statsmodels.git
4 years agoMerge statsmodels (0.12.1-2) import into refs/heads/workingbranch
Drew Parsons [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Merge statsmodels (0.12.1-2) import into refs/heads/workingbranch

4 years agoscipy_1.6_test_bytestring
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
scipy_1.6_test_bytestring

===================================================================

Gbp-Pq: Name scipy_1.6_test_bytestring.patch

4 years agoIgnore test failures on arm64, warn on armel
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Ignore test failures on arm64, warn on armel

arm64 - TestZeroInflatedModel_probit convergence issues
armel - 21 crashes, 2 wrong answers (ignored in d/rules)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/968210
Forwarded: no (current form does not work on non-multiarch systems)

Gbp-Pq: Name 968210_ignore_tests.patch

4 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

4 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch

4 years agoDynamicFactor test fail on ppc64el
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
DynamicFactor test fail on ppc64el

Warn on use and xfail test

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_dynamicfactor_ppc64el.patch

4 years agoMarkov* broken on armhf
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Markov* broken on armhf

Warn on use, and xfail tests

I suspect https://github.com/statsmodels/statsmodels/pull/5826
but that improved it enough on amd64 that
reverting it isn't a good solution.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_regimeswitching_armhf.patch

4 years agoFix typos
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Fix typos

Origin: lintian
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name spelling.patch

4 years agoUse local requirejs
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Use local requirejs

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_local_requirejs.patch

4 years agoAvoid NaN crash in test_structural
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Avoid NaN crash in test_structural

Out-of-range frequency.cycle starting values make untransform_params return NaN,
which crashes summary()

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name fix_test_bounds.patch

4 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Don't fail documentation build on examples exceptions

If example code outputs an error when run,
ipython (ipython:: blocks) now fails the whole build by default,
and tools/nbgenerate.py (.ipynb files) now leaves out that file
(leaving a broken link in the examples index).

As some examples use downloaded data and are hence expected to be
unrunnable on a Debian buildd, this instead keeps them
(::ipython with error output, .ipynb without output).

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

4 years agoDon't try to use a theme we don't have
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Don't try to use a theme we don't have

Upstream switched to sphinx_material in
1d7aafad5c3ad634c9ae2122881c1809c2ccbcbe
and Debian doesn't have that theme.

(I haven't investigated packaging it, which might be a better long-term option.)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (except maybe the version fix? or is that no longer needed at all?)

Gbp-Pq: Name no_sphinx_material.patch

4 years agoMake the module reference tables appear
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

4 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Xfail or loosen tolerances on flaky tests

The test_nondiagonal_obs_cov one hasn't yet been seen in Debian
but is known in upstream CI:
https://github.com/statsmodels/statsmodels/pull/6475#issuecomment-581151072

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: no

Gbp-Pq: Name 944054_flaky_tests.patch

4 years agoDon't try to write to the source directory
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

4 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

4 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Loosen tolerances on some tests on i386

Failure logs:
test_smoothing
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0
test_multivariate_switch_univariate
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.12.0-1&stamp=1599693472&raw=0

As it only fails on i386 and isn't far wrong,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

4 years agoUse example data from an R package we have
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

4 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

4 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

4 years agoto prevent failed test on i386
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

4 years agoUse cached datasets in tests and examples
Debian Science Maintainers [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Use cached datasets in tests and examples

Also remove a download that isn't actually used in that example.

This allows the tests to pass, and at least some of the examples to
be built, in an offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

4 years agostatsmodels (0.12.1-2) unstable; urgency=medium
Drew Parsons [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
statsmodels (0.12.1-2) unstable; urgency=medium

  * Team upload.
  * debian patch scipy_1.6_test_bytestring.patch uses string rather
    than bytes in expected message with scipy 1.6 in test_arma_kwargs
    (test_gls.py)
  * Standards-Version: 4.5.1

[dgit import unpatched statsmodels 0.12.1-2]

4 years agoImport statsmodels_0.12.1-2.debian.tar.xz
Drew Parsons [Sun, 17 Jan 2021 14:02:15 +0000 (14:02 +0000)]
Import statsmodels_0.12.1-2.debian.tar.xz

[dgit import tarball statsmodels 0.12.1-2 statsmodels_0.12.1-2.debian.tar.xz]

5 years agoMerge statsmodels (0.12.1-1) import into refs/heads/workingbranch
Rebecca N. Palmer [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Merge statsmodels (0.12.1-1) import into refs/heads/workingbranch

