Package: release.debian.org
Severity: normal
X-Debbugs-Cc: lmfit...@packages.debian.org, sanv...@debian.org,
pi...@debian.org, cjwat...@debian.org, dpars...@debian.org
Control: affects -1 + src:lmfit-py
User: release.debian....@packages.debian.org
Usertags: unblock
Please unblock package lmfit-py
It needs manual intervention to migrate.
This release is compatible with both uncertainties in testing and
uncertainties in unstable, and it's a pre-requisite for uncertainties
to migrate to testing (some day).
The fixes come directly from upstream, and they are now complete
in 1.3.3-4 after Paul spotted a funny debug leftover in 1.3.3-3.
There were really three upstream commits to be applied,
while version 1.3.3-3 only had one.
After this, I'd like to try adding Breaks to uncertainties
against both lmfit-py (already in salsa) and pymatgen to see if we can
rely on autopkgtests and avoid more manual interventions.
[ The uncertainties package is 24 days old and that would reset
the counter again, but so be it ]
[ Checklist ]
[X] all changes are documented in the d/changelog
[X] I reviewed all changes and I approve them
[X] attach debdiff against the package in testing
[ Cc to several involved parties for their information ]
unblock lmfit-py/1.3.3-4
diff --git a/debian/changelog b/debian/changelog
index 021c0ba..4169ca0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,23 @@
+lmfit-py (1.3.3-4) unstable; urgency=medium
+
+ * Team upload.
+ [ Andreas Tille ]
+ * Do not check for reproduciblility in Salsa CI.
+ [ Santiago Vila ]
+ * Cherry-pick two fixes from upstream:
+ - Update fix-test-failure-with-new-uncertainties.patch. Closes: #1106426.
+ - Do not test for the content of warning messages from upstream libraries.
+ They can change.
+
+ -- Santiago Vila <sanv...@debian.org> Sun, 08 Jun 2025 00:50:00 +0200
+
+lmfit-py (1.3.3-3) unstable; urgency=medium
+
+ * Team upload.
+ * Fix test failure with new uncertainties. Closes: #1106426.
+
+ -- Santiago Vila <sanv...@debian.org> Mon, 26 May 2025 19:45:00 +0200
+
lmfit-py (1.3.3-2) unstable; urgency=medium
* Team upload.
diff --git a/debian/patches/drop-test-confidence-warnings.patch
b/debian/patches/drop-test-confidence-warnings.patch
new file mode 100644
index 0000000..b5d921b
--- /dev/null
+++ b/debian/patches/drop-test-confidence-warnings.patch
@@ -0,0 +1,23 @@
+From: Matthew Newville <newvi...@cars.uchicago.edu>
+Subject: do not test for warnings from upstream code that might change or be
suppressed or altered
+Origin:
https://github.com/lmfit/lmfit-py/commit/f4c5a83f6259fc46ab76f5d75de2537ba9d72b0a
+
+--- a/tests/test_confidence.py
++++ b/tests/test_confidence.py
+@@ -191,16 +191,6 @@
+ lmfit.conf_interval(minimizer, out_lsq)
+
+
+-def test_confidence_warnings(data, pars):
+- """Make sure the proper warnings are emitted when needed."""
+- minimizer = lmfit.Minimizer(residual, pars, fcn_args=data)
+- out = minimizer.minimize(method='leastsq')
+-
+- with pytest.warns(UserWarning) as record:
+- lmfit.conf_interval(minimizer, out, maxiter=1)
+- assert 'maxiter=1 reached and prob' in str(record[0].message)
+-
+-
+ def test_confidence_with_trace(data, pars):
+ """Test calculation of confidence intervals with trace."""
+ minimizer = lmfit.Minimizer(residual, pars, fcn_args=data)
diff --git a/debian/patches/fix-test-failure-with-new-uncertainties.patch
b/debian/patches/fix-test-failure-with-new-uncertainties.patch
new file mode 100644
index 0000000..b74553d
--- /dev/null
+++ b/debian/patches/fix-test-failure-with-new-uncertainties.patch
@@ -0,0 +1,32 @@
+From: Matthew Newville <newvi...@cars.uchicago.edu>
+Subject: capture and ignore std_dev=0 warnings from uncertainties package
+Origin:
https://github.com/lmfit/lmfit-py/commit/a2830038ae769e2eff39bbb7f8a168dbfade2f34
+Origin:
https://github.com/lmfit/lmfit-py/commit/045a58ea75527d5c3575db469a965621b5a6971e
+Bug-Debian: https://bugs.debian.org/1106426
+
+--- a/lmfit/parameter.py
++++ b/lmfit/parameter.py
+@@ -2,6 +2,7 @@
+
+ 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
+@@ -572,8 +573,13 @@
+ par.stderr = sqrt(covar[vindex, vindex])
+ stderr = getattr(par, 'stderr', 0.0)
+ if stderr is None:
+- stderr = 0.0
+- uvars[par.name] = ufloat(par.value, stderr)
++ stderr = 0.00
++ if stderr < tiny*max(tiny, abs(par.value)):
++ with warnings.catch_warnings():
++ warnings.simplefilter("ignore")
++ uvars[par.name] = ufloat(par.value, stderr)
++ else:
++ uvars[par.name] = ufloat(par.value, stderr)
+
+ corr_uvars = None
+ if covar is not None:
diff --git a/debian/patches/series b/debian/patches/series
index dbdf307..0865ded 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,5 @@
deactivate_test.patch
0004-jupyter_sphinx-is-not-yet-working-on-Debian.patch
exclude_test_for_32bit.patch
+fix-test-failure-with-new-uncertainties.patch
+drop-test-confidence-warnings.patch
diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml
new file mode 100644
index 0000000..768dd12
--- /dev/null
+++ b/debian/salsa-ci.yml
@@ -0,0 +1,6 @@
+---
+include:
+ -
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
+
+variables:
+ SALSA_CI_DISABLE_REPROTEST: 1
