Merge pull request #759 from reneeotten/last_changes_before_release

(Last) minor changes before release?

Author: newville

.codecov.yml

@@ -1,8 +1,7 @@
 codecov:
   token: 11c28e95-6e64-4829-9887-04e4cd661bf6
-
-comment:
-  after_n_builds: 8
+  comment:
+    after_n_builds: 8
 
 coverage:
   status:

THANKS.txt

@@ -55,7 +55,7 @@ Roam, Alexander Stark, Alexandre Beelen, Andrey Aristov, Nicholas Zobrist,
 Ethan Welty, Julius Zimmermann, Mark Dean, Arun Persaud, Ray Osborn, @lneuhaus,
 Marcel Stimberg, Yoshiera Huang, Leon Foks, Sebastian Weigand, Florian LB,
 Michael Hudson-Doyle, Ruben Verweij, @jedzill4, @spalato, Jens Hedegaard Nielsen,
-Martin Majli, Kristian Meyer, and many others.
+Martin Majli, Kristian Meyer, @azelcer, Ivan Usov, and many others.
 
 The lmfit code obviously depends on, and owes a very large debt to the code
 in scipy.optimize. Several discussions on the SciPy-user and lmfit mailing

azure-pipelines.yml

@@ -44,7 +44,7 @@ stages:
             python setup.py install
           displayName: 'Install lmfit'
         - script: |
-            sudo apt update && sudo apt install -qq -y texlive-latex-extra latexmk
+            sudo apt-get update && sudo apt-get install -qq -y texlive-latex-extra latexmk
           displayName: 'Install TeX Live'
         - script: |
             cd doc ; make all
@@ -74,7 +74,7 @@ stages:
             versionSpec: '$(python.version)'
           displayName: 'Use Python $(python.version)'
         - script: |
-            sudo apt update && sudo apt install -yq --no-install-suggests --no-install-recommends \
+            sudo apt-get update && sudo apt-get install -yq --no-install-suggests --no-install-recommends \
             libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache \
             swig libmpc-dev
           displayName: 'Install dependencies'
@@ -130,7 +130,7 @@ stages:
             versionSpec: '$(python.version)'
           displayName: 'Use Python $(python.version)'
         - script: |
-            sudo apt update && sudo apt install -yq --no-install-suggests --no-install-recommends \
+            sudo apt-get update && sudo apt-get install -yq --no-install-suggests --no-install-recommends \
             libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache \
             swig libmpc-dev
           displayName: 'Install dependencies'
@@ -206,10 +206,10 @@ stages:
       steps:
         - script: |
             sudo add-apt-repository ppa:deadsnakes/nightly
-            sudo apt update && sudo apt install -y --no-install-recommends python3.10-dev python3.10-distutils
+            sudo apt-get update && sudo apt-get install -y --no-install-recommends python3.10-dev python3.10-distutils
           displayName: Install Python development version from the deadsnakes PPA
         - script: |
-            sudo apt update && sudo apt install -yq --no-install-suggests --no-install-recommends \
+            sudo apt-get update && sudo apt-get install -yq --no-install-suggests --no-install-recommends \
             libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache \
             swig libmpc-dev
           displayName: 'Install dependencies'

doc/whatsnew.rst

@@ -14,8 +14,8 @@ consult the `lmfit GitHub repository`_.
 
 .. _whatsnew_103_label:
 
-Version 1.0.3 Release Notes (unreleased)
-========================================
+Version 1.0.3 Release Notes (October 14, 2021)
+==============================================
 
 Potentially breaking change:
 
@@ -39,6 +39,7 @@ Bug fixes/enhancements:
   ``float``, ``int``, or ``complex`` return value to a ``numpy.ndarray`` (Issue #684 and PR #754)
 - fix ``dho`` (Damped Harmonic Oscillator) lineshape (PR #755; @rayosborn)
 - reset ``Minimizer._abort`` to ``False`` before starting a new fit (Issue #756 and PR #757; @azelcer)
+- fix typo in ``guess_from_peak2d`` (@ivan-usovl; PR #758)
 
 Various:
 
@@ -54,6 +55,7 @@ Various:
 - mark ``test_manypeaks_speed.py`` as flaky to avoid intermittent test failures (repeat up to 5 times; PR #745)
 - update scipy dependency to >= 1.14.0 (PR #751)
 - improvement to output of examples in sphinx-gallery and use higher resolution figures (PR #753)
+- remove deprecated functions ``lmfit.printfuncs.report_errors`` and ``asteval`` argument in ``Parameters`` class (PR #759)
 
