Rename integer charge to charge number #1136

namurphy · 2021-05-11T23:42:48Z

This PR replaces usage of the term "integer charge" and code elements named like integer_charge with the term "charge number" and charge_number. This is because charge number is the technical name for this concept (see #1126). The things named after "integer charge" are going to be kept for a few releases and then removed.

As part of this PR, I'm likely going to use a variant of the astropy.utils.decorators.deprecated decorator.

Closes #1126. Closes #945.

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Codecov Report

Merging #1136 (bfaeac6) into master (68801c2) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1136      +/-   ##
==========================================
+ Coverage   96.90%   96.92%   +0.01%     
==========================================
  Files          70       71       +1     
  Lines        6953     6992      +39     
==========================================
+ Hits         6738     6777      +39     
  Misses        215      215

Impacted Files	Coverage Δ
plasmapy/particles/__init__.py	`100.00% <ø> (ø)`
plasmapy/particles/symbols.py	`100.00% <ø> (ø)`
plasmapy/utils/__init__.py	`100.00% <ø> (ø)`
plasmapy/diagnostics/thomson.py	`100.00% <100.00%> (ø)`
plasmapy/dispersion/two_fluid_dispersion.py	`100.00% <100.00%> (ø)`
plasmapy/formulary/collisions.py	`97.19% <100.00%> (ø)`
plasmapy/formulary/parameters.py	`99.09% <100.00%> (ø)`
plasmapy/formulary/radiation.py	`100.00% <100.00%> (ø)`
plasmapy/particles/atomic.py	`100.00% <100.00%> (ø)`
plasmapy/particles/decorators.py	`100.00% <100.00%> (ø)`
... and 12 more

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StanczakDominik

LGTM in general; test failures seem to point to a mis-import probably since 5d2d129; the doc failure is unrelated (see Element). A couple of docstring mishaps in there.

docs/particles/ionization_states.rst

docs/particles/particle_class.rst

...since changes to integer_charge should be made known to the end user.

...and use ReST markup for ionic notation while I'm at it.

namurphy · 2021-05-12T14:19:21Z

I'm not sure why sections of docstrings ended up getting repeated. It could have been a mishap with auto-renaming via PyCharm, though it could have been a side effect of coding while listening to a BBC dramatization of my favorite book series. 🐉 In any case, I'll need to double check for this problem before this gets merged, and I have a few other things I need to finish up too. Thanks for finding that!

namurphy · 2021-05-12T14:28:14Z

StanczakDominik · 2021-05-13T15:22:26Z

Probably don't need to have exhaustive tests for integer_charge if it's just going to be a deprecated alias for charge_number!

namurphy · 2021-05-13T15:54:32Z

Probably don't need to have exhaustive tests for integer_charge if it's just going to be a deprecated alias for charge_number!

Very true. I was planning on having maybe one or two tests for each function/method...just enough to make sure it works.

plasmapy/particles/tests/test_ionization_state.py

plasmapy/particles/atomic.py

…rge_number

rocco8773

Add a stub file in docs/api_static for plasmapy.utils.decorators.deprecation.

plasmapy/utils/decorators/deprecation.py

Co-authored-by: Erik Everson <eteverson@gmail.com>

plasmapy/particles/tests/test_ionization_collection.py

rocco8773 · 2021-05-18T03:15:23Z

plasmapy/particles/tests/test_atomic.py

+def test_integer_charge():
+    with pytest.warns(PlasmaPyFutureWarning):
+        assert integer_charge("Fe 20+") == 20


If you want to be thorough, then it would be worthwhile to do a mock test here to ensure integer_charge calls charge_number. It's a bit overkill, but it does enforce the connection between the two.

It's probably more effort than is worth it for a deprecated feature, though this idea is worth keeping in mind for future features that we intend to keep around for a while.

rocco8773 · 2021-05-18T03:27:24Z

Do you want to merge #1073 first because it sure looks like you branched this PR off of that one? If so, that would avoid the scope creep of this PR.

namurphy · 2021-05-18T03:40:01Z

Do you want to merge #1073 first because it sure looks like you branched this PR off of that one? If so, that would avoid the scope creep of this PR.

