Fixed Improper Method Call: __exit__()

[fazledyn-or]

Description

While triaging your project, our bug fixing tool generated the following message(s)-

In file: openpmd_hdf5.py, class: HDF5Reader, there is a special method __exit__ that contains an unexpected number of parameters. Each call to this method will result in a TypeError. iCR suggested that special methods should have an expected number of parameters. More infomation can be found in the Python documentation on the various special method.

Proof of Concept / Explanation

Let's take the code example below. We're using a sample HDF5 file from this link.

from plasmapy.plasma.sources.openpmd_hdf5 import HDF5Reader

hdf5 = "example.h5"
print("Before entering context")
with HDF5Reader(hdf5) as f:
    print("Inside the context")
print("After exiting context")

Output:

(env) ataf@openrefactory:~/BFAS/Source/PlasmaPy$ python3 _test.py 
Before entering context
Inside the context
Traceback (most recent call last):
  File "/home/ataf/BFAS/Source/PlasmaPy/_test.py", line 5, in <module>
    with HDF5Reader(hdf5) as f:
TypeError: HDF5Reader.__exit__() takes 1 positional argument but 4 were given

However, after changing the __exit__ method, we get the following output -

(env) ataf@openrefactory:~/BFAS/Source/PlasmaPy$ python3 _test.py 
Before entering context
Inside the context
After exiting context

If the HDF5Reader class is to be used as a context manager, you must change the __exit__ method as suggested in this PR. Otherwise, you can delete both __enter__ and __exit__ methods to avoid confusion.

Changes

• Modified the method signature of __exit__ according to documentation

Previously Found & Fixed

• https://www.github.com/OCR-D/core/pull/1130

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The meaning of a signoff depends on the project, but it typically certifies that committer has the rights to submit this work under the same license and agrees to a Developer Certificate of Origin (see https://developercertificate.org/ for more information).
- Git Commit SignOff documentation

Sponsorship and Support

This work is done by the security researchers from OpenRefactory and is supported by the Open Source Security Foundation (OpenSSF): Project Alpha-Omega. Alpha-Omega is a project partnering with open source software project maintainers to systematically find new, as-yet-undiscovered vulnerabilities in open source code - and get them fixed – to improve global software supply chain security.

The bug is found by running the Intelligent Code Repair (iCR) tool by OpenRefactory and then manually triaging the results.

[github-actions]

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (ee973c8) 96.91% compared to head (4733c46) 96.91%.
Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2402   +/-   ##
=======================================
  Coverage   96.91%   96.91%           
=======================================
  Files         104      104           
  Lines        9118     9118           
=======================================
  Hits         8837     8837           
  Misses        281      281           

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[namurphy]

Thank you for making this fix! I had been meaning to look into this further after we added the # noqa comments, but haven't had a chance. Great catch!