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Codecov Report

Attention: Patch coverage is 97.48744% with 5 lines in your changes missing coverage. Please review.

Project coverage is 94.43%. Comparing base (9a0b172) to head (8487be7).
Report is 119 commits behind head on main.

@@            Coverage Diff             @@
##             main    #2911      +/-   ##
==========================================
- Coverage   94.75%   94.43%   -0.33%     
==========================================
  Files         108      108              
  Lines        9631     9681      +50     
  Branches     1451     1462      +11     
==========================================
+ Hits         9126     9142      +16     
- Misses        324      346      +22     
- Partials      181      193      +12     

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@namurphy I added some additional print output which is causing doctest to fail - how does one reset that to accept the new test output as 'normal'?

@namurphy I added some additional print output which is causing doctest to fail - how does one reset that to accept the new test output as 'normal'?

That's a good question! We can do that by updating the example section of each docstring directly to have the new output rather than the old. So it'd be something like changing a docstring from

>>> simulation.run()
>>> simulation.whatevs()

to

>>> simulation.run()
Awesomely running awesome simulation.
Finished in 4.6 gigaseconds.
>>> simulation.whatevs()

That's a good question! We can do that by updating the example section of each docstring directly to have the new output rather than the old. So it'd be something like changing a docstring from

Ah, awesome, I understand how that works now! Thanks!

The error in the tests is probably coming from the fact that the test uses the np.reshape(shape = ?) keyword argument, but that keyword argument was only added in numpy 2.1. In the older versions of numpy, shape could only be a positional argument, and maybe on the 3.11 CI tests environment, one of the earlier numpy versions is installed? The better question is, why wasn't this a problem before...

=========================== short test summary info ===========================
FAILED tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py::test_NIST_particle_stopping[ALUMINUM-density0-energy_projected_range_list0] - TypeError: reshape() got an unexpected keyword argument 'shape'
FAILED tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py::test_NIST_particle_stopping[SILICON-density1-energy_projected_range_list1] - TypeError: reshape() got an unexpected keyword argument 'shape'

EDIT: Looks like that worked!

@PlasmaPy/plasmapy-reviewers Can we get this merged in the next few weeks? I've left comments trying to explain what was done - please tag me with any further questions.

@namurphy I'm working on addressing these, but I think one of the recent changes has broken pre-commit on windows. It works for me on old branches (not up to date with main), but on main now I get:

PS C:\Users\pvheu\GitHub\PlasmaPy> pre-commit run --all-files
[INFO] Installing environment for https://github.com/mattlqx/pre-commit-search-and-replace.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('rbenv', 'init', '-')
return code: 1
stdout:
    Executable `bash` not found
stderr: (none)
Check the log at C:\Users\pvheu\.cache\pre-commit\pre-commit.log

With the unhelpful log:

### version information

pre-commit version: 4.0.1
git --version: git version 2.31.0.windows.1
sys.version:
3.12.7 (main, Oct 16 2024, 00:21:24) [MSC v.1929 64 bit (AMD64)]
sys.executable: C:\Users\pvheu.virtualenvs\dev312\Scripts\python.exe
os.name: nt
sys.platform: win32

### error information

An unexpected error has occurred: CalledProcessError: command: ('rbenv', 'init', '-')
return code: 1
stdout:
Executable bash not found
stderr: (none)

Traceback (most recent call last):
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\error_handler.py", line 73, in error_handler
yield
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\main.py", line 417, in main
return run(args.config, store, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\commands\run.py", line 442, in run
install_hook_envs(to_install, store)
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\repository.py", line 229, in install_hook_envs
_hook_install(hook)
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\repository.py", line 85, in _hook_install
lang.install_environment(
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\languages\ruby.py", line 125, in install_environment
lang_base.setup_cmd(prefix, ('rbenv', 'init', '-'))
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\lang_base.py", line 86, in setup_cmd
cmd_output_b(*cmd, cwd=prefix.prefix_dir, **kwargs)
File "C:\Users\pvheu.virtualenvs\dev312\Lib\site-packages\pre_commit\util.py", line 111, in cmd_output_b
raise CalledProcessError(returncode, cmd, stdout_b, stderr_b)
pre_commit.util.CalledProcessError: command: ('rbenv', 'init', '-')
return code: 1
stdout:
Executable bash not found
stderr: (none)

pre-commit.ci autofix

Hi @namurphy

1. If I'm understanding this correctly, the erf formulation for the mask in soften_edges will change all of the values on the grid. At the center of the grid, the original values would be multiplied by a value that is really close to, but slightly less than, one. Is there a mask we could apply that doesn't affect quantities toward the center of the grid? Or alternatively, should we add an admonition to the docstring that mentions this?

Yes, I don't see a clean way to fix this and it's a very minor problem since the ERF is very close to one away from the edge, so I've just mentioned it in the docstring.

2. If this mask is applied to the magnetic field, I believe this would cause the resulting magnetic field to violate the divergence constraint

Yes, good point, I've added a note to that effect.

Ok, I think all the comments are addressed - my pre-commit is still broken locally, but I was able to run it through the comment bot, so it's passing now.

pre-commit.ci autofix