I'd rather merge this one first and then go back to #1073 and enjoy the wonders of resolving git conflicts. Thanks for the quick review!

(Also: it's amazing how productive I can be when I'm procrastinating writing emails that I don't want to write.)

Looks like the stub file is in there, and I didn't see any more issues being raised!

Rename integer charge to charge number

f9157eb

namurphy added 2 commits May 11, 2021 21:01

Add PlasmaPy future/deprecation warnings

0fd185e

Create wrappers of Astropy deprecation decorator

0ed25fb

github-actions bot added the plasmapy.utils Related to the plasmapy.utils subpackage label May 12, 2021

namurphy added 2 commits May 11, 2021 21:59

Move deprecated decorators

5d2d129

Update test of integer_charge a little bit

c419ab6

StanczakDominik requested changes May 12, 2021

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namurphy added 4 commits May 12, 2021 10:02

Remove redundant redundancies

c892f98

Change exception to PlasmaPyFutureWarning

a8358a3

...since changes to integer_charge should be made known to the end user.

Remove extra redundant redundancy

58669a2

Remove another extra redundant redundancy

963c718

...and use ReST markup for ionic notation while I'm at it.

namurphy added 9 commits May 16, 2021 18:21

Update changelog

fb33eb0

Deprecate integer_charge function

a5b5ece

Merge branch 'master' of github.com:PlasmaPy/PlasmaPy into charge_number

c49738c

Test deprecated integer charge

d328e55

Add Ion*.integer_charge attributes & deprecate

789cd76

Use full path in docs

202e864

Fix possible ReST problem with inline markup

63e3177

Update changelog for integer charge → charge number

35fdf59

Test IonizationState.integer_charges

9f0de5c

namurphy commented May 17, 2021

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namurphy commented May 17, 2021

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namurphy commented May 17, 2021

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namurphy added 3 commits May 17, 2021 17:51

Minor fixes to particles

a0f7c5a

Add changelog entry for @deprecated decorator

c513460

Merge branch 'charge_number' of github.com:namurphy/PlasmaPy into cha…

a72ffb2

…rge_number

namurphy mentioned this pull request May 17, 2021

Remove deprecated integer_charge objects in plasmapy.particles in version ≳ 0.9.0 #1143

Closed

namurphy marked this pull request as ready for review May 17, 2021 22:05

namurphy requested a review from rocco8773 as a code owner May 17, 2021 22:05

namurphy requested a review from a team May 17, 2021 22:06

rocco8773 previously requested changes May 17, 2021

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namurphy added 2 commits May 17, 2021 18:56

Add stub file in api_static for deprecated

935e02b

Minor doc fix

47a93da

namurphy mentioned this pull request May 17, 2021

Improve consistency and ReST formatting in documentation #1073

Merged

rocco8773 reviewed May 18, 2021

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namurphy and others added 2 commits May 17, 2021 20:46

Workaround for docs of deprecated decorator

ba5cdb0

Co-authored-by: Erik Everson <eteverson@gmail.com>

Slight edits to deprecation.py

fde7f4f

rocco8773 reviewed May 18, 2021

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rocco8773 reviewed May 18, 2021

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One more charge_number → integer_charge change in tests

8291537

Merge branch 'master' of github.com:PlasmaPy/PlasmaPy into charge_number

bfaeac6

namurphy enabled auto-merge (squash) May 18, 2021 03:40

StanczakDominik approved these changes May 18, 2021

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namurphy merged commit d5859dc into PlasmaPy:master May 18, 2021

namurphy deleted the charge_number branch May 18, 2021 14:16

rocco8773 mentioned this pull request Dec 10, 2021

Hollweg dispersion solver #1189

Merged

3 tasks

namurphy mentioned this pull request Jul 7, 2022

Remove integer_charge attributes #1633

Merged

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Rename integer charge to charge number #1136

Rename integer charge to charge number #1136

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Rename integer charge to charge number #1136

Rename integer charge to charge number #1136

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