Correct init_vals

[newville]

Description

This ensures that result.init_vals is the "user" / "external" values, and adds a new attribute result._init_vals_internal to store the initial "internal" values which are needed as initial values.

This addresses #820

When running tests, I saw some deprecations and addressed some of those, but it seems there are other deprecation warnings that might need more work.

Type of Changes

• Bug fix
• New feature
• Refactoring / maintenance
• Documentation / examples

Tested on

import sys, lmfit, numpy, scipy, asteval, uncertainties
print('Python: {}\n\nlmfit: {}, scipy: {}, numpy: {}, asteval: {}, uncertainties: {}'
... .format(sys.version, lmfit.version, scipy.version, numpy.version,
... asteval.version, uncertainties.version))
Python: 3.9.13 | packaged by conda-forge | (main, May 27 2022, 17:00:52)
[Clang 13.0.1 ]

lmfit: 1.0.3.post69+g99952a2.d20221031, scipy: 1.9.0, numpy: 1.23.2, asteval: 0.9.27.post12+ge349473, uncertainties: 3.1.7

Verification

Have you

• included docstrings that follow PEP 257?

• referenced existing Issue and/or provided relevant link to mailing list?

• verified that existing tests pass locally?

• verified that the documentation builds locally?

• squashed/minimized your commits and written descriptive commit messages?

• added or updated existing tests to cover the changes?
• updated the documentation and/or added an entry to the release notes (doc/whatsnew.rst)?
• added an example?

closes #820

[codecov]

Codecov Report

Merging #821 (1a8f035) into master (4173760) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #821      +/-   ##
==========================================
+ Coverage   93.71%   93.73%   +0.01%     
==========================================
  Files           9        9              
  Lines        3487     3498      +11     
==========================================
+ Hits         3268     3279      +11     
  Misses        219      219              

Impacted Files	Coverage Δ
lmfit/minimizer.py	90.70% <100.00%> (+0.02%)	⬆️
lmfit/lineshapes.py	100.00% <0.00%> (ø)

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[reneeotten]

@newville we would need to look in which SciPy version the keyword(s) are deprecated. It it's still present in our lowers supported version we will need to use a different approach (as we've done for other minimizers as well). Should we bump supported NumPy/SciPy versions for the next release?

I'll take a look at the other code changes later today.

[newville]

@reneeotten I see messages about deprecations of the dreaded topic of maxiter in favor of maxfun within scipy (scheduled for scipy 1.11) when running tests locally. In a first pass, I fixed one of those, but other changes that I tried in our minimizer.py was causing several of our tests to fail.

I think that issue (probably should have been raised separately from this issue on init_vals) probably needs more attention. Will raise a separate issue.

[newville]

I should have mentioned that the changes at 1a8f035 were to suppress warnings when testing locally with Python 3.11

[newville]

merging this...