5 years agoImport statsmodels_0.12.1.orig.tar.gz
Rebecca N. Palmer [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Import statsmodels_0.12.1.orig.tar.gz

[dgit import orig statsmodels_0.12.1.orig.tar.gz]

5 years agoIgnore test failures on arm64, warn on armel
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Ignore test failures on arm64, warn on armel

arm64 - TestZeroInflatedModel_probit convergence issues
armel - 21 crashes, 2 wrong answers (ignored in d/rules)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/968210
Forwarded: no (current form does not work on non-multiarch systems)

Gbp-Pq: Name 968210_ignore_tests.patch

5 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

5 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch

5 years agoDynamicFactor test fail on ppc64el
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
DynamicFactor test fail on ppc64el

Warn on use and xfail test

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_dynamicfactor_ppc64el.patch

5 years agoMarkov* broken on armhf
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Markov* broken on armhf

Warn on use, and xfail tests

I suspect https://github.com/statsmodels/statsmodels/pull/5826
but that improved it enough on amd64 that
reverting it isn't a good solution.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_regimeswitching_armhf.patch

5 years agoFix typos
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Fix typos

Origin: lintian
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name spelling.patch

5 years agoUse local requirejs
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Use local requirejs

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_local_requirejs.patch

5 years agoAvoid NaN crash in test_structural
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Avoid NaN crash in test_structural

Out-of-range frequency.cycle starting values make untransform_params return NaN,
which crashes summary()

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name fix_test_bounds.patch

5 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Don't fail documentation build on examples exceptions

If example code outputs an error when run,
ipython (ipython:: blocks) now fails the whole build by default,
and tools/nbgenerate.py (.ipynb files) now leaves out that file
(leaving a broken link in the examples index).

As some examples use downloaded data and are hence expected to be
unrunnable on a Debian buildd, this instead keeps them
(::ipython with error output, .ipynb without output).

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

5 years agoDon't try to use a theme we don't have
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Don't try to use a theme we don't have

Upstream switched to sphinx_material in
1d7aafad5c3ad634c9ae2122881c1809c2ccbcbe
and Debian doesn't have that theme.

(I haven't investigated packaging it, which might be a better long-term option.)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (except maybe the version fix? or is that no longer needed at all?)

Gbp-Pq: Name no_sphinx_material.patch

5 years agoMake the module reference tables appear
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

5 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Xfail or loosen tolerances on flaky tests

The test_nondiagonal_obs_cov one hasn't yet been seen in Debian
but is known in upstream CI:
https://github.com/statsmodels/statsmodels/pull/6475#issuecomment-581151072

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: no

Gbp-Pq: Name 944054_flaky_tests.patch

5 years agoDon't try to write to the source directory
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

5 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

5 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Loosen tolerances on some tests on i386

Failure logs:
test_smoothing
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0
test_multivariate_switch_univariate
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.12.0-1&stamp=1599693472&raw=0

As it only fails on i386 and isn't far wrong,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

5 years agoUse example data from an R package we have
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

5 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

5 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

5 years agoto prevent failed test on i386
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

5 years agoUse cached datasets in tests and examples
Debian Science Maintainers [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Use cached datasets in tests and examples

Also remove a download that isn't actually used in that example.

This allows the tests to pass, and at least some of the examples to
be built, in an offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

5 years agostatsmodels (0.12.1-1) unstable; urgency=medium
Rebecca N. Palmer [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
statsmodels (0.12.1-1) unstable; urgency=medium

  * Upstream bugfix release.

[dgit import unpatched statsmodels 0.12.1-1]

5 years agoImport statsmodels_0.12.1-1.debian.tar.xz
Rebecca N. Palmer [Thu, 5 Nov 2020 07:28:38 +0000 (07:28 +0000)]
Import statsmodels_0.12.1-1.debian.tar.xz

[dgit import tarball statsmodels 0.12.1-1 statsmodels_0.12.1-1.debian.tar.xz]

5 years agoMerge statsmodels (0.12.0-2) import into refs/heads/workingbranch
Rebecca N. Palmer [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Merge statsmodels (0.12.0-2) import into refs/heads/workingbranch

5 years agoIgnore test failures on arm64, warn on armel
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Ignore test failures on arm64, warn on armel

arm64 - TestZeroInflatedModel_probit convergence issues
armel - 21 crashes, 2 wrong answers (ignored in d/rules)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/968210
Forwarded: no (current form does not work on non-multiarch systems)