 
 .. _whatsnew_102_label:

lmfit/__init__.py

@@ -38,8 +38,7 @@
 from .confidence import conf_interval, conf_interval2d
 from .minimizer import Minimizer, MinimizerException, minimize
 from .parameter import Parameter, Parameters
-from .printfuncs import (ci_report, fit_report, report_ci, report_errors,
-                         report_fit)
+from .printfuncs import ci_report, fit_report, report_ci, report_fit
 from .model import Model, CompositeModel
 from . import lineshapes, models
 

lmfit/parameter.py

@@ -2,7 +2,6 @@
 
 from copy import deepcopy
 import json
-import warnings
 
 from asteval import Interpreter, get_ast_names, valid_symbol_name
 from numpy import arcsin, array, cos, inf, isclose, sin, sqrt
@@ -45,30 +44,18 @@ class Parameters(dict):
 
     """
 
-    def __init__(self, asteval=None, usersyms=None):
+    def __init__(self, usersyms=None):
         """
         Arguments
         ---------
-        asteval : :class:`asteval.Interpreter`, optional
-            Instance of the `asteval.Interpreter` to use for constraint
-            expressions. If None (default), a new interpreter will be
-            created. **Warning: deprecated**, use `usersyms` if possible!
         usersyms : dict, optional
             Dictionary of symbols to add to the
             :class:`asteval.Interpreter` (default is None).
 
         """
         super().__init__(self)
 
-        self._asteval = asteval
-        if asteval is None:
-            self._asteval = Interpreter()
-        else:
-            msg = ("The use of the 'asteval' argument for the Parameters class"
-                   " was deprecated in lmfit v0.9.12 and will be removed in a "
-                   "later release. Please use the 'usersyms' argument instead!")
-            warnings.warn(FutureWarning(msg))
-            self._asteval = asteval
+        self._asteval = Interpreter()
 
         _syms = {}
         _syms.update(SCIPY_FUNCTIONS)
@@ -101,7 +88,7 @@ def __deepcopy__(self, memo):
         all individual Parameter objects are copied.
 
         """
-        _pars = self.__class__(asteval=None)
+        _pars = self.__class__()
 
         # find the symbols that were added by users, not during construction
         unique_symbols = {key: self._asteval.symtable[key]

lmfit/printfuncs.py

@@ -2,7 +2,6 @@
 
 from math import log10
 import re
-import warnings
 
 import numpy as np
 
@@ -341,14 +340,6 @@ def cell(x, cat='td'):
     return ''.join(html)
 
 
-def report_errors(params, **kws):
-    """Print a report for fitted params: see error_report()."""
-    warnings.warn("The function 'report_errors' is deprecated as of lmfit "
-                  "0.9.14 and will be removed in the next release. Please "
-                  "use 'report_fit' instead.", FutureWarning)
-    print(fit_report(params, **kws))
-
-
 def report_fit(params, **kws):
     """Print a report of the fitting results."""
     print(fit_report(params, **kws))

tests/test_parameters.py

@@ -4,7 +4,6 @@
 from copy import copy, deepcopy
 import pickle
 
-import asteval
 import numpy as np
 from numpy.testing import assert_allclose
 import pytest
@@ -45,21 +44,9 @@ def test_check_ast_errors():
         pars.add('par1', expr='2.0*par2')
 
 
-def test_parameters_init_with_asteval():
-    """Test for initialization of the Parameters class with asteval."""
-    ast_int = asteval.Interpreter()
-
-    msg = ("The use of the 'asteval' argument for the Parameters class was "
-           "deprecated in lmfit v0.9.12 and will be removed in a later "
-           "release. Please use the 'usersyms' argument instead!")
-    with pytest.warns(FutureWarning, match=msg):
-        pars = lmfit.Parameters(asteval=ast_int)
-    assert pars._asteval == ast_int
-
-
 def test_parameters_init_with_usersyms():
     """Test for initialization of the Parameters class with usersyms."""
-    pars = lmfit.Parameters(asteval=None, usersyms={'test': np.sin})
+    pars = lmfit.Parameters(usersyms={'test': np.sin})
     assert 'test' in pars._asteval.symtable
 
 

tests/test_printfuncs.py

@@ -4,7 +4,7 @@
 
 import lmfit
 from lmfit import (Minimizer, Parameters, ci_report, conf_interval, fit_report,
-                   report_ci, report_errors, report_fit)
+                   report_ci, report_fit)
 from lmfit.lineshapes import gaussian
 from lmfit.models import GaussianModel
 from lmfit.printfuncs import alphanumeric_sort, getfloat_attr, gformat
@@ -222,12 +222,6 @@ def test_report_fit(fitresult, capsys):
         assert header in captured.out
 
 
-def test_report_errors_deprecated(fitresult):
-    """Verify that a FutureWarning is shown when calling report_errors."""
-    with pytest.warns(FutureWarning):
-        report_errors(params=fitresult.params)
-
-
 def test_report_leastsq_no_errorbars(fitresult):
     """Verify correct message when uncertainties could not be estimated."""
     # general warning is shown