================
  Files          48       48           
  Lines        6382     6383    +1     
=======================================
+ Hits         5631     5632    +1     
  Misses        751      751           

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