Gbp-Pq: Name 968210_ignore_tests.patch

5 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

5 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch

5 years agoDynamicFactor test fail on ppc64el
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
DynamicFactor test fail on ppc64el

Warn on use and xfail test

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_dynamicfactor_ppc64el.patch

5 years agoMarkov* broken on armhf
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Markov* broken on armhf

Warn on use, and xfail tests

I suspect https://github.com/statsmodels/statsmodels/pull/5826
but that improved it enough on amd64 that
reverting it isn't a good solution.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_regimeswitching_armhf.patch

5 years agoFix typos
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Fix typos

Origin: lintian
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name spelling.patch

5 years agoUse local requirejs
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Use local requirejs

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_local_requirejs.patch

5 years agoAvoid NaN crash in test_structural
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Avoid NaN crash in test_structural

Out-of-range frequency.cycle starting values make untransform_params return NaN,
which crashes summary()

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name fix_test_bounds.patch

5 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Don't fail documentation build on examples exceptions

If example code outputs an error when run,
ipython (ipython:: blocks) now fails the whole build by default,
and tools/nbgenerate.py (.ipynb files) now leaves out that file
(leaving a broken link in the examples index).

As some examples use downloaded data and are hence expected to be
unrunnable on a Debian buildd, this instead keeps them
(::ipython with error output, .ipynb without output).

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

5 years agoDon't try to use a theme we don't have
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Don't try to use a theme we don't have

Upstream switched to sphinx_material in
1d7aafad5c3ad634c9ae2122881c1809c2ccbcbe
and Debian doesn't have that theme.

(I haven't investigated packaging it, which might be a better long-term option.)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (except maybe the version fix? or is that no longer needed at all?)

Gbp-Pq: Name no_sphinx_material.patch

5 years agoMake the module reference tables appear
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

5 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Xfail or loosen tolerances on flaky tests

The test_nondiagonal_obs_cov one hasn't yet been seen in Debian
but is known in upstream CI:
https://github.com/statsmodels/statsmodels/pull/6475#issuecomment-581151072

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: no

Gbp-Pq: Name 944054_flaky_tests.patch

5 years agoDon't try to write to the source directory
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

5 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

5 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Loosen tolerances on some tests on i386

Failure logs:
test_smoothing
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0
test_multivariate_switch_univariate
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.12.0-1&stamp=1599693472&raw=0

As it only fails on i386 and isn't far wrong,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

5 years agoUse example data from an R package we have
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

5 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

5 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

5 years agoto prevent failed test on i386
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

5 years agoUse cached datasets in tests and examples
Debian Science Maintainers [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Use cached datasets in tests and examples

Also remove a download that isn't actually used in that example.

This allows the tests to pass, and at least some of the examples to
be built, in an offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

5 years agostatsmodels (0.12.0-2) unstable; urgency=medium
Rebecca N. Palmer [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
statsmodels (0.12.0-2) unstable; urgency=medium

  * Loosen some test tolerances on i386.
  * Require scipy >= 1.5 to avoid autopkgtest failure.

[dgit import unpatched statsmodels 0.12.0-2]

5 years agoImport statsmodels_0.12.0-2.debian.tar.xz
Rebecca N. Palmer [Fri, 11 Sep 2020 06:24:40 +0000 (07:24 +0100)]
Import statsmodels_0.12.0-2.debian.tar.xz

[dgit import tarball statsmodels 0.12.0-2 statsmodels_0.12.0-2.debian.tar.xz]

5 years agoImport statsmodels_0.12.0.orig.tar.gz
Rebecca N. Palmer [Tue, 8 Sep 2020 17:35:08 +0000 (18:35 +0100)]
Import statsmodels_0.12.0.orig.tar.gz

[dgit import orig statsmodels_0.12.0.orig.tar.gz]

5 years agoMerge statsmodels (0.11.1-3) import into refs/heads/workingbranch
Rebecca N. Palmer [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Merge statsmodels (0.11.1-3) import into refs/heads/workingbranch

5 years agoIgnore new deprecation warnings
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Ignore new deprecation warnings

Origin: upstream 8873ab357c9a2a7d3eeeeb1cf1ac63d72a687a75
Bug-Debian: https://bugs.debian.org/964700
Author: Kevin Sheppard
Forwarded: not-needed

Gbp-Pq: Name numpy119_compat.patch

5 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

5 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch

5 years agoDynamicFactor test fail on ppc64el
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
DynamicFactor test fail on ppc64el

Warn on use and xfail test

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_dynamicfactor_ppc64el.patch

5 years agoMarkov* broken on armhf
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Markov* broken on armhf

Warn on use, and xfail tests

I suspect https://github.com/statsmodels/statsmodels/pull/5826
but that improved it enough on amd64 that
reverting it isn't a good solution.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_regimeswitching_armhf.patch

5 years agoDon't require warnings that not all arches produce
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Don't require warnings that not all arches produce

numpy 0/0 (in tvalues): armel doesn't
scipy.stats NaN: Upstream already note i386 doesn't,
we find ppc64el and s390x don't either

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/956882
Forwarded: no

Gbp-Pq: Name dont_require_warnings.patch

5 years agoFix typos
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Fix typos

Origin: lintian
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name spelling.patch

5 years agoUse local requirejs
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Use local requirejs

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_local_requirejs.patch

5 years agoAvoid NaN crash in test_structural
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Avoid NaN crash in test_structural

Out-of-range frequency.cycle starting values make untransform_params return NaN,
which crashes summary()

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name fix_test_bounds.patch

5 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Don't fail documentation build on examples exceptions

If example code outputs an error when run,
ipython (ipython:: blocks) now fails the whole build by default,
and tools/nbgenerate.py (.ipynb files) now leaves out that file
(leaving a broken link in the examples index).

As some examples use downloaded data and are hence expected to be
unrunnable on a Debian buildd, this instead keeps them
(::ipython with error output, .ipynb without output).

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

5 years agoDon't try to use a theme we don't have
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Don't try to use a theme we don't have

Upstream switched to sphinx_material in
1d7aafad5c3ad634c9ae2122881c1809c2ccbcbe
and Debian doesn't have that theme.

(I haven't investigated packaging it, which might be a better long-term option.)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (except maybe the version fix? or is that no longer needed at all?)

Gbp-Pq: Name no_sphinx_material.patch

5 years agoInclude offset and exposure in GEEResults.fittedvalues
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Include offset and exposure in GEEResults.fittedvalues

and remove misleading documentation from GLMResults.fittedvalues

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/statsmodels/statsmodels/issues/5253
Forwarded: https://github.com/statsmodels/statsmodels/issues/5253#issuecomment-578980169

Gbp-Pq: Name up5253_gee_offset.patch

5 years agoMake the module reference tables appear
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

5 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Xfail or loosen tolerances on flaky tests

The test_nondiagonal_obs_cov one hasn't yet been seen in Debian
but is known in upstream CI:
https://github.com/statsmodels/statsmodels/pull/6475#issuecomment-581151072

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: no

Gbp-Pq: Name 944054_flaky_tests.patch

5 years agoDon't try to write to the source directory
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

5 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

5 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Loosen tolerances on some tests on i386

Failure log
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0

As it only fails on i386 (not x32) and isn't far over tolerance,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

5 years agoUse example data from an R package we have
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

5 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

5 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

5 years agoto prevent failed test on i386
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

5 years agoUse cached datasets in tests and examples
Debian Science Maintainers [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Use cached datasets in tests and examples

Also remove a download that isn't actually used in that example.

This allows the tests to pass, and at least some of the examples to
be built, in an offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

5 years agostatsmodels (0.11.1-3) unstable; urgency=medium
Rebecca N. Palmer [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
statsmodels (0.11.1-3) unstable; urgency=medium

  * Tests: ignore harmless new warnings.  Closes: #964700.
  * Add matplotlib etc to autopkgtest Depends to skip fewer tests.

[dgit import unpatched statsmodels 0.11.1-3]

5 years agoImport statsmodels_0.11.1-3.debian.tar.xz
Rebecca N. Palmer [Fri, 10 Jul 2020 05:46:36 +0000 (06:46 +0100)]
Import statsmodels_0.11.1-3.debian.tar.xz

[dgit import tarball statsmodels 0.11.1-3 statsmodels_0.11.1-3.debian.tar.xz]

5 years agoMerge statsmodels (0.11.1-2) import into refs/heads/workingbranch
Rebecca N. Palmer [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Merge statsmodels (0.11.1-2) import into refs/heads/workingbranch

5 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

5 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch